Starting phenix.real_space_refine on Thu Feb 15 20:03:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td0_25819/02_2024/7td0_25819_trim_updated.pdb" } resolution = 2.83 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= -0.000 sd= 0.963 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 56 5.16 5 C 4363 2.51 5 N 1148 2.21 5 O 1269 1.98 5 H 6471 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 315": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13308 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4397 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 7, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 4797 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3358 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 727 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.57, per 1000 atoms: 0.42 Number of scatterers: 13308 At special positions: 0 Unit cell: (96.824, 95.76, 126.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 1 15.00 O 1269 8.00 N 1148 7.00 C 4363 6.00 H 6471 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 190 " distance=2.02 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=2.33 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " distance=1.89 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=0, symmetry=0 Time building additional restraints: 10.85 Conformation dependent library (CDL) restraints added in 1.5 seconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 40.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'R' and resid 30 through 36 Processing helix chain 'R' and resid 47 through 76 Processing helix chain 'R' and resid 83 through 105 Processing helix chain 'R' and resid 110 through 115 Processing helix chain 'R' and resid 118 through 151 removed outlier: 3.589A pdb=" N PHE R 151 " --> pdb=" O HIS R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 184 Proline residue: R 182 - end of helix Processing helix chain 'R' and resid 204 through 236 Processing helix chain 'R' and resid 252 through 283 removed outlier: 3.662A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 293 through 310 removed outlier: 3.798A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 316 through 321 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 11 through 31 removed outlier: 3.731A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.812A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.803A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.872A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.813A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.882A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.623A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.366A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.842A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 987 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: 5.00 Time building geometry restraints manager: 11.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6446 1.03 - 1.23: 41 1.23 - 1.42: 2936 1.42 - 1.62: 3938 1.62 - 1.81: 82 Bond restraints: 13443 Sorted by residual: bond pdb=" C PHE R 25 " pdb=" O PHE R 25 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.14e-02 7.69e+03 9.36e+00 bond pdb=" N CYS R 24 " pdb=" CA CYS R 24 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.29e-02 6.01e+03 7.64e+00 bond pdb=" N TYR R 26 " pdb=" H TYR R 26 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" N TYR R 26 " pdb=" CA TYR R 26 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.66e+00 bond pdb=" N PHE R 25 " pdb=" H PHE R 25 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 13438 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 161 107.09 - 113.81: 15671 113.81 - 120.54: 4538 120.54 - 127.27: 3689 127.27 - 134.00: 67 Bond angle restraints: 24126 Sorted by residual: angle pdb=" CA PHE R 25 " pdb=" C PHE R 25 " pdb=" O PHE R 25 " ideal model delta sigma weight residual 120.57 116.07 4.50 1.26e+00 6.30e-01 1.27e+01 angle pdb=" CA CYS R 24 " pdb=" C CYS R 24 " pdb=" O CYS R 24 " ideal model delta sigma weight residual 121.44 118.16 3.28 1.17e+00 7.31e-01 7.85e+00 angle pdb=" CA PHE R 25 " pdb=" C PHE R 25 " pdb=" N TYR R 26 " ideal model delta sigma weight residual 116.41 120.54 -4.13 1.53e+00 4.27e-01 7.29e+00 angle pdb=" N MET A 53 " pdb=" CA MET A 53 " pdb=" C MET A 53 " ideal model delta sigma weight residual 111.82 109.05 2.77 1.16e+00 7.43e-01 5.71e+00 angle pdb=" C GLN A 52 " pdb=" N MET A 53 " pdb=" CA MET A 53 " ideal model delta sigma weight residual 120.31 123.79 -3.48 1.52e+00 4.33e-01 5.23e+00 ... (remaining 24121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5968 17.71 - 35.42: 332 35.42 - 53.13: 80 53.13 - 70.84: 21 70.84 - 88.54: 6 Dihedral angle restraints: 6407 sinusoidal: 3274 harmonic: 3133 Sorted by residual: dihedral pdb=" CA ASP A 341 " pdb=" CB ASP A 341 " pdb=" CG ASP A 341 " pdb=" OD1 ASP A 341 " ideal model delta sinusoidal sigma weight residual -30.00 -86.48 56.48 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " pdb=" OD1 ASP B 258 " ideal model delta sinusoidal sigma weight residual -30.00 -86.35 56.35 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " pdb=" CD GLU A 297 " pdb=" OE1 GLU A 297 " ideal model delta sinusoidal sigma weight residual 0.00 88.54 -88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 748 0.031 - 0.061: 243 0.061 - 0.092: 68 0.092 - 0.123: 38 0.123 - 0.153: 14 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CA PHE R 25 " pdb=" N PHE R 25 " pdb=" C PHE R 25 " pdb=" CB PHE R 25 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA MET A 53 " pdb=" N MET A 53 " pdb=" C MET A 53 " pdb=" CB MET A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1108 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 52 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C GLN A 52 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN A 52 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 52 " -0.010 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" N MET A 53 " 0.030 2.00e-02 2.50e+03 pdb=" CA MET A 53 " -0.008 2.00e-02 2.50e+03 pdb=" H MET A 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 26 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" N ASN R 27 " 0.030 2.00e-02 2.50e+03 pdb=" CA ASN R 27 " -0.008 2.00e-02 2.50e+03 pdb=" H ASN R 27 " -0.013 2.00e-02 2.50e+03 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 495 2.18 - 2.79: 26368 2.79 - 3.39: 36337 3.39 - 4.00: 47651 4.00 - 4.60: 73900 Nonbonded interactions: 184751 Sorted by model distance: nonbonded pdb=" O ALA B 106 " pdb=" H GLY B 109 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASP B 254 " pdb=" H ALA B 257 " model vdw 1.639 1.850 nonbonded pdb=" O VAL A 342 " pdb="HD21 ASN A 346 " model vdw 1.674 1.850 nonbonded pdb=" HH TYR A 320 " pdb=" OD1 ASP A 341 " model vdw 1.675 1.850 nonbonded pdb=" HZ1 LYS B 57 " pdb=" OE1 GLU A 216 " model vdw 1.677 1.850 ... (remaining 184746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.880 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: 0.210 Extract box with map and model: 4.040 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.730 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 0.036 6972 Z= 0.163 Angle : 0.453 4.591 9480 Z= 0.273 Chirality : 0.039 0.153 1111 Planarity : 0.003 0.042 1199 Dihedral : 12.581 88.544 2381 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.72 % Allowed : 8.93 % Favored : 90.35 % 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: -1.88 (0.25), residues: 889 helix: -0.14 (0.24), residues: 376 sheet: -1.51 (0.35), residues: 174 loop : -2.30 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.009 0.001 PHE B 151 TYR 0.016 0.001 TYR R 26 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 71 MET cc_start: 0.7065 (mtp) cc_final: 0.6757 (mtp) REVERT: R 77 ASN cc_start: 0.6978 (m-40) cc_final: 0.6525 (m-40) REVERT: B 49 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7451 (ttm-80) REVERT: B 118 ASP cc_start: 0.7274 (p0) cc_final: 0.7008 (p0) REVERT: B 256 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.8025 (mtm-85) REVERT: B 323 ASP cc_start: 0.6327 (t0) cc_final: 0.6040 (t0) REVERT: A 209 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7708 (ptpt) REVERT: A 261 ASP cc_start: 0.7605 (p0) cc_final: 0.7323 (p0) REVERT: A 306 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7337 (mm-40) REVERT: G 58 GLU cc_start: 0.6822 (mm-30) cc_final: 0.5931 (pm20) outliers start: 5 outliers final: 2 residues processed: 178 average time/residue: 1.7999 time to fit residues: 343.4488 Evaluate side-chains 143 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain B residue 67 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6972 Z= 0.237 Angle : 0.477 4.889 9480 Z= 0.264 Chirality : 0.039 0.139 1111 Planarity : 0.003 0.045 1199 Dihedral : 5.538 59.734 982 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.03 % Allowed : 15.85 % Favored : 81.12 % 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: -0.48 (0.27), residues: 889 helix: 1.30 (0.26), residues: 376 sheet: -0.93 (0.36), residues: 172 loop : -1.83 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.001 PHE B 151 TYR 0.008 0.001 TYR A 296 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 26 TYR cc_start: 0.7619 (m-80) cc_final: 0.6656 (m-80) REVERT: R 36 ARG cc_start: 0.7106 (tpp-160) cc_final: 0.6773 (tpp-160) REVERT: R 71 MET cc_start: 0.7181 (mtp) cc_final: 0.6749 (mtp) REVERT: R 77 ASN cc_start: 0.6905 (m-40) cc_final: 0.6473 (m-40) REVERT: R 204 ASP cc_start: 0.7045 (m-30) cc_final: 0.6689 (m-30) REVERT: R 212 ILE cc_start: 0.7109 (mt) cc_final: 0.6888 (mm) REVERT: B 323 ASP cc_start: 0.6267 (t0) cc_final: 0.6037 (t0) REVERT: A 261 ASP cc_start: 0.7694 (p0) cc_final: 0.7400 (p0) REVERT: A 349 LYS cc_start: 0.7252 (tttm) cc_final: 0.6993 (tttp) REVERT: G 58 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6008 (pm20) outliers start: 21 outliers final: 13 residues processed: 159 average time/residue: 1.7313 time to fit residues: 296.4290 Evaluate side-chains 156 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 297 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6972 Z= 0.256 Angle : 0.484 4.870 9480 Z= 0.269 Chirality : 0.040 0.146 1111 Planarity : 0.004 0.047 1199 Dihedral : 5.722 52.533 980 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.03 % Allowed : 16.86 % Favored : 79.11 % 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 (0.28), residues: 889 helix: 1.76 (0.26), residues: 377 sheet: -0.70 (0.37), residues: 172 loop : -1.70 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 195 PHE 0.013 0.001 PHE B 151 TYR 0.008 0.001 TYR A 296 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7106 (tpp-160) cc_final: 0.6861 (tpp80) REVERT: R 53 MET cc_start: 0.7898 (ttp) cc_final: 0.7698 (ttt) REVERT: R 71 MET cc_start: 0.7094 (mtp) cc_final: 0.6764 (mtp) REVERT: R 77 ASN cc_start: 0.6984 (m-40) cc_final: 0.6567 (m-40) REVERT: R 145 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: R 189 ILE cc_start: 0.7911 (mt) cc_final: 0.7674 (tt) REVERT: R 204 ASP cc_start: 0.7131 (m-30) cc_final: 0.6785 (m-30) REVERT: R 212 ILE cc_start: 0.7138 (mt) cc_final: 0.6934 (mm) REVERT: B 49 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7691 (ttm110) REVERT: B 170 ASP cc_start: 0.7145 (t0) cc_final: 0.6942 (t70) REVERT: A 29 LYS cc_start: 0.7362 (ttmt) cc_final: 0.7009 (tppp) REVERT: A 261 ASP cc_start: 0.7690 (p0) cc_final: 0.7421 (p0) REVERT: A 349 LYS cc_start: 0.7231 (tttm) cc_final: 0.6984 (tttp) REVERT: G 21 MET cc_start: 0.3847 (tmm) cc_final: 0.3557 (tmm) REVERT: G 58 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6029 (pm20) outliers start: 28 outliers final: 17 residues processed: 162 average time/residue: 1.6359 time to fit residues: 286.2695 Evaluate side-chains 163 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 297 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6972 Z= 0.247 Angle : 0.484 4.931 9480 Z= 0.269 Chirality : 0.040 0.148 1111 Planarity : 0.004 0.068 1199 Dihedral : 5.772 57.392 980 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.18 % Allowed : 18.16 % Favored : 77.67 % 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: 0.18 (0.28), residues: 889 helix: 1.96 (0.26), residues: 378 sheet: -0.54 (0.38), residues: 172 loop : -1.71 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 195 PHE 0.012 0.001 PHE B 151 TYR 0.007 0.001 TYR A 296 ARG 0.011 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7123 (tpp-160) cc_final: 0.6748 (tpt90) REVERT: R 71 MET cc_start: 0.7117 (mtp) cc_final: 0.6821 (mtp) REVERT: R 77 ASN cc_start: 0.6999 (m-40) cc_final: 0.6548 (m-40) REVERT: R 204 ASP cc_start: 0.7212 (m-30) cc_final: 0.6887 (m-30) REVERT: R 212 ILE cc_start: 0.7136 (mt) cc_final: 0.6927 (mm) REVERT: B 49 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7712 (ttm110) REVERT: B 101 MET cc_start: 0.8629 (mtm) cc_final: 0.8320 (mtm) REVERT: B 134 ARG cc_start: 0.7175 (mtm110) cc_final: 0.6774 (mtp-110) REVERT: B 170 ASP cc_start: 0.7190 (t0) cc_final: 0.6980 (t70) REVERT: A 29 LYS cc_start: 0.7508 (ttmt) cc_final: 0.7129 (tppp) REVERT: A 261 ASP cc_start: 0.7773 (p0) cc_final: 0.7498 (p0) REVERT: A 349 LYS cc_start: 0.7235 (tttm) cc_final: 0.6979 (tttp) REVERT: G 50 LEU cc_start: 0.8466 (mp) cc_final: 0.8259 (mt) REVERT: G 58 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6086 (pm20) outliers start: 29 outliers final: 21 residues processed: 166 average time/residue: 1.5665 time to fit residues: 281.4123 Evaluate side-chains 167 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6972 Z= 0.313 Angle : 0.530 5.057 9480 Z= 0.295 Chirality : 0.041 0.147 1111 Planarity : 0.004 0.052 1199 Dihedral : 5.972 55.278 980 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.61 % Allowed : 18.73 % Favored : 76.66 % 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: 0.07 (0.28), residues: 889 helix: 1.78 (0.27), residues: 382 sheet: -0.52 (0.39), residues: 168 loop : -1.72 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.002 0.001 HIS R 147 PHE 0.014 0.002 PHE B 151 TYR 0.007 0.001 TYR A 296 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7178 (tpp-160) cc_final: 0.6590 (mmt180) REVERT: R 71 MET cc_start: 0.7127 (mtp) cc_final: 0.6829 (mtp) REVERT: R 77 ASN cc_start: 0.6924 (m-40) cc_final: 0.6517 (m-40) REVERT: R 145 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: R 204 ASP cc_start: 0.7232 (m-30) cc_final: 0.6961 (m-30) REVERT: R 212 ILE cc_start: 0.7140 (mt) cc_final: 0.6924 (mm) REVERT: B 49 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7726 (ttm110) REVERT: B 68 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6893 (ttt90) REVERT: B 101 MET cc_start: 0.8661 (mtm) cc_final: 0.8348 (mtm) REVERT: B 134 ARG cc_start: 0.7237 (mtm110) cc_final: 0.6920 (mtm180) REVERT: A 29 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7102 (tppp) REVERT: A 261 ASP cc_start: 0.7770 (p0) cc_final: 0.7485 (p0) REVERT: A 349 LYS cc_start: 0.7270 (tttm) cc_final: 0.7021 (tttp) REVERT: G 58 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6119 (pm20) outliers start: 32 outliers final: 24 residues processed: 165 average time/residue: 1.6601 time to fit residues: 295.5292 Evaluate side-chains 168 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6972 Z= 0.241 Angle : 0.491 4.926 9480 Z= 0.272 Chirality : 0.040 0.151 1111 Planarity : 0.004 0.052 1199 Dihedral : 5.742 53.669 980 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.03 % Allowed : 20.03 % Favored : 75.94 % 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 (0.28), residues: 889 helix: 1.96 (0.26), residues: 382 sheet: -0.49 (0.39), residues: 167 loop : -1.62 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 40 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 104 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7162 (tpp-160) cc_final: 0.6862 (tpt90) REVERT: R 41 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6761 (mm) REVERT: R 71 MET cc_start: 0.7131 (mtp) cc_final: 0.6836 (mtp) REVERT: R 77 ASN cc_start: 0.6988 (m-40) cc_final: 0.6410 (m-40) REVERT: R 145 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: R 204 ASP cc_start: 0.7283 (m-30) cc_final: 0.7023 (m-30) REVERT: R 212 ILE cc_start: 0.7143 (mt) cc_final: 0.6936 (mm) REVERT: B 49 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7704 (ttm110) REVERT: B 101 MET cc_start: 0.8587 (mtm) cc_final: 0.8148 (mtm) REVERT: B 134 ARG cc_start: 0.7227 (mtm110) cc_final: 0.6890 (mtm180) REVERT: B 175 GLN cc_start: 0.8105 (mp10) cc_final: 0.7813 (mp10) REVERT: A 29 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7123 (tppp) REVERT: A 261 ASP cc_start: 0.7809 (p0) cc_final: 0.7538 (p0) REVERT: A 349 LYS cc_start: 0.7234 (tttm) cc_final: 0.6998 (tttp) REVERT: G 58 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6128 (pm20) outliers start: 28 outliers final: 21 residues processed: 161 average time/residue: 1.5747 time to fit residues: 277.0737 Evaluate side-chains 167 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 125 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6972 Z= 0.216 Angle : 0.475 5.693 9480 Z= 0.263 Chirality : 0.039 0.151 1111 Planarity : 0.004 0.052 1199 Dihedral : 5.539 56.141 980 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.61 % Allowed : 20.17 % Favored : 75.22 % 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: 0.39 (0.29), residues: 889 helix: 2.10 (0.26), residues: 382 sheet: -0.46 (0.39), residues: 167 loop : -1.56 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 151 TYR 0.007 0.001 TYR R 26 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7196 (tpp-160) cc_final: 0.6897 (tpt90) REVERT: R 71 MET cc_start: 0.7081 (mtp) cc_final: 0.6797 (mtp) REVERT: R 204 ASP cc_start: 0.7254 (m-30) cc_final: 0.7008 (m-30) REVERT: R 212 ILE cc_start: 0.7137 (mt) cc_final: 0.6931 (mm) REVERT: B 49 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7735 (ttm110) REVERT: B 101 MET cc_start: 0.8606 (mtm) cc_final: 0.8251 (mtm) REVERT: B 134 ARG cc_start: 0.7214 (mtm110) cc_final: 0.6887 (mtm180) REVERT: A 29 LYS cc_start: 0.7482 (ttmt) cc_final: 0.7039 (tppp) REVERT: A 32 ARG cc_start: 0.7145 (mtp180) cc_final: 0.6777 (ttm110) REVERT: A 261 ASP cc_start: 0.7819 (p0) cc_final: 0.7528 (p0) REVERT: A 349 LYS cc_start: 0.7237 (tttm) cc_final: 0.6990 (tttp) REVERT: G 58 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6278 (mp0) outliers start: 32 outliers final: 26 residues processed: 167 average time/residue: 1.5797 time to fit residues: 285.4867 Evaluate side-chains 170 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6972 Z= 0.171 Angle : 0.456 6.140 9480 Z= 0.251 Chirality : 0.039 0.151 1111 Planarity : 0.003 0.050 1199 Dihedral : 5.284 56.689 980 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.18 % Allowed : 20.75 % Favored : 75.07 % 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: 0.59 (0.29), residues: 889 helix: 2.29 (0.26), residues: 382 sheet: -0.38 (0.40), residues: 167 loop : -1.48 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 40 PHE 0.010 0.001 PHE A 189 TYR 0.007 0.001 TYR R 26 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.6890 (tpt90) REVERT: R 71 MET cc_start: 0.7055 (mtp) cc_final: 0.6743 (mtp) REVERT: R 212 ILE cc_start: 0.7157 (mt) cc_final: 0.6952 (mm) REVERT: B 49 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7732 (ttm110) REVERT: B 101 MET cc_start: 0.8575 (mtm) cc_final: 0.8267 (mtm) REVERT: B 134 ARG cc_start: 0.7196 (mtm110) cc_final: 0.6871 (mtm180) REVERT: A 29 LYS cc_start: 0.7468 (ttmt) cc_final: 0.7099 (tppp) REVERT: A 32 ARG cc_start: 0.7105 (mtp180) cc_final: 0.6754 (ttm110) REVERT: A 261 ASP cc_start: 0.7799 (p0) cc_final: 0.7503 (p0) REVERT: A 349 LYS cc_start: 0.7205 (tttm) cc_final: 0.6962 (tttp) REVERT: G 58 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6306 (mp0) outliers start: 29 outliers final: 22 residues processed: 165 average time/residue: 1.7116 time to fit residues: 304.7841 Evaluate side-chains 166 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6972 Z= 0.181 Angle : 0.471 8.198 9480 Z= 0.256 Chirality : 0.039 0.150 1111 Planarity : 0.003 0.051 1199 Dihedral : 5.192 55.020 980 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.46 % Allowed : 21.61 % 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: 0.68 (0.29), residues: 889 helix: 2.35 (0.26), residues: 382 sheet: -0.35 (0.39), residues: 167 loop : -1.41 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.010 0.001 PHE B 151 TYR 0.009 0.001 TYR R 26 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7188 (tpp-160) cc_final: 0.6601 (mmt180) REVERT: R 71 MET cc_start: 0.7059 (mtp) cc_final: 0.6751 (mtp) REVERT: R 212 ILE cc_start: 0.7158 (mt) cc_final: 0.6954 (mm) REVERT: B 49 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7734 (ttm110) REVERT: B 101 MET cc_start: 0.8593 (mtm) cc_final: 0.8281 (mtm) REVERT: A 29 LYS cc_start: 0.7472 (ttmt) cc_final: 0.7101 (tppp) REVERT: A 32 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6748 (ttm110) REVERT: A 261 ASP cc_start: 0.7785 (p0) cc_final: 0.7505 (p0) REVERT: A 349 LYS cc_start: 0.7198 (tttm) cc_final: 0.6948 (tttp) REVERT: G 58 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6314 (mp0) outliers start: 24 outliers final: 19 residues processed: 157 average time/residue: 1.6341 time to fit residues: 277.0390 Evaluate side-chains 159 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6972 Z= 0.210 Angle : 0.489 8.487 9480 Z= 0.266 Chirality : 0.039 0.149 1111 Planarity : 0.005 0.116 1199 Dihedral : 5.175 53.827 980 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.46 % Allowed : 22.19 % Favored : 74.35 % 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: 0.65 (0.29), residues: 889 helix: 2.30 (0.26), residues: 382 sheet: -0.36 (0.39), residues: 167 loop : -1.38 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 40 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR R 26 ARG 0.017 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue MET 254 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 33 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ARG cc_start: 0.7190 (tpp-160) cc_final: 0.6614 (mmt180) REVERT: R 71 MET cc_start: 0.7064 (mtp) cc_final: 0.6756 (mtp) REVERT: R 212 ILE cc_start: 0.7161 (mt) cc_final: 0.6957 (mm) REVERT: B 49 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7727 (ttm110) REVERT: B 101 MET cc_start: 0.8582 (mtm) cc_final: 0.8261 (mtm) REVERT: A 29 LYS cc_start: 0.7485 (ttmt) cc_final: 0.7103 (tppp) REVERT: A 32 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6747 (ttm110) REVERT: A 261 ASP cc_start: 0.7803 (p0) cc_final: 0.7525 (p0) REVERT: A 349 LYS cc_start: 0.7202 (tttm) cc_final: 0.6950 (tttp) REVERT: G 58 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6323 (mp0) outliers start: 24 outliers final: 23 residues processed: 157 average time/residue: 1.5542 time to fit residues: 264.5428 Evaluate side-chains 163 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 113 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.171061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137218 restraints weight = 23431.565| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.28 r_work: 0.3310 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6972 Z= 0.249 Angle : 0.508 8.219 9480 Z= 0.278 Chirality : 0.040 0.151 1111 Planarity : 0.005 0.104 1199 Dihedral : 5.227 51.537 980 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.75 % Allowed : 22.19 % Favored : 74.06 % 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: 0.57 (0.29), residues: 889 helix: 2.23 (0.26), residues: 381 sheet: -0.41 (0.39), residues: 167 loop : -1.39 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 147 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 26 ARG 0.019 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6004.30 seconds wall clock time: 105 minutes 49.85 seconds (6349.85 seconds total)