Starting phenix.real_space_refine on Tue Feb 20 14:01:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/02_2024/6v9q_21126_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/02_2024/6v9q_21126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/02_2024/6v9q_21126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/02_2024/6v9q_21126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/02_2024/6v9q_21126_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/02_2024/6v9q_21126_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. 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 Zn 4 6.06 5 P 60 5.49 5 S 151 5.16 5 C 17670 2.51 5 N 4836 2.21 5 O 5369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 58": "NH1" <-> "NH2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 274": "NH1" <-> "NH2" Residue "I TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ARG 286": "NH1" <-> "NH2" Residue "G PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 291": "NH1" <-> "NH2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 291": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 102": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28090 Number of models: 1 Model: "" Number of chains: 13 Chain: "K" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 36} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3573 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 8 Chain: "J" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3075 Classifications: {'peptide': 378} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 359} Chain breaks: 2 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3050 Classifications: {'peptide': 374} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 355} Chain breaks: 3 Chain: "G" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2453 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 2 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2731 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2713 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "E" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1113 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 4 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6062 SG CYS J 150 47.157 20.700 66.358 1.00102.18 S ATOM 6146 SG CYS J 161 42.892 16.042 84.318 1.00100.75 S ATOM 8946 SG CYS I 128 72.664 48.965 21.648 1.00 93.85 S ATOM 8967 SG CYS I 131 68.984 48.100 23.124 1.00 93.80 S ATOM 9137 SG CYS I 150 71.768 45.717 24.459 1.00 94.95 S ATOM 9221 SG CYS I 161 79.152 60.111 14.422 1.00 97.87 S ATOM 9349 SG CYS I 178 77.076 63.435 15.202 1.00 94.48 S ATOM 9370 SG CYS I 181 77.859 62.368 11.483 1.00 96.74 S Time building chain proxies: 14.92, per 1000 atoms: 0.53 Number of scatterers: 28090 At special positions: 0 Unit cell: (125.28, 201.96, 174.96, 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) Zn 4 29.99 S 151 16.00 P 60 15.00 O 5369 8.00 N 4836 7.00 C 17670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 10.41 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 150 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 131 " pdb=" ZN I 402 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 178 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 181 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 161 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" ND1 HIS J 153 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 150 " pdb=" ZN J 402 " pdb="ZN ZN J 402 " - pdb=" SG CYS J 161 " 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6358 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 50 sheets defined 33.3% alpha, 15.5% beta 5 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 8.66 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.561A pdb=" N ALA A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 removed outlier: 3.735A pdb=" N LEU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.625A pdb=" N TRP A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 4.533A pdb=" N THR A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.563A pdb=" N GLY A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.541A pdb=" N ASN A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.352A pdb=" N LYS A 517 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 519 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.717A pdb=" N ALA A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.606A pdb=" N ALA A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'J' and resid 13 through 25 removed outlier: 3.839A pdb=" N ILE J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG J 20 " --> pdb=" O SER J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 44 Processing helix chain 'J' and resid 48 through 52 removed outlier: 3.552A pdb=" N THR J 51 " --> pdb=" O GLY J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.551A pdb=" N ALA J 79 " --> pdb=" O PHE J 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.537A pdb=" N ALA J 93 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.632A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE J 144 " --> pdb=" O LEU J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.537A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.766A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 224 " --> pdb=" O ARG J 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 231 " --> pdb=" O TRP J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 246 removed outlier: 3.677A pdb=" N VAL J 241 " --> pdb=" O HIS J 237 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN J 246 " --> pdb=" O GLN J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 265 removed outlier: 3.593A pdb=" N ILE J 255 " --> pdb=" O PHE J 251 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 279 Processing helix chain 'J' and resid 297 through 307 Processing helix chain 'J' and resid 325 through 333 removed outlier: 3.615A pdb=" N THR J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 369 through 380 Processing helix chain 'J' and resid 386 through 390 removed outlier: 4.050A pdb=" N PHE J 389 " --> pdb=" O ASN J 386 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 390 " --> pdb=" O ARG J 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 386 through 390' Processing helix chain 'I' and resid 13 through 25 removed outlier: 3.839A pdb=" N ILE I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.604A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.551A pdb=" N THR I 51 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.552A pdb=" N ALA I 79 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 93 removed outlier: 3.536A pdb=" N ALA I 93 " --> pdb=" O LEU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.632A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 173 Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.536A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 231 removed outlier: 3.766A pdb=" N TRP I 221 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL I 224 " --> pdb=" O ARG I 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 231 " --> pdb=" O TRP I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 246 removed outlier: 3.678A pdb=" N VAL I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 246 " --> pdb=" O GLN I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 265 removed outlier: 3.594A pdb=" N ILE I 255 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 297 through 307 Processing helix chain 'I' and resid 325 through 333 removed outlier: 3.614A pdb=" N THR I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL I 330 " --> pdb=" O LEU I 326 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 386 through 390 removed outlier: 4.050A pdb=" N PHE I 389 " --> pdb=" O ASN I 386 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 390 " --> pdb=" O ARG I 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 386 through 390' Processing helix chain 'G' and resid 105 through 123 Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.930A pdb=" N ASN G 135 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.615A pdb=" N PHE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 199 removed outlier: 3.812A pdb=" N MET G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 269 removed outlier: 3.526A pdb=" N ALA G 267 " --> pdb=" O LYS G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 312 removed outlier: 3.737A pdb=" N GLN G 311 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN G 312 " --> pdb=" O SER G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 321 removed outlier: 4.117A pdb=" N GLU G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL G 319 " --> pdb=" O HIS G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 344 removed outlier: 3.545A pdb=" N ASN G 340 " --> pdb=" O PHE G 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.558A pdb=" N VAL B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.873A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.880A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 3.781A pdb=" N MET B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.576A pdb=" N ALA B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.508A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 removed outlier: 4.054A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 3.897A pdb=" N ASP B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.837A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 138 " --> pdb=" O MET C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.857A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.680A pdb=" N MET C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.554A pdb=" N ALA C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.853A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 321 removed outlier: 3.554A pdb=" N ILE C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 319 " --> pdb=" O HIS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 removed outlier: 3.604A pdb=" N ASP C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.890A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.782A pdb=" N PHE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.620A pdb=" N MET D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 314 through 321 removed outlier: 4.017A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.691A pdb=" N LEU D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.906A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.829A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 199 removed outlier: 3.754A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.529A pdb=" N ALA E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.593A pdb=" N GLN E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 321 removed outlier: 4.034A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 344 removed outlier: 3.770A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 removed outlier: 4.020A pdb=" N GLN F 67 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 Processing helix chain 'F' and resid 125 through 137 removed outlier: 3.838A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.823A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 3.935A pdb=" N MET F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.546A pdb=" N ALA F 267 " --> pdb=" O LYS F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.628A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 4.091A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 344 removed outlier: 3.758A pdb=" N ASP F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 35 removed outlier: 4.406A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR H 33 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 80 removed outlier: 3.952A pdb=" N LEU H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.502A pdb=" N ALA H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.560A pdb=" N PHE H 138 " --> pdb=" O PRO H 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 203 removed outlier: 4.646A pdb=" N LEU A 597 " --> pdb=" O TYR A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 7.206A pdb=" N ILE A 590 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU A 572 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU A 592 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR A 570 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 594 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 16.048A pdb=" N SER A 566 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 568 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237 removed outlier: 5.973A pdb=" N LEU A 261 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 443 removed outlier: 4.013A pdb=" N SER A 437 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AB1, first strand: chain 'J' and resid 95 through 100 removed outlier: 3.669A pdb=" N THR J 97 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA J 107 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 322 through 323 removed outlier: 3.511A pdb=" N PHE J 367 " --> pdb=" O MET J 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 95 through 100 removed outlier: 3.669A pdb=" N THR I 97 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA I 107 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.511A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.506A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 24 current: chain 'G' and resid 151 through 158 removed outlier: 6.448A pdb=" N TRP G 152 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP G 170 " --> pdb=" O TRP G 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.727A pdb=" N ARG G 28 " --> pdb=" O TRP G 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 84 through 93 current: chain 'G' and resid 248 through 251 Processing sheet with id=AB8, first strand: chain 'G' and resid 270 through 272 Processing sheet with id=AB9, first strand: chain 'G' and resid 289 through 290 removed outlier: 3.717A pdb=" N THR G 295 " --> pdb=" O HIS G 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 23 current: chain 'B' and resid 151 through 155 removed outlier: 6.559A pdb=" N TRP B 152 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 170 " --> pdb=" O TRP B 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 93 current: chain 'B' and resid 248 through 251 Processing sheet with id=AC4, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AC5, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'B' and resid 289 through 290 removed outlier: 3.718A pdb=" N THR B 295 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AC8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.802A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 152 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 170 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.110A pdb=" N PHE C 20 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL C 22 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 14.136A pdb=" N ARG C 255 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 35 through 41 removed outlier: 8.473A pdb=" N SER C 243 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN C 72 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AD3, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.718A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AD5, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.941A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP D 152 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 170 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.114A pdb=" N PHE D 20 " --> pdb=" O PRO D 257 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N VAL D 22 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 14.029A pdb=" N ARG D 255 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AD8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AD9, first strand: chain 'D' and resid 289 through 290 removed outlier: 3.612A pdb=" N THR D 295 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AE2, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.502A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 152 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E 170 " --> pdb=" O TRP E 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 29 through 31 removed outlier: 4.187A pdb=" N PHE E 20 " --> pdb=" O PRO E 257 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N VAL E 22 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 14.005A pdb=" N ARG E 255 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AE5, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AE6, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.665A pdb=" N THR E 295 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 102 through 103 Processing sheet with id=AE8, first strand: chain 'F' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 23 current: chain 'F' and resid 151 through 158 removed outlier: 6.557A pdb=" N TRP F 152 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP F 170 " --> pdb=" O TRP F 152 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 93 current: chain 'F' and resid 248 through 251 Processing sheet with id=AF1, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AF2, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AF3, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AF4, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AF5, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.666A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 8.96 Time building geometry restraints manager: 11.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6795 1.33 - 1.45: 6552 1.45 - 1.57: 15234 1.57 - 1.69: 120 1.69 - 1.81: 219 Bond restraints: 28920 Sorted by residual: bond pdb=" N GLU G 280 " pdb=" CA GLU G 280 " ideal model delta sigma weight residual 1.453 1.489 -0.036 9.20e-03 1.18e+04 1.50e+01 bond pdb=" N VAL J 268 " pdb=" CA VAL J 268 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL H 42 " pdb=" CA VAL H 42 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 bond pdb=" N GLU G 277 " pdb=" CA GLU G 277 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" N ASP G 273 " pdb=" CA ASP G 273 " ideal model delta sigma weight residual 1.458 1.487 -0.029 9.00e-03 1.23e+04 1.03e+01 ... (remaining 28915 not shown) Histogram of bond angle deviations from ideal: 94.93 - 103.01: 296 103.01 - 111.08: 11191 111.08 - 119.16: 12850 119.16 - 127.23: 14668 127.23 - 135.31: 500 Bond angle restraints: 39505 Sorted by residual: angle pdb=" N ALA E 205 " pdb=" CA ALA E 205 " pdb=" C ALA E 205 " ideal model delta sigma weight residual 111.02 118.93 -7.91 1.25e+00 6.40e-01 4.00e+01 angle pdb=" N ALA C 205 " pdb=" CA ALA C 205 " pdb=" C ALA C 205 " ideal model delta sigma weight residual 111.02 118.66 -7.64 1.25e+00 6.40e-01 3.74e+01 angle pdb=" N ALA F 205 " pdb=" CA ALA F 205 " pdb=" C ALA F 205 " ideal model delta sigma weight residual 111.02 118.33 -7.31 1.25e+00 6.40e-01 3.42e+01 angle pdb=" C GLU C 96 " pdb=" N LEU C 97 " pdb=" CA LEU C 97 " ideal model delta sigma weight residual 120.29 128.36 -8.07 1.42e+00 4.96e-01 3.23e+01 angle pdb=" N MET A 564 " pdb=" CA MET A 564 " pdb=" C MET A 564 " ideal model delta sigma weight residual 110.91 117.55 -6.64 1.17e+00 7.31e-01 3.22e+01 ... (remaining 39500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 16882 34.87 - 69.74: 354 69.74 - 104.60: 32 104.60 - 139.47: 1 139.47 - 174.34: 5 Dihedral angle restraints: 17274 sinusoidal: 7497 harmonic: 9777 Sorted by residual: dihedral pdb=" O4' U K 42 " pdb=" C1' U K 42 " pdb=" N1 U K 42 " pdb=" C2 U K 42 " ideal model delta sinusoidal sigma weight residual 200.00 44.90 155.10 1 1.50e+01 4.44e-03 8.14e+01 dihedral pdb=" O4' C K 38 " pdb=" C1' C K 38 " pdb=" N1 C K 38 " pdb=" C2 C K 38 " ideal model delta sinusoidal sigma weight residual 232.00 57.66 174.34 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C K 12 " pdb=" C1' C K 12 " pdb=" N1 C K 12 " pdb=" C2 C K 12 " ideal model delta sinusoidal sigma weight residual 200.00 76.85 123.15 1 1.50e+01 4.44e-03 6.60e+01 ... (remaining 17271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3521 0.079 - 0.159: 727 0.159 - 0.238: 97 0.238 - 0.318: 26 0.318 - 0.397: 3 Chirality restraints: 4374 Sorted by residual: chirality pdb=" CG LEU G 112 " pdb=" CB LEU G 112 " pdb=" CD1 LEU G 112 " pdb=" CD2 LEU G 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB THR D 146 " pdb=" CA THR D 146 " pdb=" OG1 THR D 146 " pdb=" CG2 THR D 146 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C3' C K 46 " pdb=" C4' C K 46 " pdb=" O3' C K 46 " pdb=" C2' C K 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 4371 not shown) Planarity restraints: 4822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 11 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO H 12 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 9 " 0.018 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR D 9 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR D 9 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 9 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 9 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 9 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 9 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 9 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 194 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO A 195 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " -0.043 5.00e-02 4.00e+02 ... (remaining 4819 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 283 2.61 - 3.18: 22430 3.18 - 3.76: 42349 3.76 - 4.33: 61001 4.33 - 4.90: 100201 Nonbonded interactions: 226264 Sorted by model distance: nonbonded pdb=" O2' A K 44 " pdb=" O5' A K 45 " model vdw 2.040 2.440 nonbonded pdb=" O2' A K 44 " pdb=" OP1 A K 45 " model vdw 2.102 2.440 nonbonded pdb=" O SER G 95 " pdb=" OG SER G 95 " model vdw 2.132 2.440 nonbonded pdb=" O SER F 95 " pdb=" OG SER F 95 " model vdw 2.134 2.440 nonbonded pdb=" O SER D 95 " pdb=" OG SER D 95 " model vdw 2.149 2.440 ... (remaining 226259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'C' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'D' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'E' and (resid 1 through 36 or resid 73 through 350)) selection = (chain 'F' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'G' and (resid 1 through 228 or resid 242 through 350)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 265 or resid 270 through 391 or resid 401 throug \ h 402)) } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 6.500 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 79.370 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.150 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.008 0.110 28920 Z= 0.544 Angle : 1.123 11.907 39505 Z= 0.660 Chirality : 0.068 0.397 4374 Planarity : 0.008 0.083 4822 Dihedral : 14.169 174.339 10916 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 1.56 % Allowed : 5.41 % Favored : 93.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.97 % 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: -4.27 (0.11), residues: 3269 helix: -3.89 (0.09), residues: 1090 sheet: -1.51 (0.22), residues: 497 loop : -2.47 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 274 HIS 0.019 0.002 HIS D 335 PHE 0.037 0.004 PHE G 307 TYR 0.053 0.004 TYR D 9 ARG 0.011 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 745 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6215 (tpp) cc_final: 0.4174 (mpt) REVERT: A 522 PHE cc_start: 0.8157 (m-80) cc_final: 0.7938 (m-80) REVERT: A 543 TYR cc_start: 0.7174 (t80) cc_final: 0.6775 (t80) REVERT: A 570 TYR cc_start: 0.7983 (m-80) cc_final: 0.7445 (m-80) REVERT: J 2 PHE cc_start: 0.5111 (t80) cc_final: 0.4836 (t80) REVERT: J 154 ASN cc_start: 0.5804 (m110) cc_final: 0.4611 (p0) REVERT: J 238 PHE cc_start: 0.6493 (t80) cc_final: 0.6002 (t80) REVERT: I 38 LYS cc_start: 0.8334 (tttt) cc_final: 0.7773 (tttt) REVERT: I 86 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: I 154 ASN cc_start: 0.6573 (m110) cc_final: 0.6330 (t0) REVERT: I 177 ILE cc_start: 0.7149 (mm) cc_final: 0.6815 (pt) REVERT: G 193 MET cc_start: 0.8677 (mtt) cc_final: 0.8464 (mtp) REVERT: G 331 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7861 (mt) REVERT: B 113 VAL cc_start: 0.7782 (t) cc_final: 0.7412 (m) REVERT: E 180 ASP cc_start: 0.8752 (m-30) cc_final: 0.8508 (m-30) REVERT: E 193 MET cc_start: 0.9059 (mtt) cc_final: 0.8794 (mtm) REVERT: F 204 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6793 (tm) REVERT: H 44 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: H 102 ARG cc_start: 0.6393 (pmt100) cc_final: 0.5169 (ttm170) REVERT: H 109 LYS cc_start: 0.8186 (mttt) cc_final: 0.7799 (mmtt) outliers start: 46 outliers final: 12 residues processed: 778 average time/residue: 1.5628 time to fit residues: 1392.3565 Evaluate side-chains 380 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 365 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 1.9990 chunk 253 optimal weight: 0.0570 chunk 140 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 0.0370 chunk 194 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 226 HIS A 227 GLN A 235 HIS A 420 HIS A 486 ASN A 610 ASN J 60 ASN J 66 ASN J 143 HIS J 237 HIS J 313 GLN J 381 GLN I 47 ASN I 60 ASN I 66 ASN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 HIS I 296 HIS I 324 ASN G 299 HIS G 315 HIS G 328 GLN B 42 GLN B 77 HIS B 84 HIS B 114 GLN B 299 HIS B 348 GLN C 77 HIS C 110 GLN C 184 ASN C 241 GLN C 299 HIS C 315 HIS D 77 HIS D 84 HIS D 110 GLN D 299 HIS E 42 GLN E 55 GLN E 77 HIS E 299 HIS F 99 GLN F 299 HIS F 328 GLN H 16 ASN H 32 ASN H 39 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28920 Z= 0.186 Angle : 0.629 10.802 39505 Z= 0.325 Chirality : 0.042 0.240 4374 Planarity : 0.006 0.066 4822 Dihedral : 15.157 178.048 4548 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.57 % Allowed : 14.14 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.83 (0.13), residues: 3269 helix: -2.01 (0.13), residues: 1102 sheet: -0.85 (0.24), residues: 468 loop : -2.07 (0.13), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 312 HIS 0.011 0.001 HIS A 85 PHE 0.023 0.002 PHE J 235 TYR 0.023 0.002 TYR J 219 ARG 0.006 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 420 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6757 (tpp) cc_final: 0.4938 (mpt) REVERT: A 210 TYR cc_start: 0.8791 (m-80) cc_final: 0.8528 (m-80) REVERT: A 543 TYR cc_start: 0.7088 (t80) cc_final: 0.6794 (t80) REVERT: A 570 TYR cc_start: 0.7833 (m-80) cc_final: 0.7241 (m-80) REVERT: J 1 MET cc_start: 0.1840 (ttp) cc_final: 0.0948 (tmm) REVERT: J 169 TYR cc_start: 0.4014 (p90) cc_final: 0.3380 (p90) REVERT: I 177 ILE cc_start: 0.7161 (mm) cc_final: 0.6851 (pt) REVERT: I 258 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5972 (tp30) REVERT: I 342 MET cc_start: 0.4653 (OUTLIER) cc_final: 0.4418 (ttm) REVERT: I 348 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4859 (pt) REVERT: G 193 MET cc_start: 0.8820 (mtt) cc_final: 0.8553 (mtt) REVERT: G 204 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6030 (tp) REVERT: B 162 ASN cc_start: 0.7329 (p0) cc_final: 0.7078 (p0) REVERT: B 172 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7452 (ttm170) REVERT: B 294 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8363 (m) REVERT: C 42 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: C 210 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7194 (ttm170) REVERT: D 3 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8593 (mp) REVERT: D 63 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: D 96 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: E 176 THR cc_start: 0.8831 (m) cc_final: 0.8627 (m) REVERT: E 180 ASP cc_start: 0.8731 (m-30) cc_final: 0.8482 (m-30) REVERT: E 193 MET cc_start: 0.8960 (mtt) cc_final: 0.8729 (mtt) REVERT: E 277 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6158 (mp0) REVERT: E 287 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.5531 (p90) REVERT: F 146 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8223 (p) REVERT: H 73 TYR cc_start: 0.7882 (t80) cc_final: 0.7523 (t80) REVERT: H 102 ARG cc_start: 0.6238 (pmt100) cc_final: 0.5377 (tpt170) REVERT: H 109 LYS cc_start: 0.8187 (mttt) cc_final: 0.7870 (mttm) REVERT: H 137 SER cc_start: 0.8912 (p) cc_final: 0.8673 (p) REVERT: H 162 ASN cc_start: 0.8072 (m-40) cc_final: 0.7668 (m110) outliers start: 135 outliers final: 44 residues processed: 508 average time/residue: 1.3303 time to fit residues: 793.9277 Evaluate side-chains 382 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 326 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 342 MET Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 155 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 303 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 301 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS J 313 GLN J 381 GLN I 42 GLN I 50 GLN I 80 GLN I 154 ASN G 35 ASN B 114 GLN C 110 GLN C 241 GLN D 110 GLN E 55 GLN F 99 GLN H 71 GLN ** H 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28920 Z= 0.223 Angle : 0.608 9.792 39505 Z= 0.312 Chirality : 0.043 0.265 4374 Planarity : 0.005 0.063 4822 Dihedral : 14.899 178.684 4537 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.04 % Allowed : 15.56 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.92 (0.13), residues: 3269 helix: -0.84 (0.15), residues: 1108 sheet: -0.70 (0.23), residues: 499 loop : -1.74 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 161 HIS 0.024 0.001 HIS H 150 PHE 0.024 0.002 PHE H 163 TYR 0.017 0.002 TYR B 175 ARG 0.006 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 343 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6155 (mm-30) REVERT: A 177 MET cc_start: 0.6322 (tpp) cc_final: 0.4833 (mpt) REVERT: A 247 MET cc_start: 0.8563 (tpt) cc_final: 0.7913 (tpt) REVERT: A 543 TYR cc_start: 0.7128 (t80) cc_final: 0.6908 (t80) REVERT: A 570 TYR cc_start: 0.7942 (m-80) cc_final: 0.7431 (m-80) REVERT: J 169 TYR cc_start: 0.4004 (p90) cc_final: 0.3549 (p90) REVERT: J 217 LYS cc_start: 0.7529 (mmmm) cc_final: 0.6816 (mmmt) REVERT: J 331 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7628 (ttm) REVERT: J 384 GLU cc_start: 0.6881 (pt0) cc_final: 0.6598 (pt0) REVERT: I 99 MET cc_start: 0.6977 (mtm) cc_final: 0.6607 (mtm) REVERT: I 177 ILE cc_start: 0.7147 (mm) cc_final: 0.6832 (pt) REVERT: I 234 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5982 (pm20) REVERT: I 258 GLU cc_start: 0.6583 (mm-30) cc_final: 0.5974 (tp30) REVERT: I 304 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6074 (mp) REVERT: I 332 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6685 (mt) REVERT: I 342 MET cc_start: 0.5091 (OUTLIER) cc_final: 0.4495 (ttm) REVERT: I 348 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.5199 (pt) REVERT: G 193 MET cc_start: 0.8855 (mtt) cc_final: 0.8561 (mtt) REVERT: G 220 MET cc_start: 0.8468 (ttp) cc_final: 0.8221 (ttm) REVERT: G 329 GLU cc_start: 0.7228 (tt0) cc_final: 0.7028 (tt0) REVERT: B 58 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8055 (mttm) REVERT: B 115 LEU cc_start: 0.8920 (tp) cc_final: 0.8678 (tp) REVERT: B 172 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7584 (ttm170) REVERT: B 215 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 294 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8350 (m) REVERT: B 314 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: C 42 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: C 58 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7953 (mmmm) REVERT: D 63 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: D 96 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: D 287 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7465 (p90) REVERT: E 176 THR cc_start: 0.8823 (m) cc_final: 0.8585 (m) REVERT: E 193 MET cc_start: 0.9061 (mtt) cc_final: 0.8748 (mtt) REVERT: E 220 MET cc_start: 0.7477 (ttt) cc_final: 0.7168 (ttt) REVERT: E 222 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7815 (mtm-85) REVERT: E 287 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.5975 (p90) REVERT: F 293 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7805 (p0) REVERT: H 102 ARG cc_start: 0.6268 (pmt100) cc_final: 0.5380 (tpt170) REVERT: H 109 LYS cc_start: 0.8224 (mttt) cc_final: 0.7857 (mmtt) REVERT: H 152 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7992 (mt) REVERT: H 162 ASN cc_start: 0.8070 (m-40) cc_final: 0.7611 (m110) outliers start: 149 outliers final: 65 residues processed: 452 average time/residue: 1.3918 time to fit residues: 743.8545 Evaluate side-chains 392 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 307 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 342 MET Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 0.0270 chunk 228 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 322 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN I 50 GLN I 80 GLN I 154 ASN G 35 ASN B 114 GLN C 110 GLN C 349 HIS D 110 GLN H 32 ASN ** H 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28920 Z= 0.208 Angle : 0.576 9.398 39505 Z= 0.296 Chirality : 0.042 0.220 4374 Planarity : 0.005 0.054 4822 Dihedral : 14.651 179.962 4529 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.67 % Allowed : 16.75 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.41 (0.14), residues: 3269 helix: -0.22 (0.15), residues: 1115 sheet: -0.36 (0.24), residues: 482 loop : -1.61 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 142 HIS 0.007 0.001 HIS C 335 PHE 0.027 0.001 PHE H 163 TYR 0.017 0.002 TYR B 175 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 325 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7451 (m-80) cc_final: 0.7159 (m-80) REVERT: A 177 MET cc_start: 0.6413 (tpp) cc_final: 0.5068 (mpt) REVERT: A 247 MET cc_start: 0.8722 (tpt) cc_final: 0.8034 (tpt) REVERT: A 543 TYR cc_start: 0.7155 (t80) cc_final: 0.6898 (t80) REVERT: A 562 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6780 (mt0) REVERT: A 570 TYR cc_start: 0.7995 (m-80) cc_final: 0.7512 (m-80) REVERT: J 95 ASN cc_start: 0.4988 (OUTLIER) cc_final: 0.4471 (m-40) REVERT: J 169 TYR cc_start: 0.3947 (p90) cc_final: 0.3545 (p90) REVERT: J 217 LYS cc_start: 0.7565 (mmmm) cc_final: 0.6832 (mmmt) REVERT: J 384 GLU cc_start: 0.6819 (pt0) cc_final: 0.6480 (pt0) REVERT: I 99 MET cc_start: 0.6983 (mtm) cc_final: 0.6487 (mtm) REVERT: I 168 ASP cc_start: 0.7187 (t0) cc_final: 0.6921 (t0) REVERT: I 177 ILE cc_start: 0.7217 (mm) cc_final: 0.6863 (pt) REVERT: I 234 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5908 (pm20) REVERT: I 258 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6056 (tp30) REVERT: I 342 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4586 (ttm) REVERT: G 2 LYS cc_start: 0.8401 (mmmm) cc_final: 0.7539 (tptt) REVERT: G 112 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8208 (mm) REVERT: G 193 MET cc_start: 0.8868 (mtt) cc_final: 0.8535 (mtt) REVERT: G 329 GLU cc_start: 0.7226 (tt0) cc_final: 0.7017 (tt0) REVERT: G 349 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6489 (t70) REVERT: B 39 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8934 (pp) REVERT: B 58 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8007 (mttm) REVERT: B 215 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8810 (mm) REVERT: B 294 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8424 (m) REVERT: C 42 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: D 63 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: D 96 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: D 287 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7392 (p90) REVERT: E 176 THR cc_start: 0.8833 (m) cc_final: 0.8587 (m) REVERT: E 193 MET cc_start: 0.9091 (mtt) cc_final: 0.8811 (mtt) REVERT: E 220 MET cc_start: 0.7609 (ttt) cc_final: 0.7335 (ttt) REVERT: E 222 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7810 (mtm-85) REVERT: E 287 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.5984 (p90) REVERT: F 146 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8422 (p) REVERT: F 164 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: F 292 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: F 293 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7601 (p0) REVERT: H 102 ARG cc_start: 0.6275 (pmt100) cc_final: 0.5382 (tpt170) REVERT: H 109 LYS cc_start: 0.8244 (mttt) cc_final: 0.7893 (mmtt) REVERT: H 150 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6213 (t-90) outliers start: 138 outliers final: 64 residues processed: 429 average time/residue: 1.3570 time to fit residues: 680.9747 Evaluate side-chains 380 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 295 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 288 ARG Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 342 MET Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 240 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 23 ASN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 80 GLN I 154 ASN B 114 GLN B 184 ASN C 55 GLN C 84 HIS C 110 GLN D 110 GLN E 55 GLN H 32 ASN H 162 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28920 Z= 0.293 Angle : 0.634 9.459 39505 Z= 0.325 Chirality : 0.044 0.213 4374 Planarity : 0.005 0.057 4822 Dihedral : 14.659 179.563 4529 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 4.91 % Allowed : 16.98 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.23 (0.14), residues: 3269 helix: 0.02 (0.16), residues: 1115 sheet: -0.33 (0.24), residues: 489 loop : -1.55 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 142 HIS 0.009 0.001 HIS C 335 PHE 0.027 0.002 PHE H 163 TYR 0.019 0.002 TYR G 9 ARG 0.007 0.001 ARG H 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 310 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7391 (m-80) cc_final: 0.7147 (m-80) REVERT: A 177 MET cc_start: 0.6124 (tpp) cc_final: 0.4636 (mpt) REVERT: A 443 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.6445 (m-70) REVERT: A 543 TYR cc_start: 0.7197 (t80) cc_final: 0.6960 (t80) REVERT: A 562 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6897 (mt0) REVERT: J 95 ASN cc_start: 0.5041 (OUTLIER) cc_final: 0.4529 (m-40) REVERT: J 210 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7061 (mtpp) REVERT: J 331 MET cc_start: 0.7880 (ttt) cc_final: 0.7673 (ttm) REVERT: J 384 GLU cc_start: 0.6939 (pt0) cc_final: 0.6596 (pt0) REVERT: I 99 MET cc_start: 0.6888 (mtm) cc_final: 0.6541 (mtm) REVERT: I 177 ILE cc_start: 0.7172 (mm) cc_final: 0.6812 (pt) REVERT: I 234 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5906 (pm20) REVERT: G 112 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8265 (mm) REVERT: G 193 MET cc_start: 0.8854 (mtt) cc_final: 0.8478 (mtt) REVERT: G 329 GLU cc_start: 0.7214 (tt0) cc_final: 0.6979 (tt0) REVERT: B 39 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9021 (pp) REVERT: B 44 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: B 58 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8029 (mttm) REVERT: B 178 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7815 (ttm110) REVERT: B 215 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 294 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8476 (m) REVERT: B 314 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: C 42 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: D 63 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: D 96 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: D 287 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7383 (p90) REVERT: D 346 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7820 (mtm) REVERT: E 57 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7894 (pt) REVERT: E 193 MET cc_start: 0.9120 (mtt) cc_final: 0.8806 (mtt) REVERT: E 220 MET cc_start: 0.7700 (ttt) cc_final: 0.7441 (ttt) REVERT: E 222 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.7848 (mtm-85) REVERT: E 277 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6236 (mp0) REVERT: E 287 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.6014 (p90) REVERT: F 42 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7028 (mm-40) REVERT: F 43 MET cc_start: 0.8165 (mtp) cc_final: 0.7742 (mmt) REVERT: F 164 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: F 292 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: F 293 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7736 (p0) REVERT: H 102 ARG cc_start: 0.6386 (pmt100) cc_final: 0.5400 (tpt170) REVERT: H 109 LYS cc_start: 0.8211 (mttt) cc_final: 0.7944 (mttm) REVERT: H 152 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8291 (mt) outliers start: 145 outliers final: 75 residues processed: 426 average time/residue: 1.3265 time to fit residues: 665.1129 Evaluate side-chains 387 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 286 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 288 ARG Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 155 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 268 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 25 ASN I 50 GLN I 154 ASN I 345 GLN B 110 GLN B 114 GLN C 110 GLN D 110 GLN E 55 GLN H 32 ASN H 162 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28920 Z= 0.279 Angle : 0.622 10.330 39505 Z= 0.317 Chirality : 0.044 0.262 4374 Planarity : 0.005 0.056 4822 Dihedral : 14.622 179.586 4529 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 4.94 % Allowed : 18.00 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.09 (0.14), residues: 3269 helix: 0.20 (0.16), residues: 1112 sheet: -0.24 (0.23), residues: 506 loop : -1.54 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 142 HIS 0.007 0.001 HIS C 335 PHE 0.029 0.002 PHE H 163 TYR 0.018 0.002 TYR B 175 ARG 0.007 0.001 ARG H 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 296 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7389 (m-80) cc_final: 0.7119 (m-80) REVERT: A 177 MET cc_start: 0.6121 (tpp) cc_final: 0.4523 (mpt) REVERT: A 247 MET cc_start: 0.8806 (tpt) cc_final: 0.8049 (tpt) REVERT: A 443 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6365 (m-70) REVERT: A 543 TYR cc_start: 0.7204 (t80) cc_final: 0.6934 (t80) REVERT: A 562 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6969 (mt0) REVERT: A 574 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: J 11 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5427 (p0) REVERT: J 95 ASN cc_start: 0.5138 (OUTLIER) cc_final: 0.4636 (m-40) REVERT: J 169 TYR cc_start: 0.4136 (p90) cc_final: 0.3264 (p90) REVERT: J 331 MET cc_start: 0.7851 (ttt) cc_final: 0.7634 (ttm) REVERT: J 384 GLU cc_start: 0.6941 (pt0) cc_final: 0.6606 (pt0) REVERT: I 99 MET cc_start: 0.6887 (mtm) cc_final: 0.6502 (mtm) REVERT: I 177 ILE cc_start: 0.7180 (mm) cc_final: 0.6773 (pt) REVERT: I 234 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6088 (pm20) REVERT: I 311 LEU cc_start: 0.6706 (tm) cc_final: 0.6355 (pp) REVERT: G 112 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8245 (mm) REVERT: G 193 MET cc_start: 0.8852 (mtt) cc_final: 0.8546 (mtt) REVERT: G 329 GLU cc_start: 0.7174 (tt0) cc_final: 0.6947 (tt0) REVERT: B 39 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9007 (pp) REVERT: B 178 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7706 (ttm110) REVERT: B 215 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8857 (mm) REVERT: B 294 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8489 (m) REVERT: C 39 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8873 (pp) REVERT: C 42 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: D 63 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: D 96 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: D 287 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7399 (p90) REVERT: D 346 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7859 (mtm) REVERT: E 57 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7935 (pt) REVERT: E 193 MET cc_start: 0.9131 (mtt) cc_final: 0.8871 (mtt) REVERT: E 220 MET cc_start: 0.7701 (ttt) cc_final: 0.7404 (ttt) REVERT: E 222 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7836 (mtm-85) REVERT: E 287 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.6131 (p90) REVERT: F 42 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.6905 (mm-40) REVERT: F 164 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: F 292 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: F 293 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7771 (p0) REVERT: H 102 ARG cc_start: 0.6300 (pmt100) cc_final: 0.5355 (tpt170) REVERT: H 109 LYS cc_start: 0.8226 (mttt) cc_final: 0.7954 (mttm) REVERT: H 150 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.6097 (t-90) REVERT: H 152 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8326 (mt) REVERT: H 162 ASN cc_start: 0.8226 (m110) cc_final: 0.7593 (m-40) REVERT: H 168 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6619 (mtt-85) outliers start: 146 outliers final: 86 residues processed: 415 average time/residue: 1.3532 time to fit residues: 659.4103 Evaluate side-chains 392 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 279 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 288 ARG Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 168 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 272 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 599 ASN J 23 ASN I 50 GLN I 80 GLN I 345 GLN B 114 GLN C 110 GLN D 110 GLN E 55 GLN H 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28920 Z= 0.165 Angle : 0.545 9.850 39505 Z= 0.279 Chirality : 0.040 0.194 4374 Planarity : 0.004 0.052 4822 Dihedral : 14.337 176.450 4529 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 4.36 % Allowed : 18.61 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.75 (0.14), residues: 3269 helix: 0.59 (0.16), residues: 1105 sheet: 0.02 (0.24), residues: 487 loop : -1.43 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 142 HIS 0.006 0.001 HIS J 225 PHE 0.028 0.001 PHE H 163 TYR 0.017 0.001 TYR C 275 ARG 0.005 0.000 ARG H 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 305 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7386 (m-80) cc_final: 0.7120 (m-80) REVERT: A 177 MET cc_start: 0.6300 (tpp) cc_final: 0.4751 (mpt) REVERT: A 247 MET cc_start: 0.8792 (tpt) cc_final: 0.8045 (tpt) REVERT: A 543 TYR cc_start: 0.7179 (t80) cc_final: 0.6935 (t80) REVERT: A 562 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6867 (mt0) REVERT: A 574 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: J 11 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5354 (p0) REVERT: J 154 ASN cc_start: 0.5683 (m110) cc_final: 0.4771 (p0) REVERT: J 169 TYR cc_start: 0.4124 (p90) cc_final: 0.3274 (p90) REVERT: J 210 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7009 (mtpp) REVERT: J 384 GLU cc_start: 0.6938 (pt0) cc_final: 0.6642 (pt0) REVERT: I 99 MET cc_start: 0.6934 (mtm) cc_final: 0.6595 (mtm) REVERT: I 177 ILE cc_start: 0.7155 (mm) cc_final: 0.6740 (pt) REVERT: I 234 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6050 (pm20) REVERT: I 311 LEU cc_start: 0.6831 (tm) cc_final: 0.6473 (pp) REVERT: I 332 LEU cc_start: 0.7108 (mt) cc_final: 0.6783 (mt) REVERT: G 112 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8227 (mm) REVERT: G 193 MET cc_start: 0.8825 (mtt) cc_final: 0.8492 (mtt) REVERT: G 329 GLU cc_start: 0.7234 (tt0) cc_final: 0.7027 (tt0) REVERT: B 39 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8988 (pp) REVERT: B 44 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: B 178 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7893 (ttm110) REVERT: B 204 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6565 (tm) REVERT: B 294 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8380 (m) REVERT: C 42 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8344 (mt0) REVERT: C 58 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8178 (mmmm) REVERT: D 63 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: D 96 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: D 287 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7366 (p90) REVERT: E 17 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: E 193 MET cc_start: 0.9054 (mtt) cc_final: 0.8827 (mtt) REVERT: E 220 MET cc_start: 0.7697 (ttt) cc_final: 0.7337 (ttt) REVERT: E 222 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7805 (mtm-85) REVERT: E 277 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5868 (mp0) REVERT: E 287 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6087 (p90) REVERT: F 146 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8322 (p) REVERT: F 164 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: F 169 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: F 293 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7704 (p0) REVERT: H 102 ARG cc_start: 0.6326 (pmt100) cc_final: 0.5336 (tpt170) REVERT: H 109 LYS cc_start: 0.8202 (mttt) cc_final: 0.7946 (mmtt) REVERT: H 150 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6396 (t-90) outliers start: 129 outliers final: 70 residues processed: 404 average time/residue: 1.3469 time to fit residues: 638.4792 Evaluate side-chains 378 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 285 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 288 ARG Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 253 optimal weight: 0.8980 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN I 50 GLN I 80 GLN I 345 GLN B 110 GLN B 114 GLN C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28920 Z= 0.265 Angle : 0.610 11.550 39505 Z= 0.311 Chirality : 0.043 0.212 4374 Planarity : 0.005 0.054 4822 Dihedral : 14.402 178.441 4529 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 4.53 % Allowed : 18.84 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.76 (0.14), residues: 3269 helix: 0.55 (0.16), residues: 1114 sheet: 0.00 (0.24), residues: 494 loop : -1.43 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 142 HIS 0.006 0.001 HIS C 335 PHE 0.028 0.002 PHE H 163 TYR 0.016 0.002 TYR G 9 ARG 0.008 0.000 ARG H 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 280 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7409 (m-80) cc_final: 0.7108 (m-80) REVERT: A 177 MET cc_start: 0.5983 (tpp) cc_final: 0.4661 (mpt) REVERT: A 443 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6373 (m-70) REVERT: A 543 TYR cc_start: 0.7231 (t80) cc_final: 0.6948 (t80) REVERT: A 562 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: J 11 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5393 (p0) REVERT: J 95 ASN cc_start: 0.5297 (OUTLIER) cc_final: 0.4881 (m-40) REVERT: J 154 ASN cc_start: 0.5676 (m110) cc_final: 0.4768 (p0) REVERT: J 210 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7006 (mtpp) REVERT: J 384 GLU cc_start: 0.6965 (pt0) cc_final: 0.6623 (pt0) REVERT: I 99 MET cc_start: 0.6923 (mtm) cc_final: 0.6475 (mtm) REVERT: I 177 ILE cc_start: 0.7249 (mm) cc_final: 0.6812 (pt) REVERT: I 234 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: G 112 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8283 (mm) REVERT: G 193 MET cc_start: 0.8843 (mtt) cc_final: 0.8518 (mtt) REVERT: G 329 GLU cc_start: 0.7167 (tt0) cc_final: 0.6958 (tt0) REVERT: B 39 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9023 (pp) REVERT: B 215 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8855 (mm) REVERT: C 39 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8883 (pp) REVERT: C 42 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: C 58 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8182 (mmmm) REVERT: D 63 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: D 96 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: D 287 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7436 (p90) REVERT: D 346 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8019 (mtm) REVERT: E 57 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7903 (pt) REVERT: E 220 MET cc_start: 0.7720 (ttt) cc_final: 0.7449 (ttt) REVERT: E 222 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7851 (mtm-85) REVERT: E 277 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5993 (mp0) REVERT: E 287 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.6056 (p90) REVERT: F 164 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: F 293 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7744 (p0) REVERT: H 102 ARG cc_start: 0.6264 (pmt100) cc_final: 0.5318 (tpt170) REVERT: H 109 LYS cc_start: 0.8204 (mttt) cc_final: 0.7947 (mttm) REVERT: H 150 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6143 (t-90) outliers start: 134 outliers final: 81 residues processed: 389 average time/residue: 1.3665 time to fit residues: 623.4316 Evaluate side-chains 377 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 275 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 288 ARG Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 155 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 0.0670 chunk 308 optimal weight: 0.9980 chunk 281 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 271 optimal weight: 0.1980 chunk 283 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN I 50 GLN I 80 GLN I 154 ASN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN B 184 ASN C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28920 Z= 0.151 Angle : 0.541 12.552 39505 Z= 0.275 Chirality : 0.040 0.205 4374 Planarity : 0.004 0.050 4822 Dihedral : 14.135 175.336 4529 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 3.62 % Allowed : 20.06 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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 (0.15), residues: 3269 helix: 0.89 (0.16), residues: 1106 sheet: 0.19 (0.24), residues: 483 loop : -1.33 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 71 HIS 0.006 0.001 HIS E 349 PHE 0.028 0.001 PHE H 163 TYR 0.016 0.001 TYR C 275 ARG 0.008 0.000 ARG H 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 293 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7414 (m-80) cc_final: 0.7212 (m-80) REVERT: A 128 LYS cc_start: 0.8069 (pmmt) cc_final: 0.7418 (tttp) REVERT: A 177 MET cc_start: 0.6239 (tpp) cc_final: 0.5001 (mpt) REVERT: A 247 MET cc_start: 0.8713 (tpt) cc_final: 0.8297 (tpt) REVERT: A 526 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7107 (mp0) REVERT: A 543 TYR cc_start: 0.7212 (t80) cc_final: 0.6996 (t80) REVERT: A 562 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6822 (mt0) REVERT: J 11 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5396 (p0) REVERT: J 154 ASN cc_start: 0.5443 (m110) cc_final: 0.4615 (p0) REVERT: J 169 TYR cc_start: 0.4220 (p90) cc_final: 0.3138 (p90) REVERT: J 210 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6988 (mtpp) REVERT: J 217 LYS cc_start: 0.7649 (mmmm) cc_final: 0.6971 (mmmt) REVERT: J 384 GLU cc_start: 0.6969 (pt0) cc_final: 0.6664 (pt0) REVERT: I 66 ASN cc_start: 0.8084 (m-40) cc_final: 0.7807 (m110) REVERT: I 99 MET cc_start: 0.6823 (mtm) cc_final: 0.6431 (mtm) REVERT: I 177 ILE cc_start: 0.7224 (mm) cc_final: 0.6762 (pt) REVERT: I 311 LEU cc_start: 0.6860 (tm) cc_final: 0.6455 (pp) REVERT: I 342 MET cc_start: 0.6090 (ttt) cc_final: 0.5746 (ttt) REVERT: G 112 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8224 (mm) REVERT: G 193 MET cc_start: 0.8828 (mtt) cc_final: 0.8466 (mtt) REVERT: G 311 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7978 (mp10) REVERT: G 329 GLU cc_start: 0.7090 (tt0) cc_final: 0.6867 (tt0) REVERT: B 39 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8910 (pp) REVERT: B 178 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7883 (ttm110) REVERT: B 204 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6627 (tm) REVERT: C 39 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8825 (pp) REVERT: C 42 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: C 58 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8212 (mmmm) REVERT: D 96 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: D 287 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7317 (p90) REVERT: E 17 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: E 277 GLU cc_start: 0.6226 (mm-30) cc_final: 0.5829 (mp0) REVERT: E 287 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.6052 (p90) REVERT: F 146 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8162 (p) REVERT: F 164 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: F 293 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7548 (p0) REVERT: H 102 ARG cc_start: 0.6257 (pmt100) cc_final: 0.5299 (tpt170) REVERT: H 109 LYS cc_start: 0.8237 (mttt) cc_final: 0.8010 (mttm) REVERT: H 150 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6384 (t-90) outliers start: 107 outliers final: 62 residues processed: 378 average time/residue: 1.3591 time to fit residues: 604.9224 Evaluate side-chains 354 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 275 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 288 ARG Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 151 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 0.8980 chunk 317 optimal weight: 0.0670 chunk 193 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 332 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 313 GLN ** J 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 80 GLN I 154 ASN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN B 184 ASN C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28920 Z= 0.164 Angle : 0.550 13.068 39505 Z= 0.278 Chirality : 0.040 0.180 4374 Planarity : 0.004 0.068 4822 Dihedral : 14.004 175.092 4526 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 3.18 % Allowed : 20.87 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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 (0.15), residues: 3269 helix: 0.98 (0.16), residues: 1108 sheet: 0.31 (0.25), residues: 461 loop : -1.30 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 71 HIS 0.009 0.001 HIS E 349 PHE 0.031 0.001 PHE H 163 TYR 0.016 0.001 TYR C 275 ARG 0.007 0.000 ARG H 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 280 time to evaluate : 4.564 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8038 (pmmt) cc_final: 0.7356 (ttpp) REVERT: A 177 MET cc_start: 0.6249 (tpp) cc_final: 0.5001 (mpt) REVERT: A 247 MET cc_start: 0.8734 (tpt) cc_final: 0.8381 (tpt) REVERT: A 543 TYR cc_start: 0.7240 (t80) cc_final: 0.6999 (t80) REVERT: A 562 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6745 (mt0) REVERT: J 1 MET cc_start: 0.2830 (ttm) cc_final: 0.2347 (tmm) REVERT: J 11 ASP cc_start: 0.5913 (OUTLIER) cc_final: 0.5377 (p0) REVERT: J 154 ASN cc_start: 0.5174 (m110) cc_final: 0.4578 (p0) REVERT: J 169 TYR cc_start: 0.4328 (p90) cc_final: 0.3237 (p90) REVERT: J 210 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6999 (mtpp) REVERT: J 217 LYS cc_start: 0.7681 (mmmm) cc_final: 0.7018 (mmmt) REVERT: J 384 GLU cc_start: 0.6965 (pt0) cc_final: 0.6665 (pt0) REVERT: I 66 ASN cc_start: 0.8048 (m-40) cc_final: 0.7777 (m110) REVERT: I 99 MET cc_start: 0.6929 (mtm) cc_final: 0.6577 (mtm) REVERT: I 177 ILE cc_start: 0.7231 (mm) cc_final: 0.6781 (pt) REVERT: I 311 LEU cc_start: 0.6792 (tm) cc_final: 0.6466 (pp) REVERT: G 112 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8247 (mm) REVERT: G 193 MET cc_start: 0.8839 (mtt) cc_final: 0.8480 (mtt) REVERT: G 329 GLU cc_start: 0.7116 (tt0) cc_final: 0.6769 (mt-10) REVERT: B 39 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9002 (pp) REVERT: B 110 GLN cc_start: 0.6745 (tp-100) cc_final: 0.6536 (tp40) REVERT: B 178 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7892 (ttm110) REVERT: B 215 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8700 (mm) REVERT: C 42 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: D 96 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: D 280 GLU cc_start: 0.7621 (pt0) cc_final: 0.7390 (pt0) REVERT: D 287 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7380 (p90) REVERT: E 17 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: E 57 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7873 (pt) REVERT: E 222 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7807 (mtm-85) REVERT: E 287 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.5964 (p90) REVERT: F 43 MET cc_start: 0.8112 (mtp) cc_final: 0.7860 (mmt) REVERT: F 164 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: F 293 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7659 (p0) REVERT: H 102 ARG cc_start: 0.6278 (pmt100) cc_final: 0.5319 (tpt170) REVERT: H 107 ILE cc_start: 0.8691 (mm) cc_final: 0.8456 (mt) REVERT: H 109 LYS cc_start: 0.8255 (mttt) cc_final: 0.8033 (mttm) REVERT: H 150 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6404 (t-90) outliers start: 94 outliers final: 63 residues processed: 360 average time/residue: 1.3474 time to fit residues: 570.5621 Evaluate side-chains 355 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 275 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 199 THR Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 0.7980 chunk 282 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** J 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 80 GLN I 154 ASN B 348 GLN C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108721 restraints weight = 33566.069| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.70 r_work: 0.2960 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28920 Z= 0.182 Angle : 0.561 13.317 39505 Z= 0.285 Chirality : 0.041 0.225 4374 Planarity : 0.004 0.068 4822 Dihedral : 13.988 175.831 4524 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 3.18 % Allowed : 21.01 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.38 (0.15), residues: 3269 helix: 0.99 (0.16), residues: 1108 sheet: 0.26 (0.24), residues: 483 loop : -1.29 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 71 HIS 0.010 0.001 HIS E 349 PHE 0.033 0.001 PHE H 163 TYR 0.017 0.001 TYR I 140 ARG 0.007 0.000 ARG H 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11286.96 seconds wall clock time: 201 minutes 50.18 seconds (12110.18 seconds total)