Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 23:11:11 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/12_2021/3j2p_5499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/12_2021/3j2p_5499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/12_2021/3j2p_5499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/12_2021/3j2p_5499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/12_2021/3j2p_5499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/12_2021/3j2p_5499.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.100 sd= 2.332 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 2": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "C ARG 2": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 471": "NH1" <-> "NH2" Residue "C TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9890 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4276 Classifications: {'peptide': 495} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 475} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 627 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 4276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4276 Classifications: {'peptide': 495} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 475} Chain: "D" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 627 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.53, per 1000 atoms: 0.56 Number of scatterers: 9890 At special positions: 0 Unit cell: (98.256, 146.832, 97.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 O 1642 8.00 N 1492 7.00 C 5600 6.00 H 1086 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 502 " - " NAG A 503 " " NAG C 502 " - " NAG C 503 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 153 " " NAG C 501 " - " ASN C 67 " " NAG C 502 " - " ASN C 153 " Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 28.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.597A pdb=" N GLY A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 105' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 396 through 416 removed outlier: 3.572A pdb=" N GLN A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 Processing helix chain 'A' and resid 428 through 443 removed outlier: 4.240A pdb=" N VAL A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 452 through 469 Processing helix chain 'A' and resid 473 through 483 removed outlier: 4.213A pdb=" N VAL A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'B' and resid 22 through 39 removed outlier: 4.297A pdb=" N ALA B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 53 removed outlier: 3.667A pdb=" N THR B 43 " --> pdb=" O HIS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.601A pdb=" N GLY C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 105' Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 396 through 416 removed outlier: 3.573A pdb=" N GLN C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 415 " --> pdb=" O ARG C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 423 Processing helix chain 'C' and resid 428 through 443 removed outlier: 4.243A pdb=" N VAL C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 447 Processing helix chain 'C' and resid 452 through 469 Processing helix chain 'C' and resid 473 through 483 removed outlier: 4.213A pdb=" N VAL C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'D' and resid 22 through 39 removed outlier: 4.300A pdb=" N ALA D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.667A pdb=" N THR D 43 " --> pdb=" O HIS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 71 Processing sheet with id= A, first strand: chain 'A' and resid 11 through 13 removed outlier: 5.974A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR A 138 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 20 through 25 Processing sheet with id= C, first strand: chain 'A' and resid 63 through 72 removed outlier: 4.887A pdb=" N LEU A 65 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 120 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN A 67 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N MET A 118 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= E, first strand: chain 'A' and resid 239 through 241 Processing sheet with id= F, first strand: chain 'A' and resid 305 through 308 removed outlier: 3.781A pdb=" N LYS A 305 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 337 through 340 Processing sheet with id= H, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.974A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR C 138 " --> pdb=" O ILE C 46 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 20 through 25 Processing sheet with id= J, first strand: chain 'C' and resid 63 through 72 removed outlier: 4.887A pdb=" N LEU C 65 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR C 120 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN C 67 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET C 118 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 196 through 200 Processing sheet with id= L, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= M, first strand: chain 'C' and resid 305 through 308 removed outlier: 3.776A pdb=" N LYS C 305 " --> pdb=" O GLU C 327 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 337 through 340 320 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 1086 1.14 - 1.32: 1449 1.32 - 1.50: 3769 1.50 - 1.68: 3652 1.68 - 1.86: 116 Bond restraints: 10072 Sorted by residual: bond pdb=" N LEU A 283 " pdb=" H LEU A 283 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" N LEU C 283 " pdb=" H LEU C 283 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" N THR B 34 " pdb=" H THR B 34 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" N THR D 34 " pdb=" H THR D 34 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" N THR A 182 " pdb=" H THR A 182 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.92e+01 ... (remaining 10067 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.91: 368 105.91 - 114.14: 5144 114.14 - 122.38: 7006 122.38 - 130.61: 1755 130.61 - 138.84: 63 Bond angle restraints: 14336 Sorted by residual: angle pdb=" C LEU C 221 " pdb=" N PRO C 222 " pdb=" CA PRO C 222 " ideal model delta sigma weight residual 119.84 109.97 9.87 1.25e+00 6.40e-01 6.24e+01 angle pdb=" C LEU A 221 " pdb=" N PRO A 222 " pdb=" CA PRO A 222 " ideal model delta sigma weight residual 119.84 109.98 9.86 1.25e+00 6.40e-01 6.22e+01 angle pdb=" C GLU C 79 " pdb=" N PRO C 80 " pdb=" CA PRO C 80 " ideal model delta sigma weight residual 119.84 129.28 -9.44 1.25e+00 6.40e-01 5.71e+01 angle pdb=" C THR C 142 " pdb=" N PRO C 143 " pdb=" CA PRO C 143 " ideal model delta sigma weight residual 119.84 129.24 -9.40 1.25e+00 6.40e-01 5.65e+01 angle pdb=" C THR A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta sigma weight residual 119.84 129.15 -9.31 1.25e+00 6.40e-01 5.55e+01 ... (remaining 14331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 4667 16.18 - 32.35: 384 32.35 - 48.53: 149 48.53 - 64.70: 100 64.70 - 80.88: 20 Dihedral angle restraints: 5320 sinusoidal: 2132 harmonic: 3188 Sorted by residual: dihedral pdb=" C GLU A 195 " pdb=" N GLU A 195 " pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " ideal model delta harmonic sigma weight residual -122.60 -113.79 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C GLU C 195 " pdb=" N GLU C 195 " pdb=" CA GLU C 195 " pdb=" CB GLU C 195 " ideal model delta harmonic sigma weight residual -122.60 -113.80 -8.80 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C ASN A 124 " pdb=" N ASN A 124 " pdb=" CA ASN A 124 " pdb=" CB ASN A 124 " ideal model delta harmonic sigma weight residual -122.60 -114.02 -8.58 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 5317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 830 0.083 - 0.165: 354 0.165 - 0.248: 158 0.248 - 0.330: 52 0.330 - 0.412: 18 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LEU A 278 " pdb=" N LEU A 278 " pdb=" C LEU A 278 " pdb=" CB LEU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA LEU C 278 " pdb=" N LEU C 278 " pdb=" C LEU C 278 " pdb=" CB LEU C 278 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA TRP A 391 " pdb=" N TRP A 391 " pdb=" C TRP A 391 " pdb=" CB TRP A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1409 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 502 " 0.366 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" C7 NAG A 502 " -0.092 2.00e-02 2.50e+03 pdb=" C8 NAG A 502 " 0.118 2.00e-02 2.50e+03 pdb=" N2 NAG A 502 " -0.553 2.00e-02 2.50e+03 pdb=" O7 NAG A 502 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.366 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" C7 NAG C 502 " -0.093 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.118 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.552 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 503 " -0.367 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG A 503 " 0.097 2.00e-02 2.50e+03 pdb=" C8 NAG A 503 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A 503 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG A 503 " -0.113 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.88: 74 1.88 - 2.56: 2739 2.56 - 3.24: 17314 3.24 - 3.92: 23022 3.92 - 4.60: 32760 Nonbonded interactions: 75909 Sorted by model distance: nonbonded pdb=" H GLU A 195 " pdb=" H MET A 196 " model vdw 1.198 2.100 nonbonded pdb=" H GLU C 195 " pdb=" H MET C 196 " model vdw 1.199 2.100 nonbonded pdb=" H SER B 22 " pdb=" H GLU B 23 " model vdw 1.267 2.100 nonbonded pdb=" H SER D 22 " pdb=" H GLU D 23 " model vdw 1.267 2.100 nonbonded pdb=" H ALA C 447 " pdb=" H PHE C 448 " model vdw 1.279 2.100 ... (remaining 75904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 5600 2.51 5 N 1492 2.21 5 O 1642 1.98 5 H 1086 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.460 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 28.640 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.059 8986 Z= 0.611 Angle : 1.919 13.972 12164 Z= 1.137 Chirality : 0.118 0.412 1412 Planarity : 0.021 0.312 1520 Dihedral : 17.487 80.876 3280 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 110.36 Ramachandran Plot: Outliers : 24.07 % Allowed : 29.66 % Favored : 46.27 % Rotamer Outliers : 20.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.75 (0.15), residues: 1126 helix: -5.20 (0.09), residues: 294 sheet: -3.78 (0.32), residues: 216 loop : -5.90 (0.15), residues: 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 513 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 321 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 192 outliers final: 125 residues processed: 461 average time/residue: 0.2086 time to fit residues: 132.0448 Evaluate side-chains 386 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 261 time to evaluate : 1.084 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 6 residues processed: 125 average time/residue: 0.1209 time to fit residues: 26.0616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 203 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 242 ASN A 256 GLN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 203 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 242 ASN C 248 GLN C 256 GLN C 386 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 8986 Z= 0.296 Angle : 1.034 7.745 12164 Z= 0.543 Chirality : 0.055 0.384 1412 Planarity : 0.007 0.066 1520 Dihedral : 7.746 84.415 1224 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 87.14 Ramachandran Plot: Outliers : 5.68 % Allowed : 29.66 % Favored : 64.65 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.96 (0.17), residues: 1126 helix: -4.37 (0.17), residues: 296 sheet: -3.14 (0.31), residues: 252 loop : -5.66 (0.16), residues: 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 301 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 33 residues processed: 327 average time/residue: 0.2115 time to fit residues: 97.7518 Evaluate side-chains 297 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 264 time to evaluate : 1.015 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 2 residues processed: 33 average time/residue: 0.1081 time to fit residues: 7.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0770 chunk 31 optimal weight: 0.0170 chunk 84 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 90 optimal weight: 0.0670 chunk 34 optimal weight: 20.0000 chunk 81 optimal weight: 0.0370 chunk 100 optimal weight: 9.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 276 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8986 Z= 0.175 Angle : 0.809 6.987 12164 Z= 0.414 Chirality : 0.047 0.287 1412 Planarity : 0.006 0.076 1520 Dihedral : 7.217 70.131 1224 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 76.18 Ramachandran Plot: Outliers : 5.06 % Allowed : 22.74 % Favored : 72.20 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.05 (0.19), residues: 1126 helix: -3.04 (0.22), residues: 298 sheet: -2.87 (0.28), residues: 276 loop : -5.37 (0.18), residues: 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 326 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 291 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 308 average time/residue: 0.2002 time to fit residues: 88.1789 Evaluate side-chains 278 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 259 time to evaluate : 1.064 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.1132 time to fit residues: 4.9851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 8986 Z= 0.279 Angle : 0.817 6.981 12164 Z= 0.419 Chirality : 0.047 0.254 1412 Planarity : 0.006 0.070 1520 Dihedral : 6.980 65.527 1224 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 79.34 Ramachandran Plot: Outliers : 4.62 % Allowed : 25.31 % Favored : 70.07 % Rotamer Outliers : 6.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.71 (0.20), residues: 1126 helix: -2.58 (0.23), residues: 306 sheet: -2.62 (0.29), residues: 284 loop : -5.37 (0.18), residues: 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 265 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 46 residues processed: 295 average time/residue: 0.1928 time to fit residues: 82.0163 Evaluate side-chains 295 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 249 time to evaluate : 1.072 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 2 residues processed: 46 average time/residue: 0.1068 time to fit residues: 10.0333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 9.9990 chunk 1 optimal weight: 0.0970 chunk 80 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 overall best weight: 4.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 244 HIS ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 103 ASN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS D 7 HIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 8986 Z= 0.213 Angle : 0.761 8.125 12164 Z= 0.386 Chirality : 0.045 0.262 1412 Planarity : 0.006 0.104 1520 Dihedral : 6.779 62.650 1224 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 75.28 Ramachandran Plot: Outliers : 4.17 % Allowed : 20.78 % Favored : 75.04 % Rotamer Outliers : 4.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.30 (0.21), residues: 1126 helix: -2.14 (0.24), residues: 306 sheet: -2.36 (0.30), residues: 284 loop : -5.19 (0.18), residues: 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 265 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 23 residues processed: 282 average time/residue: 0.1978 time to fit residues: 80.1810 Evaluate side-chains 275 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 1.099 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.1161 time to fit residues: 5.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 20.0000 chunk 21 optimal weight: 0.0970 chunk 63 optimal weight: 0.0370 chunk 26 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 8986 Z= 0.196 Angle : 0.722 8.464 12164 Z= 0.366 Chirality : 0.045 0.247 1412 Planarity : 0.005 0.053 1520 Dihedral : 6.509 61.173 1224 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 71.78 Ramachandran Plot: Outliers : 4.00 % Allowed : 20.96 % Favored : 75.04 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.22), residues: 1126 helix: -1.66 (0.26), residues: 306 sheet: -1.93 (0.33), residues: 264 loop : -5.00 (0.19), residues: 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 265 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 288 average time/residue: 0.1958 time to fit residues: 80.6928 Evaluate side-chains 271 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 246 time to evaluate : 1.037 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 2 residues processed: 25 average time/residue: 0.0989 time to fit residues: 5.9105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 40.0000 chunk 61 optimal weight: 0.0370 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 overall best weight: 5.1866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 8986 Z= 0.218 Angle : 0.730 8.486 12164 Z= 0.371 Chirality : 0.045 0.238 1412 Planarity : 0.005 0.047 1520 Dihedral : 6.480 61.131 1224 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 72.57 Ramachandran Plot: Outliers : 3.46 % Allowed : 21.85 % Favored : 74.69 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.22), residues: 1126 helix: -1.24 (0.27), residues: 294 sheet: -2.05 (0.35), residues: 240 loop : -4.88 (0.19), residues: 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 263 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 272 average time/residue: 0.2131 time to fit residues: 82.5485 Evaluate side-chains 262 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 1.132 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.1214 time to fit residues: 4.9428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS A 167 GLN A 203 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 8986 Z= 0.248 Angle : 0.754 9.246 12164 Z= 0.383 Chirality : 0.045 0.307 1412 Planarity : 0.005 0.051 1520 Dihedral : 6.558 62.428 1224 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 73.64 Ramachandran Plot: Outliers : 3.46 % Allowed : 22.38 % Favored : 74.16 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.23), residues: 1126 helix: -1.17 (0.28), residues: 294 sheet: -1.70 (0.34), residues: 264 loop : -4.96 (0.19), residues: 568 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 258 average time/residue: 0.2113 time to fit residues: 77.5925 Evaluate side-chains 256 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 1.142 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.1443 time to fit residues: 5.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 20.0000 chunk 100 optimal weight: 0.4980 chunk 103 optimal weight: 30.0000 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 90 optimal weight: 30.0000 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 overall best weight: 9.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 8986 Z= 0.327 Angle : 0.817 9.656 12164 Z= 0.416 Chirality : 0.048 0.218 1412 Planarity : 0.006 0.050 1520 Dihedral : 6.959 66.760 1224 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 77.25 Ramachandran Plot: Outliers : 3.37 % Allowed : 24.42 % Favored : 72.20 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.22), residues: 1126 helix: -1.60 (0.27), residues: 302 sheet: -1.81 (0.34), residues: 266 loop : -4.90 (0.20), residues: 558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 241 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 252 average time/residue: 0.2126 time to fit residues: 75.2026 Evaluate side-chains 248 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 1.057 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.1044 time to fit residues: 4.2664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 8986 Z= 0.253 Angle : 0.767 9.981 12164 Z= 0.391 Chirality : 0.046 0.334 1412 Planarity : 0.005 0.068 1520 Dihedral : 6.798 66.445 1224 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 73.70 Ramachandran Plot: Outliers : 3.46 % Allowed : 22.11 % Favored : 74.42 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.23), residues: 1126 helix: -1.35 (0.28), residues: 294 sheet: -1.79 (0.34), residues: 266 loop : -4.84 (0.20), residues: 566 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue SER 16 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue ALA 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ALA 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue TYR 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue ALA 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue MET 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue MET 183 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue MET 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue ALA 205 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue ILE 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue LEU 253 is missing expected H atoms. Skipping. Residue SER 255 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue MET 260 is missing expected H atoms. Skipping. Residue THR 262 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue LEU 264 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue ALA 267 is missing expected H atoms. Skipping. Residue THR 268 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue MET 272 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 280 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue MET 289 is missing expected H atoms. Skipping. Residue LYS 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue MET 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue SER 300 is missing expected H atoms. Skipping. Residue MET 301 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue ILE 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue THR 319 is missing expected H atoms. Skipping. Residue ILE 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue ILE 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue TYR 326 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue ILE 335 is missing expected H atoms. Skipping. Residue ILE 339 is missing expected H atoms. Skipping. Residue MET 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue VAL 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue ILE 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue SER 363 is missing expected H atoms. Skipping. Residue VAL 365 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ALA 369 is missing expected H atoms. Skipping. Residue SER 376 is missing expected H atoms. Skipping. Residue TYR 377 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue ILE 379 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue LYS 388 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue ILE 398 is missing expected H atoms. Skipping. Residue MET 401 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue THR 404 is missing expected H atoms. Skipping. Residue THR 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ALA 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 412 is missing expected H atoms. Skipping. Residue ALA 413 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue ALA 419 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue LEU 425 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 431 is missing expected H atoms. Skipping. Residue ILE 432 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue ALA 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue TYR 444 is missing expected H atoms. Skipping. Residue ALA 446 is missing expected H atoms. Skipping. Residue ALA 447 is missing expected H atoms. Skipping. Residue SER 449 is missing expected H atoms. Skipping. Residue VAL 451 is missing expected H atoms. Skipping. Residue SER 452 is missing expected H atoms. Skipping. Residue ILE 454 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ILE 459 is missing expected H atoms. Skipping. Residue VAL 461 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue THR 464 is missing expected H atoms. Skipping. Residue ILE 466 is missing expected H atoms. Skipping. Residue MET 468 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 474 is missing expected H atoms. Skipping. Residue LEU 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue VAL 480 is missing expected H atoms. Skipping. Residue LEU 481 is missing expected H atoms. Skipping. Residue VAL 482 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue VAL 485 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue TYR 488 is missing expected H atoms. Skipping. Residue LEU 489 is missing expected H atoms. Skipping. Residue VAL 491 is missing expected H atoms. Skipping. Residue MET 492 is missing expected H atoms. Skipping. Residue VAL 493 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue ALA 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue MET 10 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue ALA 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue ALA 50 is missing expected H atoms. Skipping. Residue TYR 51 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 245 average time/residue: 0.2098 time to fit residues: 73.2190 Evaluate side-chains 241 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 230 time to evaluate : 1.102 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.0995 time to fit residues: 3.4655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 244 HIS ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139047 restraints weight = 22142.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141661 restraints weight = 11303.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143370 restraints weight = 6711.165| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 8986 Z= 0.265 Angle : 0.767 9.910 12164 Z= 0.391 Chirality : 0.046 0.234 1412 Planarity : 0.005 0.066 1520 Dihedral : 6.798 66.371 1224 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 74.77 Ramachandran Plot: Outliers : 3.37 % Allowed : 22.82 % Favored : 73.80 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.22), residues: 1126 helix: -1.51 (0.27), residues: 306 sheet: -2.05 (0.34), residues: 242 loop : -4.64 (0.20), residues: 578 =============================================================================== Job complete usr+sys time: 2204.17 seconds wall clock time: 44 minutes 49.88 seconds (2689.88 seconds total)