Starting phenix.real_space_refine on Fri Feb 16 07:00:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn2_27552/02_2024/8dn2_27552_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn2_27552/02_2024/8dn2_27552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn2_27552/02_2024/8dn2_27552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn2_27552/02_2024/8dn2_27552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn2_27552/02_2024/8dn2_27552_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn2_27552/02_2024/8dn2_27552_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.010 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9267 2.51 5 N 2258 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14102 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2814 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain breaks: 1 Chain: "A" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2778 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2755 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2726 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2692 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Unusual residues: {'HEX': 3, 'HP6': 4, 'NAG': 1, 'OCT': 1, 'UND': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Unusual residues: {'DD9': 1, 'HEX': 3, 'NAG': 1, 'NBU': 1, 'OCT': 2, 'UND': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Unusual residues: {'HEX': 2, 'HP6': 1, 'NAG': 1, 'UND': 1} Inner-chain residues flagged as termini: ['pdbres="GLY B 502 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 58 Unusual residues: {'HEX': 1, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'OCT': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Unusual residues: {'D10': 1, 'DD9': 1, 'HEX': 1, 'HP6': 2, 'NAG': 1, 'OCT': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.66, per 1000 atoms: 0.54 Number of scatterers: 14102 At special positions: 0 Unit cell: (107.07, 126.99, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2475 8.00 N 2258 7.00 C 9267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino 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=8, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 38 " " NAG B 503 " - " ASN B 38 " " NAG C 502 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 2.8 seconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 20 sheets defined 36.7% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'D' and resid 10 through 17 removed outlier: 3.718A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 87 through 92 removed outlier: 4.427A pdb=" N SER D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 221 through 243 Proline residue: D 230 - end of helix removed outlier: 3.854A pdb=" N PHE D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP D 243 " --> pdb=" O TRP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 271 Processing helix chain 'D' and resid 283 through 310 Processing helix chain 'D' and resid 386 through 416 Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 87 through 92 removed outlier: 4.185A pdb=" N SER A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 221 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.513A pdb=" N LEU A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 308 Processing helix chain 'A' and resid 386 through 418 Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 87 through 92 removed outlier: 4.767A pdb=" N SER B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 220 through 243 Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 249 through 271 Processing helix chain 'B' and resid 283 through 307 Processing helix chain 'B' and resid 385 through 418 Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 87 through 92 removed outlier: 4.596A pdb=" N SER C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 221 through 243 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 249 through 271 Processing helix chain 'C' and resid 282 through 309 removed outlier: 4.014A pdb=" N TRP C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 418 Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.966A pdb=" N LEU E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.986A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 245 through 248 No H-bonds generated for 'chain 'E' and resid 245 through 248' Processing helix chain 'E' and resid 252 through 267 removed outlier: 3.633A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 276 No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 278 through 295 removed outlier: 4.226A pdb=" N SER E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 332 Processing helix chain 'E' and resid 447 through 474 removed outlier: 3.936A pdb=" N ILE E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) Proline residue: E 460 - end of helix Processing sheet with id= A, first strand: chain 'D' and resid 166 through 169 removed outlier: 6.494A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 43 through 45 Processing sheet with id= C, first strand: chain 'D' and resid 149 through 157 Processing sheet with id= D, first strand: chain 'D' and resid 193 through 197 Processing sheet with id= E, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.457A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= G, first strand: chain 'A' and resid 149 through 157 removed outlier: 3.564A pdb=" N ALA A 212 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 195 through 197 Processing sheet with id= I, first strand: chain 'B' and resid 37 through 40 Processing sheet with id= J, first strand: chain 'B' and resid 43 through 45 Processing sheet with id= K, first strand: chain 'B' and resid 57 through 69 Processing sheet with id= L, first strand: chain 'B' and resid 149 through 157 Processing sheet with id= M, first strand: chain 'B' and resid 193 through 197 Processing sheet with id= N, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.664A pdb=" N ILE C 167 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 58 through 69 removed outlier: 4.593A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 149 through 152 Processing sheet with id= Q, first strand: chain 'E' and resid 189 through 193 removed outlier: 6.579A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP E 89 " --> pdb=" O VAL E 149 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 176 through 180 Processing sheet with id= S, first strand: chain 'E' and resid 223 through 225 Processing sheet with id= T, first strand: chain 'E' and resid 126 through 130 removed outlier: 6.930A pdb=" N THR E 158 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA E 129 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER E 156 " --> pdb=" O ALA E 129 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1731 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: 3.88 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2441 1.33 - 1.45: 3822 1.45 - 1.58: 7977 1.58 - 1.70: 0 1.70 - 1.83: 172 Bond restraints: 14412 Sorted by residual: bond pdb=" CA PHE D 387 " pdb=" C PHE D 387 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.39e-02 5.18e+03 1.24e+01 bond pdb=" N THR D 55 " pdb=" CA THR D 55 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.00e-02 1.00e+04 1.11e+01 bond pdb=" N VAL B 37 " pdb=" CA VAL B 37 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" C PRO A 87 " pdb=" O PRO A 87 " ideal model delta sigma weight residual 1.237 1.201 0.037 1.26e-02 6.30e+03 8.42e+00 bond pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.38e+00 ... (remaining 14407 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.84: 462 106.84 - 113.62: 7700 113.62 - 120.41: 5457 120.41 - 127.19: 5637 127.19 - 133.97: 164 Bond angle restraints: 19420 Sorted by residual: angle pdb=" N ILE D 388 " pdb=" CA ILE D 388 " pdb=" C ILE D 388 " ideal model delta sigma weight residual 110.72 101.30 9.42 1.01e+00 9.80e-01 8.70e+01 angle pdb=" N LEU D 386 " pdb=" CA LEU D 386 " pdb=" C LEU D 386 " ideal model delta sigma weight residual 111.07 119.86 -8.79 1.07e+00 8.73e-01 6.74e+01 angle pdb=" N VAL A 294 " pdb=" CA VAL A 294 " pdb=" C VAL A 294 " ideal model delta sigma weight residual 110.42 117.91 -7.49 9.60e-01 1.09e+00 6.09e+01 angle pdb=" N GLN C 226 " pdb=" CA GLN C 226 " pdb=" C GLN C 226 " ideal model delta sigma weight residual 111.82 120.74 -8.92 1.16e+00 7.43e-01 5.91e+01 angle pdb=" N ILE D 388 " pdb=" CA ILE D 388 " pdb=" CB ILE D 388 " ideal model delta sigma weight residual 110.58 120.84 -10.26 1.50e+00 4.44e-01 4.68e+01 ... (remaining 19415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.96: 8245 19.96 - 39.92: 354 39.92 - 59.87: 64 59.87 - 79.83: 15 79.83 - 99.79: 12 Dihedral angle restraints: 8690 sinusoidal: 3691 harmonic: 4999 Sorted by residual: dihedral pdb=" CA ILE B 419 " pdb=" C ILE B 419 " pdb=" N VAL B 420 " pdb=" CA VAL B 420 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C1 NAG E 501 " pdb=" C2 NAG E 501 " pdb=" C3 NAG E 501 " pdb=" O3 NAG E 501 " ideal model delta sinusoidal sigma weight residual -175.09 -75.30 -99.79 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" C2 NAG D 501 " pdb=" C3 NAG D 501 " pdb=" C4 NAG D 501 " pdb=" C5 NAG D 501 " ideal model delta sinusoidal sigma weight residual 53.78 -45.81 99.59 1 3.00e+01 1.11e-03 1.24e+01 ... (remaining 8687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1927 0.076 - 0.152: 208 0.152 - 0.229: 11 0.229 - 0.305: 4 0.305 - 0.381: 1 Chirality restraints: 2151 Sorted by residual: chirality pdb=" CA LEU D 386 " pdb=" N LEU D 386 " pdb=" C LEU D 386 " pdb=" CB LEU D 386 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA LEU C 224 " pdb=" N LEU C 224 " pdb=" C LEU C 224 " pdb=" CB LEU C 224 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2148 not shown) Planarity restraints: 2411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 503 " 0.307 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C7 NAG B 503 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 503 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 503 " -0.450 2.00e-02 2.50e+03 pdb=" O7 NAG B 503 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 225 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ILE C 225 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE C 225 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN C 226 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 419 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ILE B 419 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE B 419 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL B 420 " -0.022 2.00e-02 2.50e+03 ... (remaining 2408 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 7 1.96 - 2.69: 410 2.69 - 3.43: 20616 3.43 - 4.16: 31821 4.16 - 4.90: 55972 Nonbonded interactions: 108826 Sorted by model distance: nonbonded pdb=" CD2 LEU D 261 " pdb=" CE1 PHE E 282 " model vdw 1.224 3.760 nonbonded pdb=" CE1 PHE B 159 " pdb=" N GLY B 502 " model vdw 1.288 3.420 nonbonded pdb=" CE1 PHE C 159 " pdb=" N GLY C 501 " model vdw 1.330 3.420 nonbonded pdb=" CZ3 TRP B 414 " pdb=" C5 UND B 504 " model vdw 1.382 2.992 nonbonded pdb=" CD1 PHE C 159 " pdb=" N GLY C 501 " model vdw 1.755 3.420 ... (remaining 108821 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' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 308 or resid 386 through 419)) selection = (chain 'D' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.710 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.540 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.003 0.056 14412 Z= 0.225 Angle : 0.652 10.260 19420 Z= 0.389 Chirality : 0.046 0.381 2151 Planarity : 0.006 0.260 2406 Dihedral : 12.212 99.789 5420 Min Nonbonded Distance : 1.224 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.02 % Rotamer: Outliers : 2.83 % Allowed : 8.95 % Favored : 88.22 % 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: 0.00 (0.21), residues: 1673 helix: 1.90 (0.22), residues: 596 sheet: -0.46 (0.28), residues: 368 loop : -1.41 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.002 0.001 HIS A 311 PHE 0.011 0.001 PHE D 412 TYR 0.015 0.001 TYR D 301 ARG 0.003 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 437 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.8202 (pt0) cc_final: 0.7867 (pt0) REVERT: D 404 MET cc_start: 0.7747 (mtp) cc_final: 0.7451 (ptt) REVERT: A 18 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7132 (ptt) REVERT: A 73 LEU cc_start: 0.9385 (tp) cc_final: 0.9090 (tt) REVERT: A 220 MET cc_start: 0.7924 (mtt) cc_final: 0.7650 (mtm) REVERT: A 383 MET cc_start: 0.7454 (ppp) cc_final: 0.6668 (ppp) REVERT: B 55 THR cc_start: 0.9136 (p) cc_final: 0.8900 (p) REVERT: B 131 ARG cc_start: 0.8932 (ttt-90) cc_final: 0.8665 (ttt90) REVERT: B 170 TRP cc_start: 0.8339 (m100) cc_final: 0.8064 (m100) REVERT: B 211 GLU cc_start: 0.7407 (pm20) cc_final: 0.6806 (pm20) REVERT: B 252 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.7868 (mmm-85) REVERT: B 263 MET cc_start: 0.9188 (tpp) cc_final: 0.8891 (tpp) REVERT: B 276 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8172 (mtmt) REVERT: B 295 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8278 (t80) REVERT: B 393 LYS cc_start: 0.7678 (mttm) cc_final: 0.7160 (pttt) REVERT: C 17 LEU cc_start: 0.9307 (mt) cc_final: 0.9035 (mt) REVERT: C 55 THR cc_start: 0.9628 (OUTLIER) cc_final: 0.9240 (m) REVERT: C 98 LEU cc_start: 0.9152 (pt) cc_final: 0.8867 (pt) REVERT: C 147 MET cc_start: 0.7790 (mtp) cc_final: 0.7519 (tpt) REVERT: C 192 GLU cc_start: 0.8493 (tp30) cc_final: 0.8277 (tp30) REVERT: C 239 TRP cc_start: 0.8602 (m-10) cc_final: 0.8273 (m-10) REVERT: C 399 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6835 (ttm110) REVERT: E 154 ARG cc_start: 0.8857 (ttt-90) cc_final: 0.8298 (ttt-90) REVERT: E 235 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7722 (mt-10) REVERT: E 247 TYR cc_start: 0.8330 (m-80) cc_final: 0.7940 (m-80) REVERT: E 285 LEU cc_start: 0.8012 (mt) cc_final: 0.7629 (tt) REVERT: E 329 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8112 (tm-30) outliers start: 43 outliers final: 17 residues processed: 463 average time/residue: 0.2332 time to fit residues: 158.6812 Evaluate side-chains 341 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN D 305 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 67 GLN E 138 ASN E 173 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14412 Z= 0.203 Angle : 0.632 8.846 19420 Z= 0.309 Chirality : 0.044 0.255 2151 Planarity : 0.004 0.043 2406 Dihedral : 9.880 83.184 2138 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.61 % Allowed : 16.38 % Favored : 79.01 % 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: 0.25 (0.21), residues: 1673 helix: 2.09 (0.21), residues: 590 sheet: -0.11 (0.29), residues: 343 loop : -1.34 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS A 311 PHE 0.016 0.001 PHE B 409 TYR 0.024 0.001 TYR B 78 ARG 0.004 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 339 time to evaluate : 1.589 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: D 242 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: D 404 MET cc_start: 0.7774 (mtp) cc_final: 0.7490 (ptt) REVERT: D 411 MET cc_start: 0.6569 (mmt) cc_final: 0.6362 (mmt) REVERT: A 192 GLU cc_start: 0.8295 (pm20) cc_final: 0.7850 (mm-30) REVERT: A 217 GLU cc_start: 0.8326 (tp30) cc_final: 0.8002 (tp30) REVERT: A 220 MET cc_start: 0.7874 (mtt) cc_final: 0.7600 (mtm) REVERT: B 41 CYS cc_start: 0.8609 (p) cc_final: 0.8105 (p) REVERT: B 131 ARG cc_start: 0.8953 (ttt-90) cc_final: 0.8672 (ttt90) REVERT: B 170 TRP cc_start: 0.8343 (m100) cc_final: 0.7968 (m100) REVERT: B 393 LYS cc_start: 0.7700 (mttm) cc_final: 0.7191 (pttt) REVERT: C 17 LEU cc_start: 0.9295 (mt) cc_final: 0.9016 (mt) REVERT: C 116 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8845 (mtpp) REVERT: C 147 MET cc_start: 0.7824 (mtp) cc_final: 0.7454 (tpt) REVERT: C 192 GLU cc_start: 0.8451 (tp30) cc_final: 0.8239 (tp30) REVERT: C 239 TRP cc_start: 0.8676 (m-10) cc_final: 0.8341 (m-10) REVERT: C 399 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6845 (ttm110) REVERT: E 170 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8717 (mtm) REVERT: E 235 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7713 (mt-10) REVERT: E 247 TYR cc_start: 0.8384 (m-80) cc_final: 0.7989 (m-80) REVERT: E 329 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8072 (tm-30) outliers start: 70 outliers final: 49 residues processed: 379 average time/residue: 0.2309 time to fit residues: 135.9688 Evaluate side-chains 363 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 311 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14412 Z= 0.265 Angle : 0.638 9.713 19420 Z= 0.317 Chirality : 0.044 0.290 2151 Planarity : 0.004 0.050 2406 Dihedral : 8.814 78.333 2129 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.46 % Allowed : 16.84 % Favored : 77.70 % 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: 0.22 (0.21), residues: 1673 helix: 2.15 (0.22), residues: 585 sheet: -0.16 (0.29), residues: 343 loop : -1.38 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS A 311 PHE 0.024 0.001 PHE B 13 TYR 0.018 0.001 TYR E 325 ARG 0.005 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 330 time to evaluate : 1.693 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: D 103 GLU cc_start: 0.8105 (pt0) cc_final: 0.7817 (pt0) REVERT: D 242 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: D 298 LEU cc_start: 0.9248 (tp) cc_final: 0.8963 (tp) REVERT: D 404 MET cc_start: 0.7835 (mtp) cc_final: 0.7544 (ptt) REVERT: A 217 GLU cc_start: 0.8398 (tp30) cc_final: 0.8186 (tp30) REVERT: A 220 MET cc_start: 0.7913 (mtt) cc_final: 0.7561 (mtm) REVERT: A 383 MET cc_start: 0.7610 (ppp) cc_final: 0.6649 (ppp) REVERT: B 25 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7530 (p0) REVERT: B 41 CYS cc_start: 0.8610 (p) cc_final: 0.8095 (p) REVERT: B 170 TRP cc_start: 0.8368 (m100) cc_final: 0.7931 (m100) REVERT: B 393 LYS cc_start: 0.7723 (mttm) cc_final: 0.7224 (pttt) REVERT: C 17 LEU cc_start: 0.9306 (mt) cc_final: 0.9005 (mt) REVERT: C 98 LEU cc_start: 0.9050 (pt) cc_final: 0.8807 (pt) REVERT: C 147 MET cc_start: 0.7870 (mtp) cc_final: 0.7640 (tpt) REVERT: C 192 GLU cc_start: 0.8477 (tp30) cc_final: 0.8257 (tp30) REVERT: C 399 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6783 (ttm110) REVERT: E 154 ARG cc_start: 0.8916 (ttt-90) cc_final: 0.8660 (ttt-90) REVERT: E 170 MET cc_start: 0.8938 (mtm) cc_final: 0.8683 (mtm) REVERT: E 235 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7552 (mt-10) REVERT: E 247 TYR cc_start: 0.8459 (m-80) cc_final: 0.8091 (m-80) REVERT: E 329 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8026 (tm-30) REVERT: E 331 MET cc_start: 0.8628 (mmt) cc_final: 0.8402 (mmt) outliers start: 83 outliers final: 57 residues processed: 380 average time/residue: 0.2137 time to fit residues: 125.1232 Evaluate side-chains 366 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 306 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 305 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14412 Z= 0.291 Angle : 0.655 11.556 19420 Z= 0.326 Chirality : 0.044 0.294 2151 Planarity : 0.004 0.046 2406 Dihedral : 8.295 70.534 2126 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.32 % Allowed : 16.78 % Favored : 76.91 % 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: 0.14 (0.21), residues: 1673 helix: 2.00 (0.21), residues: 588 sheet: -0.29 (0.29), residues: 353 loop : -1.33 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS C 215 PHE 0.020 0.002 PHE E 282 TYR 0.019 0.002 TYR E 325 ARG 0.007 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 324 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.8164 (pt0) cc_final: 0.7841 (pt0) REVERT: D 140 MET cc_start: 0.8517 (mtm) cc_final: 0.8310 (mtm) REVERT: D 298 LEU cc_start: 0.9281 (tp) cc_final: 0.9018 (tp) REVERT: D 404 MET cc_start: 0.7789 (mtp) cc_final: 0.7526 (ptt) REVERT: A 220 MET cc_start: 0.7976 (mtt) cc_final: 0.7680 (mtm) REVERT: A 383 MET cc_start: 0.7658 (ppp) cc_final: 0.6600 (ppp) REVERT: B 25 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7584 (p0) REVERT: B 41 CYS cc_start: 0.8661 (p) cc_final: 0.8098 (p) REVERT: B 170 TRP cc_start: 0.8357 (m100) cc_final: 0.7872 (m100) REVERT: B 393 LYS cc_start: 0.7742 (mttm) cc_final: 0.7219 (pttt) REVERT: C 17 LEU cc_start: 0.9329 (mt) cc_final: 0.9028 (mt) REVERT: C 147 MET cc_start: 0.7824 (mtp) cc_final: 0.7589 (tpt) REVERT: C 192 GLU cc_start: 0.8485 (tp30) cc_final: 0.8222 (tp30) REVERT: C 239 TRP cc_start: 0.8691 (m-10) cc_final: 0.8381 (m-10) REVERT: C 399 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6870 (ttm110) REVERT: E 154 ARG cc_start: 0.8940 (ttt-90) cc_final: 0.8601 (ttt-90) REVERT: E 235 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7579 (mt-10) REVERT: E 247 TYR cc_start: 0.8483 (m-80) cc_final: 0.8083 (m-80) REVERT: E 329 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 331 MET cc_start: 0.8627 (mmt) cc_final: 0.8366 (mmt) outliers start: 96 outliers final: 74 residues processed: 377 average time/residue: 0.2246 time to fit residues: 129.7427 Evaluate side-chains 377 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 301 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 120 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14412 Z= 0.158 Angle : 0.630 9.260 19420 Z= 0.305 Chirality : 0.044 0.387 2151 Planarity : 0.003 0.029 2406 Dihedral : 7.939 64.641 2126 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.00 % Allowed : 20.07 % Favored : 74.93 % 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: 0.17 (0.21), residues: 1673 helix: 1.99 (0.21), residues: 589 sheet: -0.07 (0.29), residues: 336 loop : -1.39 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 243 HIS 0.006 0.001 HIS A 109 PHE 0.018 0.001 PHE B 13 TYR 0.019 0.001 TYR E 325 ARG 0.005 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 342 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.7033 (tpt170) cc_final: 0.6711 (tpt90) REVERT: D 116 LYS cc_start: 0.8443 (pttp) cc_final: 0.7975 (mtmm) REVERT: D 140 MET cc_start: 0.8401 (mtm) cc_final: 0.8178 (mtm) REVERT: D 163 MET cc_start: 0.8321 (ttm) cc_final: 0.7739 (mtp) REVERT: D 242 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: D 298 LEU cc_start: 0.9302 (tp) cc_final: 0.9038 (tp) REVERT: D 404 MET cc_start: 0.7709 (mtp) cc_final: 0.7462 (ptt) REVERT: A 89 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7827 (ppp) REVERT: A 220 MET cc_start: 0.7834 (mtt) cc_final: 0.7568 (mtm) REVERT: A 383 MET cc_start: 0.7755 (ppp) cc_final: 0.6738 (ppp) REVERT: B 25 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7543 (p0) REVERT: B 41 CYS cc_start: 0.8550 (p) cc_final: 0.8102 (p) REVERT: B 170 TRP cc_start: 0.8314 (m100) cc_final: 0.7698 (m100) REVERT: B 393 LYS cc_start: 0.7697 (mttm) cc_final: 0.7179 (pttt) REVERT: C 17 LEU cc_start: 0.9300 (mt) cc_final: 0.8985 (mt) REVERT: C 147 MET cc_start: 0.7791 (mtp) cc_final: 0.7437 (tpt) REVERT: C 148 ASP cc_start: 0.7963 (p0) cc_final: 0.7742 (p0) REVERT: C 192 GLU cc_start: 0.8435 (tp30) cc_final: 0.8207 (tp30) REVERT: C 239 TRP cc_start: 0.8668 (m-10) cc_final: 0.8445 (m-10) REVERT: E 235 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7592 (mt-10) REVERT: E 247 TYR cc_start: 0.8353 (m-80) cc_final: 0.7976 (m-80) REVERT: E 322 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8641 (tt) REVERT: E 329 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8011 (tm-30) REVERT: E 331 MET cc_start: 0.8609 (mmt) cc_final: 0.8356 (mmt) outliers start: 76 outliers final: 49 residues processed: 381 average time/residue: 0.2195 time to fit residues: 128.1283 Evaluate side-chains 372 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 319 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 14412 Z= 0.440 Angle : 0.755 12.307 19420 Z= 0.378 Chirality : 0.047 0.476 2151 Planarity : 0.005 0.064 2406 Dihedral : 8.031 59.428 2118 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 6.78 % Allowed : 19.41 % Favored : 73.82 % 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: -0.04 (0.21), residues: 1673 helix: 1.84 (0.21), residues: 585 sheet: -0.39 (0.29), residues: 357 loop : -1.42 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 243 HIS 0.005 0.002 HIS D 107 PHE 0.022 0.002 PHE E 282 TYR 0.023 0.002 TYR D 301 ARG 0.012 0.001 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 313 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 140 MET cc_start: 0.8564 (mtm) cc_final: 0.8293 (mtm) REVERT: D 242 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: D 404 MET cc_start: 0.7851 (mtp) cc_final: 0.7559 (ptt) REVERT: A 89 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7877 (ppp) REVERT: A 136 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8903 (pp) REVERT: A 211 GLU cc_start: 0.7922 (pp20) cc_final: 0.7670 (pm20) REVERT: A 220 MET cc_start: 0.8035 (mtt) cc_final: 0.7811 (mtm) REVERT: A 229 ILE cc_start: 0.8279 (mm) cc_final: 0.8037 (mm) REVERT: A 383 MET cc_start: 0.7700 (ppp) cc_final: 0.7463 (ppp) REVERT: B 25 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7629 (p0) REVERT: B 41 CYS cc_start: 0.8637 (p) cc_final: 0.8111 (p) REVERT: B 170 TRP cc_start: 0.8293 (m100) cc_final: 0.7831 (m100) REVERT: B 393 LYS cc_start: 0.7731 (mttm) cc_final: 0.7177 (tttt) REVERT: C 17 LEU cc_start: 0.9358 (mt) cc_final: 0.9025 (mt) REVERT: C 110 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8175 (mm-30) REVERT: C 147 MET cc_start: 0.7947 (mtp) cc_final: 0.7735 (tpt) REVERT: C 211 GLU cc_start: 0.6939 (mp0) cc_final: 0.6609 (mp0) REVERT: C 239 TRP cc_start: 0.8691 (m-10) cc_final: 0.8353 (m-10) REVERT: E 170 MET cc_start: 0.8683 (mtm) cc_final: 0.8452 (ptp) REVERT: E 208 GLN cc_start: 0.8549 (pt0) cc_final: 0.8281 (pt0) REVERT: E 235 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7483 (mt-10) REVERT: E 290 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7605 (mm-30) REVERT: E 294 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8160 (mm) REVERT: E 329 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8114 (tm-30) outliers start: 103 outliers final: 77 residues processed: 371 average time/residue: 0.2012 time to fit residues: 117.8802 Evaluate side-chains 382 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 300 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14412 Z= 0.252 Angle : 0.687 11.101 19420 Z= 0.334 Chirality : 0.045 0.479 2151 Planarity : 0.004 0.048 2406 Dihedral : 7.747 59.587 2118 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.39 % Allowed : 22.37 % Favored : 72.24 % 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: -0.01 (0.21), residues: 1673 helix: 1.86 (0.22), residues: 585 sheet: -0.29 (0.29), residues: 342 loop : -1.43 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 243 HIS 0.003 0.001 HIS A 107 PHE 0.019 0.001 PHE E 282 TYR 0.019 0.001 TYR E 325 ARG 0.006 0.000 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 322 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6963 (tpt170) cc_final: 0.6657 (tpt90) REVERT: D 116 LYS cc_start: 0.8536 (pttp) cc_final: 0.8044 (mtmm) REVERT: D 140 MET cc_start: 0.8493 (mtm) cc_final: 0.8221 (mtm) REVERT: D 163 MET cc_start: 0.8384 (ttm) cc_final: 0.7736 (mtp) REVERT: D 242 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: D 298 LEU cc_start: 0.9163 (tp) cc_final: 0.8816 (tp) REVERT: D 404 MET cc_start: 0.7766 (mtp) cc_final: 0.7487 (ptt) REVERT: A 211 GLU cc_start: 0.7829 (pp20) cc_final: 0.7510 (pm20) REVERT: A 220 MET cc_start: 0.7959 (mtt) cc_final: 0.7733 (mtm) REVERT: A 383 MET cc_start: 0.7684 (ppp) cc_final: 0.6659 (ppp) REVERT: B 25 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7619 (p0) REVERT: B 41 CYS cc_start: 0.8615 (p) cc_final: 0.8185 (p) REVERT: B 170 TRP cc_start: 0.8214 (m100) cc_final: 0.7685 (m100) REVERT: B 393 LYS cc_start: 0.7710 (mttm) cc_final: 0.7192 (pttt) REVERT: C 17 LEU cc_start: 0.9314 (mt) cc_final: 0.9003 (mt) REVERT: C 110 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 211 GLU cc_start: 0.6736 (mp0) cc_final: 0.6530 (mp0) REVERT: C 239 TRP cc_start: 0.8643 (m-10) cc_final: 0.8320 (m-10) REVERT: E 170 MET cc_start: 0.8648 (mtm) cc_final: 0.8398 (ptp) REVERT: E 235 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7569 (mt-10) REVERT: E 247 TYR cc_start: 0.8476 (m-80) cc_final: 0.8064 (m-80) REVERT: E 266 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7759 (t80) REVERT: E 329 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8078 (tm-30) REVERT: E 331 MET cc_start: 0.8637 (mmt) cc_final: 0.8395 (mmt) outliers start: 82 outliers final: 64 residues processed: 368 average time/residue: 0.2011 time to fit residues: 116.4137 Evaluate side-chains 375 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 308 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.0050 chunk 31 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14412 Z= 0.252 Angle : 0.689 10.819 19420 Z= 0.334 Chirality : 0.045 0.468 2151 Planarity : 0.004 0.053 2406 Dihedral : 7.493 59.584 2118 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.72 % Allowed : 22.63 % Favored : 71.64 % 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: -0.02 (0.21), residues: 1673 helix: 1.82 (0.22), residues: 580 sheet: -0.25 (0.29), residues: 342 loop : -1.40 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS D 201 PHE 0.022 0.001 PHE E 282 TYR 0.019 0.001 TYR E 325 ARG 0.005 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 327 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6960 (tpt170) cc_final: 0.6662 (tpt90) REVERT: D 116 LYS cc_start: 0.8526 (pttp) cc_final: 0.7976 (mtmm) REVERT: D 140 MET cc_start: 0.8467 (mtm) cc_final: 0.8184 (mtm) REVERT: D 163 MET cc_start: 0.8372 (ttm) cc_final: 0.7723 (mtp) REVERT: D 242 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: D 404 MET cc_start: 0.7765 (mtp) cc_final: 0.7487 (ptt) REVERT: A 136 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8816 (pp) REVERT: A 195 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8506 (pp) REVERT: A 219 GLN cc_start: 0.8647 (mp10) cc_final: 0.8301 (mp10) REVERT: A 220 MET cc_start: 0.7948 (mtt) cc_final: 0.7734 (mtm) REVERT: A 383 MET cc_start: 0.7754 (ppp) cc_final: 0.6720 (ppp) REVERT: B 25 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7626 (p0) REVERT: B 41 CYS cc_start: 0.8633 (p) cc_final: 0.8154 (p) REVERT: B 170 TRP cc_start: 0.8204 (m100) cc_final: 0.7840 (m100) REVERT: B 263 MET cc_start: 0.9098 (mmm) cc_final: 0.8744 (ttm) REVERT: B 393 LYS cc_start: 0.7709 (mttm) cc_final: 0.7186 (pttt) REVERT: C 17 LEU cc_start: 0.9300 (mt) cc_final: 0.8961 (mt) REVERT: C 93 ILE cc_start: 0.9386 (pt) cc_final: 0.9122 (mp) REVERT: C 110 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8121 (mm-30) REVERT: E 235 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7500 (mt-10) REVERT: E 247 TYR cc_start: 0.8473 (m-80) cc_final: 0.8059 (m-80) REVERT: E 266 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7828 (t80) REVERT: E 294 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8213 (mm) REVERT: E 329 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8108 (tm-30) REVERT: E 331 MET cc_start: 0.8641 (mmt) cc_final: 0.8399 (mmt) outliers start: 87 outliers final: 70 residues processed: 377 average time/residue: 0.2032 time to fit residues: 120.8581 Evaluate side-chains 384 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 308 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 135 optimal weight: 0.4980 chunk 141 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14412 Z= 0.220 Angle : 0.700 10.120 19420 Z= 0.336 Chirality : 0.045 0.460 2151 Planarity : 0.004 0.045 2406 Dihedral : 7.345 59.061 2118 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.53 % Allowed : 23.16 % Favored : 71.32 % 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: -0.01 (0.21), residues: 1673 helix: 1.77 (0.22), residues: 581 sheet: -0.23 (0.28), residues: 352 loop : -1.36 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 286 HIS 0.003 0.001 HIS A 311 PHE 0.022 0.001 PHE E 282 TYR 0.019 0.001 TYR E 325 ARG 0.005 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 329 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6960 (tpt170) cc_final: 0.6664 (tpt90) REVERT: D 116 LYS cc_start: 0.8488 (pttp) cc_final: 0.7948 (mtmm) REVERT: D 163 MET cc_start: 0.8345 (ttm) cc_final: 0.7740 (mtp) REVERT: D 404 MET cc_start: 0.7765 (mtp) cc_final: 0.7482 (ptt) REVERT: A 136 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8800 (pp) REVERT: A 195 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8525 (pp) REVERT: A 219 GLN cc_start: 0.8653 (mp10) cc_final: 0.8348 (mp10) REVERT: A 220 MET cc_start: 0.7918 (mtt) cc_final: 0.7686 (mtm) REVERT: A 383 MET cc_start: 0.7777 (ppp) cc_final: 0.6795 (ppp) REVERT: B 25 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7633 (p0) REVERT: B 41 CYS cc_start: 0.8629 (p) cc_final: 0.8154 (p) REVERT: B 170 TRP cc_start: 0.8168 (m100) cc_final: 0.7779 (m100) REVERT: B 393 LYS cc_start: 0.7746 (mttm) cc_final: 0.7192 (pttt) REVERT: C 17 LEU cc_start: 0.9288 (mt) cc_final: 0.8967 (mt) REVERT: C 93 ILE cc_start: 0.9383 (pt) cc_final: 0.9119 (mp) REVERT: C 110 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8102 (mm-30) REVERT: E 235 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7544 (mt-10) REVERT: E 247 TYR cc_start: 0.8433 (m-80) cc_final: 0.8031 (m-80) REVERT: E 266 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7805 (t80) REVERT: E 294 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8184 (mm) REVERT: E 322 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8699 (tt) REVERT: E 329 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8105 (tm-30) REVERT: E 331 MET cc_start: 0.8637 (mmt) cc_final: 0.8398 (mmt) outliers start: 84 outliers final: 69 residues processed: 379 average time/residue: 0.2110 time to fit residues: 126.3328 Evaluate side-chains 390 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 315 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14412 Z= 0.204 Angle : 0.695 10.607 19420 Z= 0.333 Chirality : 0.045 0.422 2151 Planarity : 0.003 0.039 2406 Dihedral : 7.113 59.360 2118 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.54 % Allowed : 24.08 % Favored : 71.38 % 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: -0.01 (0.21), residues: 1673 helix: 1.72 (0.22), residues: 583 sheet: -0.29 (0.28), residues: 360 loop : -1.29 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS A 311 PHE 0.024 0.001 PHE E 282 TYR 0.020 0.001 TYR E 325 ARG 0.005 0.000 ARG D 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 330 time to evaluate : 1.674 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: D 20 ARG cc_start: 0.6985 (tpt170) cc_final: 0.6696 (tpt90) REVERT: D 116 LYS cc_start: 0.8473 (pttp) cc_final: 0.7989 (mtmm) REVERT: D 140 MET cc_start: 0.8383 (mtm) cc_final: 0.8156 (mtm) REVERT: D 163 MET cc_start: 0.8322 (ttm) cc_final: 0.7875 (mtp) REVERT: D 404 MET cc_start: 0.7692 (mtp) cc_final: 0.7459 (ptt) REVERT: A 89 MET cc_start: 0.8114 (ppp) cc_final: 0.7700 (ppp) REVERT: A 195 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8530 (pp) REVERT: A 220 MET cc_start: 0.7867 (mtt) cc_final: 0.7626 (mtm) REVERT: A 383 MET cc_start: 0.7779 (ppp) cc_final: 0.6832 (ppp) REVERT: B 25 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7654 (p0) REVERT: B 41 CYS cc_start: 0.8582 (p) cc_final: 0.8130 (p) REVERT: B 170 TRP cc_start: 0.8115 (m100) cc_final: 0.7797 (m100) REVERT: B 263 MET cc_start: 0.8976 (mmm) cc_final: 0.8616 (ttm) REVERT: B 393 LYS cc_start: 0.7713 (mttm) cc_final: 0.7174 (pttt) REVERT: C 17 LEU cc_start: 0.9260 (mt) cc_final: 0.8937 (mt) REVERT: C 89 MET cc_start: 0.6677 (mmt) cc_final: 0.5830 (mmt) REVERT: C 93 ILE cc_start: 0.9395 (pt) cc_final: 0.9097 (mp) REVERT: C 110 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8081 (mm-30) REVERT: E 235 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7513 (mt-10) REVERT: E 247 TYR cc_start: 0.8423 (m-80) cc_final: 0.8012 (m-80) REVERT: E 294 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8171 (mm) REVERT: E 322 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8681 (tt) REVERT: E 329 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 331 MET cc_start: 0.8642 (mmt) cc_final: 0.8412 (mmt) outliers start: 69 outliers final: 57 residues processed: 372 average time/residue: 0.2068 time to fit residues: 121.4812 Evaluate side-chains 380 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 319 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104406 restraints weight = 28827.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107587 restraints weight = 15698.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109742 restraints weight = 10329.893| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14412 Z= 0.256 Angle : 0.716 10.924 19420 Z= 0.345 Chirality : 0.045 0.414 2151 Planarity : 0.004 0.039 2406 Dihedral : 7.145 59.146 2118 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.13 % Allowed : 24.14 % Favored : 70.72 % 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: -0.04 (0.21), residues: 1673 helix: 1.70 (0.22), residues: 582 sheet: -0.23 (0.28), residues: 349 loop : -1.36 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 286 HIS 0.003 0.001 HIS A 311 PHE 0.023 0.001 PHE E 282 TYR 0.021 0.001 TYR E 325 ARG 0.005 0.000 ARG D 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.15 seconds wall clock time: 57 minutes 22.69 seconds (3442.69 seconds total)