Starting phenix.real_space_refine on Sun Sep 29 11:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq6_34199/09_2024/8gq6_34199.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq6_34199/09_2024/8gq6_34199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq6_34199/09_2024/8gq6_34199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq6_34199/09_2024/8gq6_34199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq6_34199/09_2024/8gq6_34199.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq6_34199/09_2024/8gq6_34199.cif" } resolution = 3.96 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 172 5.16 5 C 14114 2.51 5 N 3850 2.21 5 O 4151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22293 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4535 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 538} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 737 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5866 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4546 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 22, 'TRANS': 540} Chain breaks: 2 Chain: "F" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5866 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 737 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4732 SG CYS E 42 97.824 132.212 203.054 1.00135.97 S ATOM 4751 SG CYS E 45 97.332 135.997 203.064 1.00137.74 S ATOM 5046 SG CYS E 83 95.455 133.950 200.438 1.00118.07 S ATOM 4975 SG CYS E 75 99.032 119.450 200.491 1.00115.91 S ATOM 5142 SG CYS E 94 100.927 123.010 199.342 1.00129.19 S ATOM 4818 SG CYS E 53 91.949 137.158 200.696 1.00143.05 S ATOM 4841 SG CYS E 56 88.516 138.753 200.124 1.00146.03 S ATOM 4925 SG CYS E 68 88.779 135.715 202.407 1.00133.77 S ATOM 21747 SG CYS D 42 132.130 62.809 51.273 1.00135.97 S ATOM 21766 SG CYS D 45 135.799 61.647 52.145 1.00137.74 S ATOM 22061 SG CYS D 83 133.073 61.294 54.944 1.00118.07 S ATOM 21990 SG CYS D 75 123.469 71.768 55.932 1.00115.91 S ATOM 22157 SG CYS D 94 126.259 71.634 56.989 1.00129.19 S ATOM 21833 SG CYS D 53 134.193 56.390 55.193 1.00143.05 S ATOM 21856 SG CYS D 56 133.279 52.693 55.048 1.00146.03 S ATOM 21940 SG CYS D 68 130.649 55.324 54.136 1.00133.77 S Time building chain proxies: 13.51, per 1000 atoms: 0.61 Number of scatterers: 22293 At special positions: 0 Unit cell: (149.184, 154.512, 258.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 172 16.00 O 4151 8.00 N 3850 7.00 C 14114 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 - 3.00 Amino acid : True - 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: 5.66 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D4001 " pdb="ZN ZN D4001 " - pdb=" ND1 HIS D 80 " pdb="ZN ZN D4001 " - pdb=" SG CYS D 45 " pdb="ZN ZN D4001 " - pdb=" SG CYS D 83 " pdb="ZN ZN D4001 " - pdb=" SG CYS D 42 " pdb=" ZN D4002 " pdb="ZN ZN D4002 " - pdb=" SG CYS D 94 " pdb="ZN ZN D4002 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D4002 " - pdb=" SG CYS D 75 " pdb=" ZN D4003 " pdb="ZN ZN D4003 " - pdb=" ND1 HIS D 82 " pdb="ZN ZN D4003 " - pdb=" SG CYS D 56 " pdb="ZN ZN D4003 " - pdb=" SG CYS D 68 " pdb="ZN ZN D4003 " - pdb=" SG CYS D 53 " pdb=" ZN E4001 " pdb="ZN ZN E4001 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 45 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 83 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 42 " pdb=" ZN E4002 " pdb="ZN ZN E4002 " - pdb=" SG CYS E 75 " pdb="ZN ZN E4002 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E4002 " - pdb=" SG CYS E 94 " pdb=" ZN E4003 " pdb="ZN ZN E4003 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 56 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 68 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 53 " Number of angles added : 12 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5270 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 24 sheets defined 49.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.570A pdb=" N LEU A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 131 through 143 removed outlier: 4.662A pdb=" N ARG A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 removed outlier: 4.535A pdb=" N THR A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.870A pdb=" N MET A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 171' Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.866A pdb=" N ARG A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.540A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'E' and resid 81 through 88 Processing helix chain 'C' and resid 26 through 46 removed outlier: 3.551A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 removed outlier: 3.950A pdb=" N HIS C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 96 removed outlier: 4.078A pdb=" N ARG C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 134 removed outlier: 4.358A pdb=" N MET C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 156 through 175 removed outlier: 3.677A pdb=" N GLY C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 195 removed outlier: 3.892A pdb=" N LEU C 195 " --> pdb=" O MET C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 228 removed outlier: 3.777A pdb=" N GLU C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Proline residue: C 208 - end of helix removed outlier: 3.753A pdb=" N ALA C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Processing helix chain 'C' and resid 257 through 273 removed outlier: 3.997A pdb=" N SER C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 292 through 304 Processing helix chain 'C' and resid 308 through 329 removed outlier: 3.879A pdb=" N THR C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 360 Processing helix chain 'C' and resid 363 through 379 removed outlier: 4.042A pdb=" N ASN C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 398 removed outlier: 4.276A pdb=" N LYS C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 421 removed outlier: 4.141A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 441 removed outlier: 3.739A pdb=" N PHE C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.986A pdb=" N ASN C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 495 removed outlier: 3.600A pdb=" N ALA C 493 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 494 " --> pdb=" O HIS C 490 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 542 Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 612 through 619 Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.654A pdb=" N VAL C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 711 Processing helix chain 'C' and resid 712 through 714 No H-bonds generated for 'chain 'C' and resid 712 through 714' Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.918A pdb=" N GLU C 725 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 746 removed outlier: 3.849A pdb=" N GLU C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.865A pdb=" N GLU C 750 " --> pdb=" O GLY C 747 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 751 " --> pdb=" O LEU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 747 through 751' Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.860A pdb=" N LEU B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 145 through 164 Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.897A pdb=" N ARG B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.980A pdb=" N SER B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'F' and resid 26 through 46 removed outlier: 3.586A pdb=" N VAL F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 67 removed outlier: 4.010A pdb=" N HIS F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 96 removed outlier: 4.095A pdb=" N ARG F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 134 removed outlier: 4.250A pdb=" N MET F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 156 through 175 removed outlier: 3.697A pdb=" N GLY F 175 " --> pdb=" O ARG F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 removed outlier: 3.902A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 removed outlier: 3.590A pdb=" N GLU F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 228 removed outlier: 4.084A pdb=" N GLN F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 226 " --> pdb=" O GLN F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 252 Processing helix chain 'F' and resid 257 through 273 removed outlier: 3.997A pdb=" N SER F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 292 through 304 Processing helix chain 'F' and resid 308 through 329 removed outlier: 3.904A pdb=" N THR F 312 " --> pdb=" O ASN F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 360 Processing helix chain 'F' and resid 363 through 379 removed outlier: 4.104A pdb=" N ASN F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 398 removed outlier: 4.293A pdb=" N LYS F 398 " --> pdb=" O ASP F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 421 removed outlier: 4.069A pdb=" N VAL F 408 " --> pdb=" O THR F 404 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 421 " --> pdb=" O VAL F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 441 removed outlier: 3.713A pdb=" N PHE F 428 " --> pdb=" O GLU F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 462 removed outlier: 3.949A pdb=" N ASN F 453 " --> pdb=" O ASP F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 495 Processing helix chain 'F' and resid 525 through 542 Processing helix chain 'F' and resid 598 through 608 Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.726A pdb=" N GLU F 619 " --> pdb=" O GLU F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 635 Processing helix chain 'F' and resid 684 through 711 removed outlier: 3.663A pdb=" N GLU F 704 " --> pdb=" O LYS F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 714 No H-bonds generated for 'chain 'F' and resid 712 through 714' Processing helix chain 'F' and resid 721 through 730 removed outlier: 3.912A pdb=" N GLU F 725 " --> pdb=" O VAL F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 746 removed outlier: 3.918A pdb=" N GLU F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 751 removed outlier: 4.051A pdb=" N GLU F 750 " --> pdb=" O GLY F 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 86 removed outlier: 3.502A pdb=" N ARG D 86 " --> pdb=" O HIS D 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 44 removed outlier: 3.576A pdb=" N ILE A 33 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 72 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 586 removed outlier: 3.543A pdb=" N ARG A 580 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 272 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 266 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE A 270 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 288 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE A 272 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 286 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A 285 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 592 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.591A pdb=" N GLY A 309 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 321 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 311 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 319 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE A 318 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA5, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.573A pdb=" N SER A 374 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 408 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 423 through 427 removed outlier: 3.586A pdb=" N TYR A 440 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 448 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 467 removed outlier: 4.106A pdb=" N SER A 463 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 474 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 503 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 508 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.611A pdb=" N CYS A 535 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU A 534 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 538 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 550 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 540 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 548 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N TYR A 549 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS A 566 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR A 551 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 564 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 560 " --> pdb=" O ASP A 555 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 502 through 503 removed outlier: 6.766A pdb=" N ASP C 558 " --> pdb=" O LYS E 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 506 through 509 removed outlier: 4.245A pdb=" N LEU E 32 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 78 through 80 Processing sheet with id=AB3, first strand: chain 'C' and resid 645 through 646 Processing sheet with id=AB4, first strand: chain 'B' and resid 40 through 44 removed outlier: 3.652A pdb=" N ILE B 33 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 72 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.628A pdb=" N SER B 285 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 286 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE B 272 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR B 288 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE B 270 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 266 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 586 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 580 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.632A pdb=" N GLY B 309 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 321 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 311 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE B 318 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 378 removed outlier: 3.765A pdb=" N SER B 374 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 400 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 423 through 427 removed outlier: 3.546A pdb=" N VAL B 433 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 440 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 448 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 463 through 467 removed outlier: 3.892A pdb=" N SER B 463 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 465 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 472 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL B 499 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 512 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 508 " --> pdb=" O ASP B 503 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 527 through 530 removed outlier: 4.825A pdb=" N LEU B 534 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 550 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR B 549 " --> pdb=" O HIS B 566 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B 566 " --> pdb=" O TYR B 549 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR B 551 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 564 " --> pdb=" O THR B 551 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 502 through 503 removed outlier: 7.071A pdb=" N ASP F 502 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP F 558 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 506 through 509 removed outlier: 6.287A pdb=" N ARG F 506 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TRP D 33 " --> pdb=" O ARG F 506 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU F 508 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU D 32 " --> pdb=" O THR F 549 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 34 " --> pdb=" O GLN F 547 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN F 547 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 645 through 646 Processing sheet with id=AC6, first strand: chain 'D' and resid 78 through 80 1102 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.21 Time building geometry restraints manager: 6.19 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: 6166 1.33 - 1.45: 3885 1.45 - 1.57: 12410 1.57 - 1.69: 0 1.69 - 1.82: 270 Bond restraints: 22731 Sorted by residual: bond pdb=" N ALA F 207 " pdb=" CA ALA F 207 " ideal model delta sigma weight residual 1.462 1.484 -0.022 7.70e-03 1.69e+04 8.33e+00 bond pdb=" N VAL B 399 " pdb=" CA VAL B 399 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.32e-02 5.74e+03 7.74e+00 bond pdb=" N GLU F 202 " pdb=" CA GLU F 202 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N GLU F 206 " pdb=" CA GLU F 206 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.01e+00 bond pdb=" N ARG B 396 " pdb=" CA ARG B 396 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.40e-02 5.10e+03 5.75e+00 ... (remaining 22726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 30012 1.54 - 3.09: 550 3.09 - 4.63: 78 4.63 - 6.17: 38 6.17 - 7.71: 6 Bond angle restraints: 30684 Sorted by residual: angle pdb=" C SER E 65 " pdb=" CA SER E 65 " pdb=" CB SER E 65 " ideal model delta sigma weight residual 117.23 110.37 6.86 1.36e+00 5.41e-01 2.54e+01 angle pdb=" N ARG B 396 " pdb=" CA ARG B 396 " pdb=" C ARG B 396 " ideal model delta sigma weight residual 113.15 107.81 5.34 1.19e+00 7.06e-01 2.01e+01 angle pdb=" CA VAL B 399 " pdb=" C VAL B 399 " pdb=" O VAL B 399 " ideal model delta sigma weight residual 121.92 117.16 4.76 1.17e+00 7.31e-01 1.66e+01 angle pdb=" CA SER E 65 " pdb=" C SER E 65 " pdb=" N GLU E 66 " ideal model delta sigma weight residual 119.98 116.76 3.22 8.50e-01 1.38e+00 1.44e+01 angle pdb=" CA GLU F 206 " pdb=" C GLU F 206 " pdb=" O GLU F 206 " ideal model delta sigma weight residual 120.82 117.16 3.66 1.05e+00 9.07e-01 1.21e+01 ... (remaining 30679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12597 17.96 - 35.93: 986 35.93 - 53.89: 184 53.89 - 71.85: 43 71.85 - 89.82: 22 Dihedral angle restraints: 13832 sinusoidal: 5726 harmonic: 8106 Sorted by residual: dihedral pdb=" CA SER C 255 " pdb=" C SER C 255 " pdb=" N THR C 256 " pdb=" CA THR C 256 " ideal model delta harmonic sigma weight residual 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS A 255 " pdb=" C LYS A 255 " pdb=" N PHE A 256 " pdb=" CA PHE A 256 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA SER F 255 " pdb=" C SER F 255 " pdb=" N THR F 256 " pdb=" CA THR F 256 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2895 0.054 - 0.107: 428 0.107 - 0.161: 56 0.161 - 0.214: 3 0.214 - 0.268: 3 Chirality restraints: 3385 Sorted by residual: chirality pdb=" CB VAL B 399 " pdb=" CA VAL B 399 " pdb=" CG1 VAL B 399 " pdb=" CG2 VAL B 399 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ARG B 397 " pdb=" N ARG B 397 " pdb=" C ARG B 397 " pdb=" CB ARG B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ARG B 396 " pdb=" N ARG B 396 " pdb=" C ARG B 396 " pdb=" CB ARG B 396 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3382 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 519 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO F 520 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 520 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 520 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 622 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO C 623 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 623 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 623 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 524 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO C 525 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 525 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 525 " 0.024 5.00e-02 4.00e+02 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 361 2.67 - 3.23: 21453 3.23 - 3.78: 35917 3.78 - 4.34: 45492 4.34 - 4.90: 74179 Nonbonded interactions: 177402 Sorted by model distance: nonbonded pdb=" OD2 ASP E 97 " pdb="ZN ZN E4002 " model vdw 2.109 2.230 nonbonded pdb=" OD2 ASP D 97 " pdb="ZN ZN D4002 " model vdw 2.122 2.230 nonbonded pdb=" O GLU C 206 " pdb=" N LEU C 210 " model vdw 2.199 3.120 nonbonded pdb=" OG SER A 374 " pdb=" O ILE A 385 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O ASP B 574 " model vdw 2.235 3.040 ... (remaining 177397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 328 or resid 330 through 598)) selection = (chain 'B' and (resid 8 through 328 or resid 342 or resid 344 through 477 or res \ id 496 through 598)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.880 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 53.950 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 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 : 0.002 0.037 22731 Z= 0.144 Angle : 0.534 7.714 30684 Z= 0.312 Chirality : 0.040 0.268 3385 Planarity : 0.003 0.065 3934 Dihedral : 13.629 89.815 8562 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 0.32 % Allowed : 14.49 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2718 helix: 1.10 (0.15), residues: 1260 sheet: -0.95 (0.31), residues: 269 loop : -2.31 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 35 HIS 0.014 0.001 HIS C 701 PHE 0.011 0.001 PHE F 205 TYR 0.015 0.001 TYR F 753 ARG 0.003 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 867 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 PHE cc_start: 0.8261 (m-10) cc_final: 0.8009 (m-80) REVERT: A 26 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7104 (mt-10) REVERT: A 29 LEU cc_start: 0.8823 (mp) cc_final: 0.8401 (mm) REVERT: A 42 PHE cc_start: 0.8764 (m-80) cc_final: 0.8344 (m-10) REVERT: A 47 MET cc_start: 0.7389 (ttt) cc_final: 0.6915 (ttt) REVERT: A 49 LEU cc_start: 0.8206 (mt) cc_final: 0.7832 (mp) REVERT: A 59 MET cc_start: 0.7402 (ttt) cc_final: 0.7027 (ttt) REVERT: A 60 PHE cc_start: 0.8229 (m-80) cc_final: 0.7604 (m-10) REVERT: A 68 LYS cc_start: 0.8583 (tptp) cc_final: 0.8304 (tptp) REVERT: A 73 HIS cc_start: 0.7355 (m-70) cc_final: 0.6968 (m-70) REVERT: A 84 ILE cc_start: 0.8494 (tp) cc_final: 0.8196 (tt) REVERT: A 87 THR cc_start: 0.8320 (t) cc_final: 0.7948 (p) REVERT: A 103 GLN cc_start: 0.7660 (tp40) cc_final: 0.7397 (tp40) REVERT: A 109 CYS cc_start: 0.8122 (t) cc_final: 0.7791 (t) REVERT: A 110 PHE cc_start: 0.8370 (t80) cc_final: 0.7917 (t80) REVERT: A 112 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7826 (tp40) REVERT: A 121 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8222 (ttp80) REVERT: A 122 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 123 TYR cc_start: 0.8191 (t80) cc_final: 0.7869 (t80) REVERT: A 124 LEU cc_start: 0.8480 (mp) cc_final: 0.8235 (mt) REVERT: A 127 LYS cc_start: 0.8383 (tppt) cc_final: 0.8045 (mmmt) REVERT: A 147 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 150 GLN cc_start: 0.7996 (mm110) cc_final: 0.7729 (mm-40) REVERT: A 159 LYS cc_start: 0.7038 (mtmt) cc_final: 0.5753 (mtpp) REVERT: A 180 ILE cc_start: 0.8385 (mt) cc_final: 0.8176 (tp) REVERT: A 183 SER cc_start: 0.8181 (t) cc_final: 0.7628 (p) REVERT: A 184 ASP cc_start: 0.7872 (p0) cc_final: 0.7365 (p0) REVERT: A 191 GLU cc_start: 0.7188 (pp20) cc_final: 0.6789 (tm-30) REVERT: A 195 ARG cc_start: 0.8327 (tmm160) cc_final: 0.8087 (ttm-80) REVERT: A 196 GLU cc_start: 0.7311 (pp20) cc_final: 0.6880 (pp20) REVERT: A 225 LEU cc_start: 0.5278 (mt) cc_final: 0.4834 (mt) REVERT: A 271 PHE cc_start: 0.7787 (m-80) cc_final: 0.7540 (m-10) REVERT: A 293 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7970 (mt-10) REVERT: A 296 TYR cc_start: 0.7668 (m-80) cc_final: 0.7241 (m-80) REVERT: A 311 VAL cc_start: 0.8227 (p) cc_final: 0.7865 (t) REVERT: A 352 TRP cc_start: 0.8050 (t60) cc_final: 0.7606 (t60) REVERT: A 361 PHE cc_start: 0.7182 (m-80) cc_final: 0.6659 (m-80) REVERT: A 379 GLU cc_start: 0.7183 (tp30) cc_final: 0.6633 (tp30) REVERT: A 381 TYR cc_start: 0.7577 (m-80) cc_final: 0.7163 (m-80) REVERT: A 383 TYR cc_start: 0.6574 (m-80) cc_final: 0.6199 (m-80) REVERT: A 403 ASP cc_start: 0.7686 (t0) cc_final: 0.6969 (t0) REVERT: A 443 PHE cc_start: 0.8714 (t80) cc_final: 0.8325 (t80) REVERT: A 502 TYR cc_start: 0.6125 (t80) cc_final: 0.5852 (t80) REVERT: A 503 ASP cc_start: 0.7912 (t0) cc_final: 0.5086 (p0) REVERT: A 587 TYR cc_start: 0.6845 (m-80) cc_final: 0.6605 (m-10) REVERT: E 23 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6342 (mp0) REVERT: E 28 ASN cc_start: 0.6374 (t0) cc_final: 0.5766 (t0) REVERT: E 48 HIS cc_start: 0.5195 (t70) cc_final: 0.4701 (t70) REVERT: E 93 VAL cc_start: 0.7122 (m) cc_final: 0.6722 (p) REVERT: C 28 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7398 (mmmm) REVERT: C 33 ILE cc_start: 0.8950 (mm) cc_final: 0.8666 (tt) REVERT: C 42 GLN cc_start: 0.8090 (mt0) cc_final: 0.7679 (mt0) REVERT: C 58 TYR cc_start: 0.8074 (t80) cc_final: 0.7829 (t80) REVERT: C 71 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7008 (tm-30) REVERT: C 72 LYS cc_start: 0.8082 (tttt) cc_final: 0.7832 (tptm) REVERT: C 83 GLU cc_start: 0.7417 (tp30) cc_final: 0.6951 (tp30) REVERT: C 91 GLU cc_start: 0.7452 (tp30) cc_final: 0.7131 (mm-30) REVERT: C 118 MET cc_start: 0.7030 (mtm) cc_final: 0.6332 (mtm) REVERT: C 145 ILE cc_start: 0.8198 (mt) cc_final: 0.7909 (tt) REVERT: C 153 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7435 (mmt90) REVERT: C 163 GLN cc_start: 0.8226 (mm110) cc_final: 0.7617 (mm110) REVERT: C 168 MET cc_start: 0.7564 (ptp) cc_final: 0.6954 (ptp) REVERT: C 188 GLN cc_start: 0.7456 (tp40) cc_final: 0.7109 (tp40) REVERT: C 192 ILE cc_start: 0.8341 (mm) cc_final: 0.8113 (mt) REVERT: C 215 GLU cc_start: 0.7721 (mp0) cc_final: 0.7494 (mp0) REVERT: C 217 PHE cc_start: 0.7881 (m-80) cc_final: 0.7389 (m-10) REVERT: C 222 GLN cc_start: 0.7625 (tp40) cc_final: 0.7220 (tm-30) REVERT: C 235 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8074 (mtmt) REVERT: C 238 GLU cc_start: 0.7179 (tp30) cc_final: 0.6517 (tm-30) REVERT: C 250 HIS cc_start: 0.7772 (t-90) cc_final: 0.7193 (t-90) REVERT: C 253 ASP cc_start: 0.6386 (p0) cc_final: 0.5912 (t70) REVERT: C 258 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7047 (mm-30) REVERT: C 262 LYS cc_start: 0.8008 (tmtm) cc_final: 0.7400 (ttpp) REVERT: C 265 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7199 (mm-30) REVERT: C 270 SER cc_start: 0.8342 (m) cc_final: 0.8070 (t) REVERT: C 287 MET cc_start: 0.7788 (ptt) cc_final: 0.5941 (ptt) REVERT: C 292 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8224 (mmtm) REVERT: C 301 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7975 (ptpp) REVERT: C 302 LEU cc_start: 0.8464 (tp) cc_final: 0.8211 (tp) REVERT: C 306 VAL cc_start: 0.8536 (t) cc_final: 0.8155 (p) REVERT: C 346 LEU cc_start: 0.7997 (tp) cc_final: 0.7658 (tp) REVERT: C 353 ASP cc_start: 0.7789 (t0) cc_final: 0.7563 (t0) REVERT: C 354 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7642 (ttp-110) REVERT: C 360 PHE cc_start: 0.7644 (m-10) cc_final: 0.7290 (m-10) REVERT: C 368 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6445 (tm-30) REVERT: C 369 THR cc_start: 0.7974 (p) cc_final: 0.7266 (t) REVERT: C 386 GLU cc_start: 0.8226 (mp0) cc_final: 0.7219 (mp0) REVERT: C 394 ASP cc_start: 0.7839 (t0) cc_final: 0.7405 (t0) REVERT: C 395 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8390 (mmtm) REVERT: C 412 LEU cc_start: 0.8724 (mt) cc_final: 0.8055 (pp) REVERT: C 413 ASP cc_start: 0.8438 (m-30) cc_final: 0.7292 (m-30) REVERT: C 418 LEU cc_start: 0.8687 (tt) cc_final: 0.8068 (tp) REVERT: C 424 GLU cc_start: 0.7511 (mp0) cc_final: 0.6755 (mp0) REVERT: C 431 TYR cc_start: 0.7810 (m-80) cc_final: 0.6904 (m-80) REVERT: C 441 LEU cc_start: 0.8306 (mt) cc_final: 0.7565 (mp) REVERT: C 457 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8556 (mmtp) REVERT: C 479 ILE cc_start: 0.7650 (mm) cc_final: 0.7423 (mm) REVERT: C 554 MET cc_start: 0.6774 (tpp) cc_final: 0.6320 (tpp) REVERT: C 603 MET cc_start: 0.7399 (tmm) cc_final: 0.7073 (tmm) REVERT: C 687 GLU cc_start: 0.6194 (pp20) cc_final: 0.4324 (tt0) REVERT: C 688 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7650 (mmm-85) REVERT: C 692 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.7969 (tpp80) REVERT: B 19 GLU cc_start: 0.7375 (pp20) cc_final: 0.6989 (pp20) REVERT: B 24 PHE cc_start: 0.8399 (m-10) cc_final: 0.8071 (m-80) REVERT: B 36 ILE cc_start: 0.8542 (mm) cc_final: 0.8275 (mt) REVERT: B 44 CYS cc_start: 0.8398 (p) cc_final: 0.8065 (p) REVERT: B 46 LYS cc_start: 0.8893 (mttt) cc_final: 0.8531 (mtpp) REVERT: B 60 PHE cc_start: 0.8344 (m-10) cc_final: 0.7777 (m-10) REVERT: B 61 MET cc_start: 0.6835 (tmm) cc_final: 0.6357 (tmm) REVERT: B 66 GLU cc_start: 0.8034 (mp0) cc_final: 0.7725 (mp0) REVERT: B 72 VAL cc_start: 0.8752 (m) cc_final: 0.8286 (p) REVERT: B 85 ILE cc_start: 0.8644 (mt) cc_final: 0.8353 (tp) REVERT: B 90 TYR cc_start: 0.7964 (m-80) cc_final: 0.7475 (m-80) REVERT: B 106 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 112 GLN cc_start: 0.7824 (mm-40) cc_final: 0.6570 (mm-40) REVERT: B 114 GLU cc_start: 0.6430 (tm-30) cc_final: 0.6075 (mm-30) REVERT: B 115 ASP cc_start: 0.7595 (p0) cc_final: 0.6968 (p0) REVERT: B 123 TYR cc_start: 0.7301 (t80) cc_final: 0.6708 (t80) REVERT: B 127 LYS cc_start: 0.7876 (tptt) cc_final: 0.7606 (tptt) REVERT: B 136 LEU cc_start: 0.8276 (mt) cc_final: 0.7858 (mm) REVERT: B 149 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7786 (tptp) REVERT: B 153 LYS cc_start: 0.8284 (tptm) cc_final: 0.8064 (tppt) REVERT: B 155 MET cc_start: 0.8009 (tpt) cc_final: 0.7272 (tpp) REVERT: B 167 ASP cc_start: 0.7176 (p0) cc_final: 0.6957 (p0) REVERT: B 184 ASP cc_start: 0.7690 (t70) cc_final: 0.7235 (t0) REVERT: B 199 MET cc_start: 0.7310 (mmp) cc_final: 0.7093 (mmp) REVERT: B 212 TYR cc_start: 0.7963 (m-10) cc_final: 0.7420 (m-80) REVERT: B 229 THR cc_start: 0.5601 (p) cc_final: 0.4609 (p) REVERT: B 263 MET cc_start: 0.6709 (mpp) cc_final: 0.6400 (mtm) REVERT: B 353 PHE cc_start: 0.8300 (t80) cc_final: 0.7448 (t80) REVERT: B 363 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8146 (mmtt) REVERT: B 381 TYR cc_start: 0.7630 (m-80) cc_final: 0.6984 (m-80) REVERT: B 383 TYR cc_start: 0.5681 (m-80) cc_final: 0.5477 (m-80) REVERT: B 403 ASP cc_start: 0.8368 (t0) cc_final: 0.8106 (t70) REVERT: B 429 ASP cc_start: 0.7710 (m-30) cc_final: 0.7085 (m-30) REVERT: B 430 CYS cc_start: 0.6040 (m) cc_final: 0.5152 (t) REVERT: B 434 MET cc_start: 0.1668 (tpt) cc_final: 0.1270 (tpt) REVERT: B 469 ASP cc_start: 0.7146 (t70) cc_final: 0.6427 (t0) REVERT: B 470 LYS cc_start: 0.7126 (mttm) cc_final: 0.6825 (mtpp) REVERT: B 529 VAL cc_start: 0.5922 (t) cc_final: 0.5098 (m) REVERT: F 28 LYS cc_start: 0.7796 (mmmm) cc_final: 0.7466 (mmmm) REVERT: F 35 ASP cc_start: 0.7551 (t0) cc_final: 0.7242 (t70) REVERT: F 60 ASN cc_start: 0.7940 (m-40) cc_final: 0.7734 (m-40) REVERT: F 64 MET cc_start: 0.6875 (tpt) cc_final: 0.6646 (tpt) REVERT: F 68 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8261 (mttm) REVERT: F 78 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7620 (ttm-80) REVERT: F 124 MET cc_start: 0.3809 (tmm) cc_final: 0.3359 (tmm) REVERT: F 126 MET cc_start: 0.8240 (tmt) cc_final: 0.7826 (tmm) REVERT: F 139 VAL cc_start: 0.7208 (m) cc_final: 0.6470 (t) REVERT: F 140 TYR cc_start: 0.7893 (t80) cc_final: 0.7393 (t80) REVERT: F 145 ILE cc_start: 0.8766 (mt) cc_final: 0.8451 (mm) REVERT: F 153 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7387 (mtt180) REVERT: F 167 ASP cc_start: 0.6934 (t0) cc_final: 0.6472 (t0) REVERT: F 168 MET cc_start: 0.7116 (ptp) cc_final: 0.6579 (ptp) REVERT: F 188 GLN cc_start: 0.7547 (tp40) cc_final: 0.7334 (mm-40) REVERT: F 193 LEU cc_start: 0.8873 (tp) cc_final: 0.8642 (tt) REVERT: F 200 VAL cc_start: 0.7432 (t) cc_final: 0.7143 (t) REVERT: F 204 ASP cc_start: 0.7763 (m-30) cc_final: 0.7472 (p0) REVERT: F 215 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7240 (mm-30) REVERT: F 219 MET cc_start: 0.7274 (mmt) cc_final: 0.7065 (mmt) REVERT: F 223 LYS cc_start: 0.7744 (tmtp) cc_final: 0.7046 (tmtt) REVERT: F 235 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8245 (mmmt) REVERT: F 240 ARG cc_start: 0.7905 (mmt180) cc_final: 0.7536 (tpp80) REVERT: F 243 GLU cc_start: 0.7471 (pp20) cc_final: 0.6946 (pp20) REVERT: F 246 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7159 (tp30) REVERT: F 249 MET cc_start: 0.7602 (ppp) cc_final: 0.7227 (ppp) REVERT: F 251 CYS cc_start: 0.8065 (t) cc_final: 0.7857 (t) REVERT: F 258 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7806 (mm-30) REVERT: F 265 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7034 (mm-30) REVERT: F 270 SER cc_start: 0.8662 (m) cc_final: 0.8085 (t) REVERT: F 295 ASP cc_start: 0.7265 (m-30) cc_final: 0.6868 (m-30) REVERT: F 302 LEU cc_start: 0.8673 (tp) cc_final: 0.8370 (tp) REVERT: F 303 PHE cc_start: 0.7607 (m-80) cc_final: 0.6851 (m-80) REVERT: F 311 LYS cc_start: 0.7672 (tmmt) cc_final: 0.7208 (ttmm) REVERT: F 316 CYS cc_start: 0.7705 (t) cc_final: 0.7493 (p) REVERT: F 319 SER cc_start: 0.8625 (t) cc_final: 0.8079 (p) REVERT: F 322 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7744 (mmt-90) REVERT: F 346 LEU cc_start: 0.7621 (tp) cc_final: 0.7347 (pp) REVERT: F 411 ILE cc_start: 0.8643 (tt) cc_final: 0.8380 (pt) REVERT: F 423 GLN cc_start: 0.7870 (tt0) cc_final: 0.7436 (tt0) REVERT: F 431 TYR cc_start: 0.6687 (m-80) cc_final: 0.6324 (m-80) REVERT: F 457 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7962 (mmtt) REVERT: F 473 MET cc_start: 0.6879 (ptm) cc_final: 0.6662 (ttm) REVERT: F 489 GLN cc_start: 0.8049 (mt0) cc_final: 0.7826 (tp-100) outliers start: 8 outliers final: 2 residues processed: 873 average time/residue: 0.3876 time to fit residues: 490.6575 Evaluate side-chains 725 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 723 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain F residue 748 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 187 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 532 ASN E 48 HIS C 60 ASN C 106 ASN C 163 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 657 HIS C 718 GLN B 71 HIS B 316 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 163 GLN F 286 HIS F 434 GLN F 606 ASN F 618 GLN F 718 GLN F 719 HIS D 47 ASN D 48 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22731 Z= 0.258 Angle : 0.667 9.033 30684 Z= 0.353 Chirality : 0.044 0.231 3385 Planarity : 0.005 0.118 3934 Dihedral : 4.526 44.083 3012 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.17 % Favored : 91.76 % Rotamer: Outliers : 3.68 % Allowed : 19.22 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2718 helix: 0.97 (0.15), residues: 1265 sheet: -0.91 (0.30), residues: 276 loop : -2.37 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 101 HIS 0.012 0.002 HIS B 306 PHE 0.020 0.002 PHE F 205 TYR 0.023 0.002 TYR B 549 ARG 0.010 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 771 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7631 (pp20) REVERT: A 20 GLN cc_start: 0.8703 (mm-40) cc_final: 0.7909 (mm110) REVERT: A 22 LYS cc_start: 0.8633 (ttmt) cc_final: 0.7837 (ttmt) REVERT: A 26 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 34 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8629 (m) REVERT: A 42 PHE cc_start: 0.8824 (m-80) cc_final: 0.8493 (m-80) REVERT: A 60 PHE cc_start: 0.8418 (m-80) cc_final: 0.7683 (m-10) REVERT: A 66 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7084 (pt0) REVERT: A 68 LYS cc_start: 0.8541 (tptp) cc_final: 0.8134 (tptp) REVERT: A 75 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.7548 (ptp-170) REVERT: A 84 ILE cc_start: 0.8596 (tp) cc_final: 0.8292 (tt) REVERT: A 87 THR cc_start: 0.8454 (t) cc_final: 0.8019 (p) REVERT: A 90 TYR cc_start: 0.7826 (m-80) cc_final: 0.7313 (m-80) REVERT: A 102 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 103 GLN cc_start: 0.7914 (tp40) cc_final: 0.7680 (tp40) REVERT: A 112 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7728 (mm-40) REVERT: A 117 LEU cc_start: 0.8287 (mt) cc_final: 0.7935 (tt) REVERT: A 121 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8278 (ttp80) REVERT: A 122 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 127 LYS cc_start: 0.8456 (tppt) cc_final: 0.8096 (mmmm) REVERT: A 159 LYS cc_start: 0.7328 (mtmt) cc_final: 0.6770 (mtmm) REVERT: A 165 HIS cc_start: 0.6375 (m90) cc_final: 0.6138 (m90) REVERT: A 170 MET cc_start: 0.6767 (mmp) cc_final: 0.6424 (mmp) REVERT: A 191 GLU cc_start: 0.7386 (pp20) cc_final: 0.7019 (tm-30) REVERT: A 196 GLU cc_start: 0.7545 (pp20) cc_final: 0.7116 (pp20) REVERT: A 225 LEU cc_start: 0.5416 (mt) cc_final: 0.5154 (mt) REVERT: A 267 GLU cc_start: 0.7596 (tp30) cc_final: 0.7167 (tp30) REVERT: A 269 MET cc_start: 0.6973 (mmp) cc_final: 0.6369 (mmp) REVERT: A 288 TYR cc_start: 0.7355 (t80) cc_final: 0.6938 (t80) REVERT: A 293 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 294 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7880 (mmmm) REVERT: A 296 TYR cc_start: 0.7139 (m-80) cc_final: 0.6739 (m-80) REVERT: A 297 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7910 (ptpt) REVERT: A 301 PRO cc_start: 0.7504 (Cg_exo) cc_final: 0.7239 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8295 (p) cc_final: 0.7902 (t) REVERT: A 352 TRP cc_start: 0.8037 (t60) cc_final: 0.7765 (t60) REVERT: A 353 PHE cc_start: 0.7868 (t80) cc_final: 0.7378 (t80) REVERT: A 354 ASP cc_start: 0.6323 (t0) cc_final: 0.5259 (t70) REVERT: A 361 PHE cc_start: 0.7187 (m-80) cc_final: 0.6492 (m-80) REVERT: A 408 GLU cc_start: 0.7482 (pm20) cc_final: 0.6890 (pm20) REVERT: A 443 PHE cc_start: 0.8639 (t80) cc_final: 0.8288 (t80) REVERT: A 511 MET cc_start: 0.6059 (tpt) cc_final: 0.5836 (tpp) REVERT: E 23 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6557 (mp0) REVERT: E 48 HIS cc_start: 0.4924 (t-90) cc_final: 0.4545 (t-90) REVERT: C 28 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7667 (tptp) REVERT: C 33 ILE cc_start: 0.8975 (mm) cc_final: 0.8630 (tt) REVERT: C 43 GLU cc_start: 0.7359 (tp30) cc_final: 0.6553 (tp30) REVERT: C 48 ASN cc_start: 0.7999 (t0) cc_final: 0.6986 (t0) REVERT: C 62 TYR cc_start: 0.7846 (t80) cc_final: 0.7555 (t80) REVERT: C 68 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8312 (mptt) REVERT: C 71 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 72 LYS cc_start: 0.8461 (tttt) cc_final: 0.7847 (tptm) REVERT: C 83 GLU cc_start: 0.7586 (tp30) cc_final: 0.7137 (tp30) REVERT: C 91 GLU cc_start: 0.7341 (tp30) cc_final: 0.7095 (mm-30) REVERT: C 118 MET cc_start: 0.7182 (mtm) cc_final: 0.6964 (mtm) REVERT: C 125 TYR cc_start: 0.4324 (t80) cc_final: 0.4092 (t80) REVERT: C 153 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7634 (mmm160) REVERT: C 163 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7729 (mm110) REVERT: C 204 ASP cc_start: 0.7067 (t0) cc_final: 0.6768 (t0) REVERT: C 215 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: C 217 PHE cc_start: 0.7834 (m-80) cc_final: 0.7427 (m-10) REVERT: C 220 GLU cc_start: 0.7242 (tp30) cc_final: 0.6796 (tp30) REVERT: C 222 GLN cc_start: 0.7710 (tp40) cc_final: 0.7354 (tm-30) REVERT: C 224 PHE cc_start: 0.6895 (m-80) cc_final: 0.5556 (m-80) REVERT: C 235 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7929 (mtmm) REVERT: C 238 GLU cc_start: 0.7329 (tp30) cc_final: 0.6721 (tm-30) REVERT: C 243 GLU cc_start: 0.8198 (pt0) cc_final: 0.7455 (pp20) REVERT: C 246 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 250 HIS cc_start: 0.7738 (t-90) cc_final: 0.7151 (t-90) REVERT: C 258 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7018 (mm-30) REVERT: C 262 LYS cc_start: 0.7928 (tmtm) cc_final: 0.7407 (ttpp) REVERT: C 270 SER cc_start: 0.8419 (m) cc_final: 0.8181 (t) REVERT: C 282 SER cc_start: 0.7515 (OUTLIER) cc_final: 0.6951 (p) REVERT: C 292 LYS cc_start: 0.8599 (mmmm) cc_final: 0.7966 (mmtm) REVERT: C 301 LYS cc_start: 0.8415 (ptpt) cc_final: 0.8136 (ptpt) REVERT: C 306 VAL cc_start: 0.8586 (t) cc_final: 0.8204 (p) REVERT: C 321 LEU cc_start: 0.8543 (mt) cc_final: 0.8306 (mt) REVERT: C 346 LEU cc_start: 0.8153 (tp) cc_final: 0.7875 (tp) REVERT: C 353 ASP cc_start: 0.7840 (t0) cc_final: 0.7586 (t0) REVERT: C 360 PHE cc_start: 0.8288 (m-10) cc_final: 0.7818 (m-10) REVERT: C 368 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6582 (tm-30) REVERT: C 369 THR cc_start: 0.8123 (p) cc_final: 0.7564 (t) REVERT: C 394 ASP cc_start: 0.7935 (t0) cc_final: 0.7576 (t0) REVERT: C 395 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8597 (mmmt) REVERT: C 409 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7299 (pt0) REVERT: C 412 LEU cc_start: 0.8702 (mt) cc_final: 0.8139 (pp) REVERT: C 413 ASP cc_start: 0.8290 (m-30) cc_final: 0.7532 (m-30) REVERT: C 418 LEU cc_start: 0.8713 (tt) cc_final: 0.8355 (tp) REVERT: C 424 GLU cc_start: 0.7324 (mp0) cc_final: 0.6971 (mp0) REVERT: C 429 GLU cc_start: 0.8081 (tp30) cc_final: 0.7879 (tp30) REVERT: C 431 TYR cc_start: 0.8080 (m-80) cc_final: 0.7265 (m-10) REVERT: C 438 ARG cc_start: 0.7856 (tpm170) cc_final: 0.7227 (tpm170) REVERT: C 457 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8676 (mmmt) REVERT: C 479 ILE cc_start: 0.7680 (mm) cc_final: 0.7379 (mt) REVERT: C 554 MET cc_start: 0.6881 (tpp) cc_final: 0.6380 (tpp) REVERT: C 603 MET cc_start: 0.7415 (tmm) cc_final: 0.6996 (tmm) REVERT: C 692 ARG cc_start: 0.8469 (tpp-160) cc_final: 0.8214 (mmp80) REVERT: B 19 GLU cc_start: 0.7607 (pp20) cc_final: 0.7033 (pp20) REVERT: B 20 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8266 (mm-40) REVERT: B 24 PHE cc_start: 0.8453 (m-10) cc_final: 0.8138 (m-80) REVERT: B 25 TYR cc_start: 0.8640 (t80) cc_final: 0.8397 (t80) REVERT: B 29 LEU cc_start: 0.8233 (mp) cc_final: 0.7971 (mp) REVERT: B 32 ASP cc_start: 0.7990 (p0) cc_final: 0.7621 (p0) REVERT: B 45 HIS cc_start: 0.8300 (m90) cc_final: 0.8011 (m170) REVERT: B 46 LYS cc_start: 0.8793 (mttt) cc_final: 0.8457 (mtpp) REVERT: B 60 PHE cc_start: 0.8479 (m-10) cc_final: 0.8252 (m-10) REVERT: B 61 MET cc_start: 0.6823 (tmm) cc_final: 0.6422 (tmm) REVERT: B 69 GLN cc_start: 0.7829 (tt0) cc_final: 0.7619 (tt0) REVERT: B 72 VAL cc_start: 0.8770 (m) cc_final: 0.8434 (p) REVERT: B 75 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7431 (ptp-110) REVERT: B 85 ILE cc_start: 0.8699 (mt) cc_final: 0.8412 (tp) REVERT: B 103 GLN cc_start: 0.7522 (pm20) cc_final: 0.6921 (pm20) REVERT: B 105 TYR cc_start: 0.8018 (t80) cc_final: 0.7589 (t80) REVERT: B 106 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7492 (mt-10) REVERT: B 112 GLN cc_start: 0.7615 (mm-40) cc_final: 0.5990 (mm110) REVERT: B 114 GLU cc_start: 0.6451 (tm-30) cc_final: 0.6149 (mm-30) REVERT: B 123 TYR cc_start: 0.7519 (t80) cc_final: 0.6862 (t80) REVERT: B 127 LYS cc_start: 0.8011 (tptt) cc_final: 0.7698 (tptt) REVERT: B 132 ASN cc_start: 0.7858 (p0) cc_final: 0.7422 (p0) REVERT: B 136 LEU cc_start: 0.8321 (mt) cc_final: 0.7967 (mm) REVERT: B 149 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7818 (tptp) REVERT: B 155 MET cc_start: 0.8070 (tpt) cc_final: 0.7246 (tpp) REVERT: B 167 ASP cc_start: 0.7437 (p0) cc_final: 0.7029 (p0) REVERT: B 170 MET cc_start: 0.7873 (mmm) cc_final: 0.7618 (mmm) REVERT: B 184 ASP cc_start: 0.7810 (t70) cc_final: 0.7278 (t0) REVERT: B 203 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7112 (mm-30) REVERT: B 212 TYR cc_start: 0.7931 (m-10) cc_final: 0.7542 (m-80) REVERT: B 242 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7847 (mmtt) REVERT: B 263 MET cc_start: 0.6857 (mpp) cc_final: 0.6465 (mtm) REVERT: B 267 GLU cc_start: 0.7033 (tp30) cc_final: 0.6677 (tp30) REVERT: B 269 MET cc_start: 0.5611 (mmp) cc_final: 0.5159 (mmp) REVERT: B 290 PRO cc_start: 0.8439 (Cg_exo) cc_final: 0.8047 (Cg_endo) REVERT: B 307 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8296 (mmtm) REVERT: B 363 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8272 (mmtp) REVERT: B 381 TYR cc_start: 0.7817 (m-80) cc_final: 0.6951 (m-80) REVERT: B 383 TYR cc_start: 0.5548 (m-80) cc_final: 0.5009 (m-80) REVERT: B 429 ASP cc_start: 0.7905 (m-30) cc_final: 0.7389 (m-30) REVERT: B 430 CYS cc_start: 0.5609 (m) cc_final: 0.5232 (t) REVERT: B 436 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6309 (tt) REVERT: B 443 PHE cc_start: 0.7661 (t80) cc_final: 0.7444 (t80) REVERT: B 469 ASP cc_start: 0.7263 (t70) cc_final: 0.6522 (t0) REVERT: B 470 LYS cc_start: 0.7086 (mttm) cc_final: 0.6603 (mtpp) REVERT: B 502 TYR cc_start: 0.6834 (t80) cc_final: 0.6240 (t80) REVERT: B 507 ASN cc_start: 0.8230 (t0) cc_final: 0.7792 (t0) REVERT: B 529 VAL cc_start: 0.6192 (t) cc_final: 0.5365 (m) REVERT: B 553 GLN cc_start: 0.6284 (tt0) cc_final: 0.6032 (tm-30) REVERT: F 28 LYS cc_start: 0.7799 (mmmm) cc_final: 0.7460 (mmmm) REVERT: F 30 VAL cc_start: 0.7136 (m) cc_final: 0.6858 (p) REVERT: F 35 ASP cc_start: 0.7352 (t0) cc_final: 0.7071 (t70) REVERT: F 62 TYR cc_start: 0.7925 (t80) cc_final: 0.7511 (t80) REVERT: F 64 MET cc_start: 0.7272 (tpt) cc_final: 0.6942 (tpt) REVERT: F 66 LEU cc_start: 0.7540 (tp) cc_final: 0.7248 (tp) REVERT: F 68 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8381 (mttm) REVERT: F 78 ARG cc_start: 0.8229 (ttm170) cc_final: 0.8014 (ttm-80) REVERT: F 79 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6803 (tp30) REVERT: F 113 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: F 126 MET cc_start: 0.8213 (tmt) cc_final: 0.7873 (tmm) REVERT: F 128 ARG cc_start: 0.6557 (mtm-85) cc_final: 0.5235 (mtm-85) REVERT: F 139 VAL cc_start: 0.7418 (m) cc_final: 0.6643 (t) REVERT: F 140 TYR cc_start: 0.7938 (t80) cc_final: 0.6929 (t80) REVERT: F 145 ILE cc_start: 0.8855 (mt) cc_final: 0.8610 (mm) REVERT: F 153 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7406 (mtt180) REVERT: F 160 HIS cc_start: 0.8135 (t-90) cc_final: 0.7880 (t-90) REVERT: F 167 ASP cc_start: 0.7045 (t0) cc_final: 0.6693 (t0) REVERT: F 168 MET cc_start: 0.7205 (ptp) cc_final: 0.6688 (ptp) REVERT: F 208 PRO cc_start: 0.8586 (Cg_exo) cc_final: 0.8379 (Cg_endo) REVERT: F 216 PHE cc_start: 0.7495 (t80) cc_final: 0.7173 (t80) REVERT: F 233 TYR cc_start: 0.7559 (t80) cc_final: 0.7146 (t80) REVERT: F 235 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8394 (mmmt) REVERT: F 240 ARG cc_start: 0.7930 (mmt180) cc_final: 0.7620 (tpp80) REVERT: F 241 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8603 (tp) REVERT: F 243 GLU cc_start: 0.7587 (pp20) cc_final: 0.7109 (pp20) REVERT: F 246 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7236 (tp30) REVERT: F 249 MET cc_start: 0.7698 (ppp) cc_final: 0.7273 (ppp) REVERT: F 258 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7784 (mm-30) REVERT: F 265 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7161 (mm-30) REVERT: F 270 SER cc_start: 0.8513 (m) cc_final: 0.8013 (t) REVERT: F 274 LYS cc_start: 0.8086 (tppt) cc_final: 0.7528 (tmmt) REVERT: F 287 MET cc_start: 0.7664 (ptm) cc_final: 0.7272 (ppp) REVERT: F 295 ASP cc_start: 0.7268 (m-30) cc_final: 0.6740 (m-30) REVERT: F 301 LYS cc_start: 0.8380 (ptpt) cc_final: 0.8138 (ttpp) REVERT: F 302 LEU cc_start: 0.8640 (tp) cc_final: 0.8432 (tp) REVERT: F 303 PHE cc_start: 0.7664 (m-80) cc_final: 0.7157 (m-80) REVERT: F 311 LYS cc_start: 0.7805 (tmmt) cc_final: 0.7401 (ttmm) REVERT: F 319 SER cc_start: 0.8612 (t) cc_final: 0.8145 (p) REVERT: F 322 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7793 (mmt-90) REVERT: F 323 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7566 (tm-30) REVERT: F 332 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: F 414 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8665 (mmtm) REVERT: F 423 GLN cc_start: 0.8021 (tt0) cc_final: 0.7588 (tt0) REVERT: F 457 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8011 (mmtt) REVERT: F 461 GLU cc_start: 0.6658 (tp30) cc_final: 0.5983 (tp30) REVERT: F 489 GLN cc_start: 0.8115 (mt0) cc_final: 0.7768 (tp-100) REVERT: F 490 HIS cc_start: 0.7004 (m90) cc_final: 0.6620 (m-70) REVERT: F 539 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: F 673 LYS cc_start: 0.8029 (ptmm) cc_final: 0.7821 (pptt) REVERT: F 725 GLU cc_start: 0.8325 (tt0) cc_final: 0.8005 (mt-10) REVERT: D 98 ASN cc_start: 0.7145 (p0) cc_final: 0.6865 (p0) outliers start: 91 outliers final: 39 residues processed: 826 average time/residue: 0.3971 time to fit residues: 486.6450 Evaluate side-chains 755 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 708 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 420 ARG Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 539 TYR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 205 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 68 optimal weight: 0.4980 chunk 247 optimal weight: 0.5980 chunk 267 optimal weight: 0.0770 chunk 220 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN C 60 ASN C 84 HIS C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS B 187 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22731 Z= 0.218 Angle : 0.661 9.864 30684 Z= 0.341 Chirality : 0.043 0.311 3385 Planarity : 0.005 0.077 3934 Dihedral : 4.452 30.689 3008 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.02 % Favored : 91.91 % Rotamer: Outliers : 4.05 % Allowed : 20.84 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2718 helix: 0.89 (0.15), residues: 1280 sheet: -1.02 (0.30), residues: 275 loop : -2.42 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 233 HIS 0.012 0.001 HIS C 84 PHE 0.024 0.002 PHE B 537 TYR 0.022 0.002 TYR C 432 ARG 0.007 0.001 ARG F 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 732 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7744 (pt) REVERT: A 19 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7544 (pp20) REVERT: A 20 GLN cc_start: 0.8707 (mm-40) cc_final: 0.7889 (mm110) REVERT: A 26 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 27 GLN cc_start: 0.8075 (mt0) cc_final: 0.7781 (mt0) REVERT: A 34 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8582 (m) REVERT: A 37 VAL cc_start: 0.8711 (t) cc_final: 0.8261 (m) REVERT: A 57 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7673 (ttp80) REVERT: A 59 MET cc_start: 0.7595 (ttt) cc_final: 0.7217 (ttp) REVERT: A 60 PHE cc_start: 0.8244 (m-80) cc_final: 0.7956 (m-10) REVERT: A 66 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6881 (pt0) REVERT: A 68 LYS cc_start: 0.8529 (tptp) cc_final: 0.8120 (tptp) REVERT: A 84 ILE cc_start: 0.8586 (tp) cc_final: 0.8250 (tt) REVERT: A 87 THR cc_start: 0.8500 (t) cc_final: 0.8075 (p) REVERT: A 88 TYR cc_start: 0.8294 (t80) cc_final: 0.7225 (t80) REVERT: A 90 TYR cc_start: 0.7862 (m-80) cc_final: 0.7436 (m-80) REVERT: A 102 GLU cc_start: 0.7230 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 103 GLN cc_start: 0.7923 (tp40) cc_final: 0.7660 (tp40) REVERT: A 106 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 112 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7745 (mm-40) REVERT: A 115 ASP cc_start: 0.7984 (p0) cc_final: 0.7072 (p0) REVERT: A 117 LEU cc_start: 0.8236 (mt) cc_final: 0.7885 (tt) REVERT: A 122 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 127 LYS cc_start: 0.8483 (tppt) cc_final: 0.8169 (mmmm) REVERT: A 147 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7359 (mt-10) REVERT: A 157 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 159 LYS cc_start: 0.6974 (mtmt) cc_final: 0.6562 (mtmm) REVERT: A 165 HIS cc_start: 0.6445 (m90) cc_final: 0.6156 (m90) REVERT: A 170 MET cc_start: 0.6737 (mmp) cc_final: 0.6382 (mmp) REVERT: A 191 GLU cc_start: 0.7307 (pp20) cc_final: 0.6990 (tm-30) REVERT: A 196 GLU cc_start: 0.7554 (pp20) cc_final: 0.7081 (pp20) REVERT: A 199 MET cc_start: 0.7686 (mmm) cc_final: 0.7363 (mmp) REVERT: A 209 ARG cc_start: 0.7416 (mtm180) cc_final: 0.7067 (mtm180) REVERT: A 225 LEU cc_start: 0.5447 (mt) cc_final: 0.5131 (mt) REVERT: A 267 GLU cc_start: 0.7534 (tp30) cc_final: 0.7315 (tp30) REVERT: A 268 MET cc_start: 0.7160 (mtt) cc_final: 0.5689 (mtt) REVERT: A 269 MET cc_start: 0.7395 (mmp) cc_final: 0.7140 (mmp) REVERT: A 294 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7871 (mmmm) REVERT: A 297 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7853 (ptpt) REVERT: A 301 PRO cc_start: 0.7478 (Cg_exo) cc_final: 0.7197 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8209 (p) cc_final: 0.7825 (t) REVERT: A 352 TRP cc_start: 0.8007 (t60) cc_final: 0.7602 (t60) REVERT: A 354 ASP cc_start: 0.6407 (t0) cc_final: 0.5719 (t0) REVERT: A 356 GLN cc_start: 0.8089 (pp30) cc_final: 0.6623 (pp30) REVERT: A 357 GLN cc_start: 0.7299 (mm-40) cc_final: 0.6566 (mm-40) REVERT: A 361 PHE cc_start: 0.7073 (m-80) cc_final: 0.6301 (m-80) REVERT: A 382 ILE cc_start: 0.7078 (mm) cc_final: 0.6816 (mm) REVERT: A 383 TYR cc_start: 0.5663 (m-80) cc_final: 0.5259 (m-80) REVERT: A 439 MET cc_start: 0.5621 (ptt) cc_final: 0.5239 (ptt) REVERT: A 443 PHE cc_start: 0.8618 (t80) cc_final: 0.8259 (t80) REVERT: A 454 MET cc_start: 0.7116 (tpp) cc_final: 0.6575 (tpp) REVERT: A 502 TYR cc_start: 0.5958 (t80) cc_final: 0.4172 (t80) REVERT: A 558 LEU cc_start: 0.6784 (tp) cc_final: 0.6422 (mt) REVERT: A 583 VAL cc_start: 0.6792 (OUTLIER) cc_final: 0.6583 (m) REVERT: E 22 PHE cc_start: 0.6772 (m-80) cc_final: 0.6498 (m-80) REVERT: E 23 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6838 (mp0) REVERT: E 48 HIS cc_start: 0.5014 (t-90) cc_final: 0.4274 (t-90) REVERT: C 28 LYS cc_start: 0.8089 (mmmm) cc_final: 0.7684 (tptp) REVERT: C 33 ILE cc_start: 0.8934 (mm) cc_final: 0.8673 (mm) REVERT: C 68 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8154 (mptt) REVERT: C 71 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7493 (tm-30) REVERT: C 72 LYS cc_start: 0.8463 (tttt) cc_final: 0.7849 (tptm) REVERT: C 83 GLU cc_start: 0.7651 (tp30) cc_final: 0.7207 (tp30) REVERT: C 91 GLU cc_start: 0.7291 (tp30) cc_final: 0.7044 (mm-30) REVERT: C 125 TYR cc_start: 0.4570 (t80) cc_final: 0.4314 (t80) REVERT: C 153 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7358 (mmm-85) REVERT: C 163 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7711 (mm110) REVERT: C 167 ASP cc_start: 0.7297 (t0) cc_final: 0.6817 (t70) REVERT: C 204 ASP cc_start: 0.7112 (t0) cc_final: 0.6870 (t0) REVERT: C 215 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: C 220 GLU cc_start: 0.7256 (tp30) cc_final: 0.6864 (tp30) REVERT: C 222 GLN cc_start: 0.7687 (tp40) cc_final: 0.7234 (tm-30) REVERT: C 224 PHE cc_start: 0.6891 (m-80) cc_final: 0.5830 (m-10) REVERT: C 235 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7892 (mtmm) REVERT: C 236 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8626 (ptmt) REVERT: C 238 GLU cc_start: 0.7306 (tp30) cc_final: 0.6737 (tm-30) REVERT: C 243 GLU cc_start: 0.8216 (pt0) cc_final: 0.7462 (pp20) REVERT: C 244 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7300 (tp30) REVERT: C 246 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 248 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8219 (p) REVERT: C 250 HIS cc_start: 0.7734 (t-90) cc_final: 0.7235 (t-90) REVERT: C 258 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 262 LYS cc_start: 0.8056 (tmtm) cc_final: 0.7451 (ttpp) REVERT: C 270 SER cc_start: 0.8434 (m) cc_final: 0.8136 (t) REVERT: C 282 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7338 (t) REVERT: C 288 LEU cc_start: 0.9036 (tp) cc_final: 0.8542 (tp) REVERT: C 292 LYS cc_start: 0.8375 (mmmm) cc_final: 0.7977 (mmtm) REVERT: C 299 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7444 (ttm) REVERT: C 301 LYS cc_start: 0.8392 (ptpt) cc_final: 0.8156 (ptpp) REVERT: C 306 VAL cc_start: 0.8620 (t) cc_final: 0.8253 (p) REVERT: C 315 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7060 (mm-30) REVERT: C 346 LEU cc_start: 0.8211 (tp) cc_final: 0.7974 (tp) REVERT: C 353 ASP cc_start: 0.7890 (t0) cc_final: 0.7473 (t70) REVERT: C 354 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7538 (ttp-110) REVERT: C 360 PHE cc_start: 0.8130 (m-10) cc_final: 0.7871 (m-10) REVERT: C 363 ASP cc_start: 0.8036 (t70) cc_final: 0.7830 (t70) REVERT: C 368 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6537 (tm-30) REVERT: C 369 THR cc_start: 0.7973 (p) cc_final: 0.7560 (t) REVERT: C 394 ASP cc_start: 0.7891 (t0) cc_final: 0.7528 (t0) REVERT: C 395 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8430 (mmmm) REVERT: C 409 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7281 (pt0) REVERT: C 412 LEU cc_start: 0.8690 (mt) cc_final: 0.8207 (pp) REVERT: C 413 ASP cc_start: 0.8323 (m-30) cc_final: 0.8038 (m-30) REVERT: C 418 LEU cc_start: 0.8681 (tt) cc_final: 0.8388 (tp) REVERT: C 424 GLU cc_start: 0.7321 (mp0) cc_final: 0.7039 (mp0) REVERT: C 431 TYR cc_start: 0.8113 (m-80) cc_final: 0.7309 (m-10) REVERT: C 438 ARG cc_start: 0.7861 (tpm170) cc_final: 0.7181 (tpm170) REVERT: C 441 LEU cc_start: 0.8160 (mt) cc_final: 0.7617 (mp) REVERT: C 454 MET cc_start: 0.8108 (tmm) cc_final: 0.7855 (tmm) REVERT: C 457 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8643 (mmmt) REVERT: C 473 MET cc_start: 0.7845 (mmt) cc_final: 0.7038 (mmt) REVERT: C 484 MET cc_start: 0.2766 (OUTLIER) cc_final: 0.2277 (tpt) REVERT: C 554 MET cc_start: 0.6795 (tpp) cc_final: 0.6317 (tpp) REVERT: C 687 GLU cc_start: 0.6455 (pp20) cc_final: 0.5808 (pt0) REVERT: C 688 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7469 (mmm-85) REVERT: C 692 ARG cc_start: 0.8445 (tpp-160) cc_final: 0.8161 (mmp80) REVERT: B 19 GLU cc_start: 0.7566 (pp20) cc_final: 0.6988 (pp20) REVERT: B 24 PHE cc_start: 0.8390 (m-10) cc_final: 0.8110 (m-80) REVERT: B 29 LEU cc_start: 0.8230 (mp) cc_final: 0.7826 (mp) REVERT: B 32 ASP cc_start: 0.7975 (p0) cc_final: 0.7520 (p0) REVERT: B 46 LYS cc_start: 0.8818 (mttt) cc_final: 0.8603 (mttt) REVERT: B 55 TYR cc_start: 0.8575 (t80) cc_final: 0.7290 (t80) REVERT: B 61 MET cc_start: 0.6859 (tmm) cc_final: 0.6373 (tmm) REVERT: B 72 VAL cc_start: 0.8859 (m) cc_final: 0.8463 (p) REVERT: B 85 ILE cc_start: 0.8677 (mt) cc_final: 0.8366 (tp) REVERT: B 105 TYR cc_start: 0.7893 (t80) cc_final: 0.7536 (t80) REVERT: B 106 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 112 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7365 (mm-40) REVERT: B 114 GLU cc_start: 0.6427 (tm-30) cc_final: 0.6145 (mm-30) REVERT: B 123 TYR cc_start: 0.7667 (t80) cc_final: 0.7009 (t80) REVERT: B 127 LYS cc_start: 0.7971 (tptt) cc_final: 0.7747 (tptt) REVERT: B 136 LEU cc_start: 0.8198 (mt) cc_final: 0.7925 (mm) REVERT: B 149 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7681 (tptp) REVERT: B 153 LYS cc_start: 0.8650 (tptm) cc_final: 0.8159 (tptm) REVERT: B 154 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7375 (mtp85) REVERT: B 155 MET cc_start: 0.7961 (tpt) cc_final: 0.7436 (tpp) REVERT: B 166 GLN cc_start: 0.4864 (mp10) cc_final: 0.4364 (mp10) REVERT: B 170 MET cc_start: 0.7818 (mmm) cc_final: 0.7577 (mmm) REVERT: B 184 ASP cc_start: 0.7834 (t70) cc_final: 0.7284 (t0) REVERT: B 199 MET cc_start: 0.7565 (mmp) cc_final: 0.7278 (mmp) REVERT: B 202 LEU cc_start: 0.7935 (mt) cc_final: 0.7685 (mt) REVERT: B 203 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 209 ARG cc_start: 0.8209 (mmt90) cc_final: 0.7589 (mmt90) REVERT: B 212 TYR cc_start: 0.7886 (m-10) cc_final: 0.7560 (m-80) REVERT: B 242 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7933 (mmtt) REVERT: B 245 VAL cc_start: 0.6930 (t) cc_final: 0.6639 (p) REVERT: B 263 MET cc_start: 0.6975 (mpp) cc_final: 0.6589 (mtm) REVERT: B 267 GLU cc_start: 0.7124 (tp30) cc_final: 0.6769 (tp30) REVERT: B 269 MET cc_start: 0.5547 (mmp) cc_final: 0.5155 (mmp) REVERT: B 307 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8121 (mmtm) REVERT: B 363 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8291 (mmtp) REVERT: B 381 TYR cc_start: 0.7706 (m-80) cc_final: 0.6915 (m-80) REVERT: B 383 TYR cc_start: 0.5577 (m-80) cc_final: 0.5108 (m-80) REVERT: B 429 ASP cc_start: 0.7882 (m-30) cc_final: 0.7035 (m-30) REVERT: B 430 CYS cc_start: 0.5726 (m) cc_final: 0.5249 (t) REVERT: B 443 PHE cc_start: 0.7666 (t80) cc_final: 0.7424 (t80) REVERT: B 469 ASP cc_start: 0.7364 (t70) cc_final: 0.6850 (t0) REVERT: B 470 LYS cc_start: 0.7013 (mttm) cc_final: 0.6690 (mtpp) REVERT: B 472 PHE cc_start: 0.6060 (m-80) cc_final: 0.5381 (m-80) REVERT: B 502 TYR cc_start: 0.6774 (t80) cc_final: 0.6158 (t80) REVERT: B 534 LEU cc_start: 0.6374 (tp) cc_final: 0.5992 (tt) REVERT: F 28 LYS cc_start: 0.7796 (mmmm) cc_final: 0.7484 (mmmm) REVERT: F 58 TYR cc_start: 0.8158 (t80) cc_final: 0.7775 (t80) REVERT: F 62 TYR cc_start: 0.7903 (t80) cc_final: 0.7261 (t80) REVERT: F 63 THR cc_start: 0.7400 (t) cc_final: 0.7099 (p) REVERT: F 64 MET cc_start: 0.7291 (tpt) cc_final: 0.6908 (tpt) REVERT: F 68 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8363 (mttm) REVERT: F 71 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6886 (tm-30) REVERT: F 78 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7960 (ttm-80) REVERT: F 79 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6707 (tp30) REVERT: F 113 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7606 (tp40) REVERT: F 116 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8256 (tpp) REVERT: F 125 TYR cc_start: 0.5541 (t80) cc_final: 0.5318 (t80) REVERT: F 126 MET cc_start: 0.8249 (tmt) cc_final: 0.7910 (tmm) REVERT: F 139 VAL cc_start: 0.7476 (m) cc_final: 0.6789 (t) REVERT: F 140 TYR cc_start: 0.7989 (t80) cc_final: 0.7490 (t80) REVERT: F 145 ILE cc_start: 0.8874 (mt) cc_final: 0.8598 (mm) REVERT: F 153 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7407 (mtt180) REVERT: F 167 ASP cc_start: 0.7110 (t0) cc_final: 0.6724 (t0) REVERT: F 168 MET cc_start: 0.7169 (ptp) cc_final: 0.6690 (ptp) REVERT: F 233 TYR cc_start: 0.7566 (t80) cc_final: 0.7040 (t80) REVERT: F 234 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8090 (tt) REVERT: F 235 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8260 (mmmm) REVERT: F 236 LYS cc_start: 0.8318 (ttmt) cc_final: 0.8064 (ttmm) REVERT: F 240 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7628 (tpp80) REVERT: F 243 GLU cc_start: 0.7541 (pp20) cc_final: 0.7096 (pp20) REVERT: F 246 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7210 (tp30) REVERT: F 249 MET cc_start: 0.7641 (ppp) cc_final: 0.7300 (ppp) REVERT: F 257 GLU cc_start: 0.7250 (pp20) cc_final: 0.6876 (pp20) REVERT: F 258 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7525 (mp0) REVERT: F 265 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7135 (mm-30) REVERT: F 270 SER cc_start: 0.8576 (m) cc_final: 0.8037 (t) REVERT: F 272 HIS cc_start: 0.6005 (m-70) cc_final: 0.5641 (m170) REVERT: F 274 LYS cc_start: 0.8074 (tppt) cc_final: 0.7537 (tmmt) REVERT: F 287 MET cc_start: 0.7510 (ptm) cc_final: 0.7033 (ppp) REVERT: F 295 ASP cc_start: 0.7242 (m-30) cc_final: 0.6723 (m-30) REVERT: F 301 LYS cc_start: 0.8228 (ptpt) cc_final: 0.7888 (pttm) REVERT: F 322 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7807 (mmt-90) REVERT: F 332 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6190 (pm20) REVERT: F 423 GLN cc_start: 0.8182 (tt0) cc_final: 0.7595 (tt0) REVERT: F 457 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7928 (mmtm) REVERT: F 461 GLU cc_start: 0.6351 (tp30) cc_final: 0.6080 (tp30) REVERT: F 489 GLN cc_start: 0.8003 (mt0) cc_final: 0.7771 (tp40) REVERT: F 490 HIS cc_start: 0.7000 (m90) cc_final: 0.6665 (m-70) REVERT: F 539 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: F 673 LYS cc_start: 0.7988 (ptmm) cc_final: 0.7749 (pptt) REVERT: F 689 LYS cc_start: 0.8020 (pttm) cc_final: 0.7808 (pttm) REVERT: F 734 PHE cc_start: 0.7048 (p90) cc_final: 0.6760 (p90) REVERT: D 42 CYS cc_start: 0.5665 (OUTLIER) cc_final: 0.5328 (m) REVERT: D 98 ASN cc_start: 0.6942 (p0) cc_final: 0.6705 (p0) outliers start: 100 outliers final: 49 residues processed: 783 average time/residue: 0.3722 time to fit residues: 429.5741 Evaluate side-chains 777 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 714 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 539 TYR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 118 optimal weight: 0.0170 chunk 166 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 235 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 77 HIS C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22731 Z= 0.233 Angle : 0.681 14.041 30684 Z= 0.351 Chirality : 0.044 0.304 3385 Planarity : 0.005 0.078 3934 Dihedral : 4.524 29.271 3006 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.01 % Favored : 90.91 % Rotamer: Outliers : 4.65 % Allowed : 21.49 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2718 helix: 0.82 (0.15), residues: 1261 sheet: -0.83 (0.31), residues: 256 loop : -2.43 (0.16), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 509 HIS 0.009 0.001 HIS F 84 PHE 0.027 0.002 PHE B 537 TYR 0.024 0.002 TYR C 125 ARG 0.010 0.001 ARG C 688 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 724 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7756 (pt) REVERT: A 19 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7559 (pp20) REVERT: A 20 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8010 (mm110) REVERT: A 26 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 29 LEU cc_start: 0.8692 (mp) cc_final: 0.8455 (mm) REVERT: A 34 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8730 (m) REVERT: A 37 VAL cc_start: 0.8606 (t) cc_final: 0.8187 (m) REVERT: A 57 ARG cc_start: 0.8120 (ptm160) cc_final: 0.7635 (ttp80) REVERT: A 59 MET cc_start: 0.7584 (ttt) cc_final: 0.7142 (ttp) REVERT: A 60 PHE cc_start: 0.8385 (m-80) cc_final: 0.7778 (m-10) REVERT: A 68 LYS cc_start: 0.8327 (tptp) cc_final: 0.8050 (tptp) REVERT: A 77 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8486 (m) REVERT: A 84 ILE cc_start: 0.8585 (tp) cc_final: 0.8234 (tt) REVERT: A 87 THR cc_start: 0.8534 (t) cc_final: 0.8162 (p) REVERT: A 88 TYR cc_start: 0.8389 (t80) cc_final: 0.7262 (t80) REVERT: A 90 TYR cc_start: 0.7924 (m-80) cc_final: 0.7527 (m-80) REVERT: A 103 GLN cc_start: 0.7957 (tp40) cc_final: 0.7679 (tp40) REVERT: A 106 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7250 (tm-30) REVERT: A 112 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8062 (tp40) REVERT: A 115 ASP cc_start: 0.7977 (p0) cc_final: 0.7131 (p0) REVERT: A 117 LEU cc_start: 0.8282 (mt) cc_final: 0.7868 (tt) REVERT: A 118 GLN cc_start: 0.8214 (tt0) cc_final: 0.7709 (tt0) REVERT: A 122 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 127 LYS cc_start: 0.8501 (tppt) cc_final: 0.8123 (mmmt) REVERT: A 147 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 157 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7052 (mm-30) REVERT: A 159 LYS cc_start: 0.7235 (mtmt) cc_final: 0.6856 (mtmm) REVERT: A 170 MET cc_start: 0.6665 (mmp) cc_final: 0.6317 (mmp) REVERT: A 191 GLU cc_start: 0.7348 (pp20) cc_final: 0.7044 (tm-30) REVERT: A 196 GLU cc_start: 0.7700 (pp20) cc_final: 0.7241 (pp20) REVERT: A 199 MET cc_start: 0.7800 (mmm) cc_final: 0.7439 (mmp) REVERT: A 209 ARG cc_start: 0.7472 (mtm180) cc_final: 0.6916 (mtm-85) REVERT: A 267 GLU cc_start: 0.7527 (tp30) cc_final: 0.6952 (tp30) REVERT: A 294 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8085 (mmmm) REVERT: A 297 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7862 (ptpt) REVERT: A 301 PRO cc_start: 0.7589 (Cg_exo) cc_final: 0.7384 (Cg_endo) REVERT: A 356 GLN cc_start: 0.8169 (pp30) cc_final: 0.6830 (pp30) REVERT: A 357 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6604 (mm-40) REVERT: A 358 ASN cc_start: 0.7915 (t0) cc_final: 0.7649 (t0) REVERT: A 361 PHE cc_start: 0.7147 (m-80) cc_final: 0.6303 (m-80) REVERT: A 382 ILE cc_start: 0.7112 (mm) cc_final: 0.6766 (pt) REVERT: A 383 TYR cc_start: 0.5695 (m-80) cc_final: 0.5290 (m-80) REVERT: A 434 MET cc_start: 0.2593 (tpt) cc_final: 0.2054 (tpt) REVERT: A 454 MET cc_start: 0.7183 (tpp) cc_final: 0.6715 (tpp) REVERT: A 502 TYR cc_start: 0.5961 (t80) cc_final: 0.5185 (t80) REVERT: A 558 LEU cc_start: 0.6890 (tp) cc_final: 0.6543 (mt) REVERT: E 23 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7221 (mp0) REVERT: E 48 HIS cc_start: 0.5008 (t-90) cc_final: 0.4158 (t-90) REVERT: E 50 MET cc_start: 0.2769 (pmm) cc_final: 0.2548 (pmm) REVERT: C 28 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7745 (tptp) REVERT: C 33 ILE cc_start: 0.9001 (mm) cc_final: 0.8751 (mm) REVERT: C 43 GLU cc_start: 0.7331 (tp30) cc_final: 0.6448 (tp30) REVERT: C 45 GLN cc_start: 0.7558 (mt0) cc_final: 0.7205 (tt0) REVERT: C 48 ASN cc_start: 0.8249 (t0) cc_final: 0.6748 (t0) REVERT: C 68 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8149 (mptt) REVERT: C 71 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 72 LYS cc_start: 0.8495 (tttt) cc_final: 0.8064 (tptm) REVERT: C 83 GLU cc_start: 0.7842 (tp30) cc_final: 0.7224 (tp30) REVERT: C 125 TYR cc_start: 0.4624 (t80) cc_final: 0.4414 (t80) REVERT: C 153 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7472 (mmm-85) REVERT: C 163 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7765 (mm110) REVERT: C 167 ASP cc_start: 0.7383 (t0) cc_final: 0.6923 (t70) REVERT: C 204 ASP cc_start: 0.7190 (t0) cc_final: 0.6980 (t0) REVERT: C 206 GLU cc_start: 0.6121 (mp0) cc_final: 0.5774 (mp0) REVERT: C 215 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: C 220 GLU cc_start: 0.7262 (tp30) cc_final: 0.6871 (tp30) REVERT: C 222 GLN cc_start: 0.7588 (tp40) cc_final: 0.7242 (tm-30) REVERT: C 224 PHE cc_start: 0.6764 (m-80) cc_final: 0.5901 (m-10) REVERT: C 235 LYS cc_start: 0.8398 (mmmt) cc_final: 0.7841 (mtmm) REVERT: C 238 GLU cc_start: 0.7400 (tp30) cc_final: 0.6739 (tm-30) REVERT: C 243 GLU cc_start: 0.8222 (pt0) cc_final: 0.7478 (pp20) REVERT: C 244 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7339 (tp30) REVERT: C 246 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 248 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8110 (p) REVERT: C 250 HIS cc_start: 0.7818 (t-90) cc_final: 0.7143 (t-90) REVERT: C 258 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7171 (mm-30) REVERT: C 262 LYS cc_start: 0.8096 (tmtm) cc_final: 0.7453 (ttpp) REVERT: C 270 SER cc_start: 0.8609 (m) cc_final: 0.8207 (t) REVERT: C 282 SER cc_start: 0.7808 (m) cc_final: 0.7403 (t) REVERT: C 288 LEU cc_start: 0.8950 (tp) cc_final: 0.8672 (tp) REVERT: C 292 LYS cc_start: 0.8472 (mmmm) cc_final: 0.8095 (mmtm) REVERT: C 295 ASP cc_start: 0.7576 (t0) cc_final: 0.7276 (t0) REVERT: C 301 LYS cc_start: 0.8404 (ptpt) cc_final: 0.8076 (ptpp) REVERT: C 306 VAL cc_start: 0.8676 (t) cc_final: 0.8364 (p) REVERT: C 315 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7118 (mm-30) REVERT: C 346 LEU cc_start: 0.8289 (tp) cc_final: 0.8039 (tp) REVERT: C 353 ASP cc_start: 0.7949 (t0) cc_final: 0.7477 (t70) REVERT: C 354 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7524 (ttp-110) REVERT: C 368 GLN cc_start: 0.7245 (tm-30) cc_final: 0.6606 (tm-30) REVERT: C 369 THR cc_start: 0.8051 (p) cc_final: 0.7697 (t) REVERT: C 394 ASP cc_start: 0.7910 (t0) cc_final: 0.7543 (t0) REVERT: C 395 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8283 (mmmm) REVERT: C 412 LEU cc_start: 0.8707 (mt) cc_final: 0.8434 (mm) REVERT: C 416 MET cc_start: 0.7248 (tpp) cc_final: 0.6764 (tpp) REVERT: C 418 LEU cc_start: 0.8764 (tt) cc_final: 0.8469 (tp) REVERT: C 423 GLN cc_start: 0.7719 (pm20) cc_final: 0.6600 (pt0) REVERT: C 424 GLU cc_start: 0.7436 (mp0) cc_final: 0.6756 (mp0) REVERT: C 431 TYR cc_start: 0.8163 (m-80) cc_final: 0.7539 (m-10) REVERT: C 433 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7475 (ptmm) REVERT: C 438 ARG cc_start: 0.7875 (tpm170) cc_final: 0.7419 (tpm170) REVERT: C 441 LEU cc_start: 0.8185 (mt) cc_final: 0.7694 (mp) REVERT: C 473 MET cc_start: 0.7938 (mmt) cc_final: 0.7153 (mmt) REVERT: C 554 MET cc_start: 0.6863 (tpp) cc_final: 0.6382 (tpp) REVERT: C 603 MET cc_start: 0.7788 (ptt) cc_final: 0.7561 (ptt) REVERT: C 687 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5920 (pt0) REVERT: C 692 ARG cc_start: 0.8453 (tpp-160) cc_final: 0.8211 (mmp80) REVERT: B 19 GLU cc_start: 0.7542 (pp20) cc_final: 0.6941 (pp20) REVERT: B 24 PHE cc_start: 0.8409 (m-10) cc_final: 0.8141 (m-80) REVERT: B 29 LEU cc_start: 0.8198 (mp) cc_final: 0.7842 (mp) REVERT: B 32 ASP cc_start: 0.7952 (p0) cc_final: 0.7255 (p0) REVERT: B 46 LYS cc_start: 0.8846 (mttt) cc_final: 0.8387 (mttm) REVERT: B 57 ARG cc_start: 0.8478 (ptm160) cc_final: 0.8151 (ttm110) REVERT: B 72 VAL cc_start: 0.8882 (m) cc_final: 0.8505 (p) REVERT: B 85 ILE cc_start: 0.8667 (mt) cc_final: 0.8369 (tp) REVERT: B 105 TYR cc_start: 0.7938 (t80) cc_final: 0.7685 (t80) REVERT: B 106 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 112 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7362 (mm-40) REVERT: B 114 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6240 (mm-30) REVERT: B 123 TYR cc_start: 0.7788 (t80) cc_final: 0.7126 (t80) REVERT: B 136 LEU cc_start: 0.8248 (mt) cc_final: 0.7940 (mm) REVERT: B 149 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7672 (tptm) REVERT: B 153 LYS cc_start: 0.8655 (tptm) cc_final: 0.7898 (ttmm) REVERT: B 154 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7465 (mtp85) REVERT: B 155 MET cc_start: 0.8033 (tpt) cc_final: 0.7431 (tpp) REVERT: B 166 GLN cc_start: 0.5303 (mp10) cc_final: 0.4521 (mp10) REVERT: B 170 MET cc_start: 0.7893 (mmm) cc_final: 0.7639 (mmm) REVERT: B 184 ASP cc_start: 0.7843 (t70) cc_final: 0.7378 (t0) REVERT: B 199 MET cc_start: 0.7638 (mmp) cc_final: 0.7274 (mmp) REVERT: B 202 LEU cc_start: 0.7958 (mt) cc_final: 0.7706 (tp) REVERT: B 203 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 209 ARG cc_start: 0.8199 (mmt90) cc_final: 0.7739 (mmt90) REVERT: B 212 TYR cc_start: 0.7873 (m-10) cc_final: 0.7537 (m-80) REVERT: B 242 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7795 (mmtt) REVERT: B 307 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8062 (mmtm) REVERT: B 360 TRP cc_start: 0.7915 (m100) cc_final: 0.6048 (m100) REVERT: B 361 PHE cc_start: 0.7643 (t80) cc_final: 0.7317 (t80) REVERT: B 363 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8311 (mmtp) REVERT: B 381 TYR cc_start: 0.7674 (m-80) cc_final: 0.6771 (m-80) REVERT: B 383 TYR cc_start: 0.5563 (m-80) cc_final: 0.5074 (m-80) REVERT: B 429 ASP cc_start: 0.7942 (m-30) cc_final: 0.7218 (m-30) REVERT: B 443 PHE cc_start: 0.7703 (t80) cc_final: 0.7428 (t80) REVERT: B 469 ASP cc_start: 0.7490 (t70) cc_final: 0.6943 (t0) REVERT: B 472 PHE cc_start: 0.6077 (m-80) cc_final: 0.5395 (m-80) REVERT: B 502 TYR cc_start: 0.6737 (t80) cc_final: 0.6112 (t80) REVERT: F 28 LYS cc_start: 0.7836 (mmmm) cc_final: 0.7518 (mmmm) REVERT: F 53 SER cc_start: 0.7780 (t) cc_final: 0.6955 (t) REVERT: F 56 GLU cc_start: 0.7779 (mp0) cc_final: 0.6953 (mp0) REVERT: F 58 TYR cc_start: 0.8187 (t80) cc_final: 0.7939 (t80) REVERT: F 62 TYR cc_start: 0.7912 (t80) cc_final: 0.7045 (t80) REVERT: F 63 THR cc_start: 0.7480 (t) cc_final: 0.7174 (p) REVERT: F 64 MET cc_start: 0.7455 (tpt) cc_final: 0.6944 (tpt) REVERT: F 68 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8393 (mttm) REVERT: F 71 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6921 (tm-30) REVERT: F 78 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7970 (ttm-80) REVERT: F 79 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6663 (tp30) REVERT: F 113 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7489 (tp40) REVERT: F 116 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8240 (tpp) REVERT: F 118 MET cc_start: 0.7353 (mtm) cc_final: 0.6995 (mtm) REVERT: F 125 TYR cc_start: 0.5608 (t80) cc_final: 0.5292 (t80) REVERT: F 126 MET cc_start: 0.8168 (tmt) cc_final: 0.7571 (tmm) REVERT: F 140 TYR cc_start: 0.8025 (t80) cc_final: 0.7104 (t80) REVERT: F 145 ILE cc_start: 0.8902 (mt) cc_final: 0.8622 (mm) REVERT: F 148 ARG cc_start: 0.8381 (ttp-170) cc_final: 0.8143 (ttm170) REVERT: F 153 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7448 (mtt180) REVERT: F 154 TYR cc_start: 0.7216 (t80) cc_final: 0.5550 (t80) REVERT: F 167 ASP cc_start: 0.7215 (t0) cc_final: 0.6812 (t0) REVERT: F 168 MET cc_start: 0.7243 (ptp) cc_final: 0.6742 (ptp) REVERT: F 233 TYR cc_start: 0.7555 (t80) cc_final: 0.7142 (t80) REVERT: F 235 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8260 (mmmm) REVERT: F 240 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7649 (tpp80) REVERT: F 243 GLU cc_start: 0.7613 (pp20) cc_final: 0.7106 (pp20) REVERT: F 246 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7245 (tp30) REVERT: F 249 MET cc_start: 0.7685 (ppp) cc_final: 0.7289 (ppp) REVERT: F 258 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7720 (mp0) REVERT: F 262 LYS cc_start: 0.8337 (tmtt) cc_final: 0.8084 (tmtt) REVERT: F 265 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7164 (mm-30) REVERT: F 270 SER cc_start: 0.8504 (m) cc_final: 0.8043 (t) REVERT: F 272 HIS cc_start: 0.5884 (m-70) cc_final: 0.5392 (m170) REVERT: F 274 LYS cc_start: 0.8061 (tppt) cc_final: 0.7593 (tmmt) REVERT: F 287 MET cc_start: 0.7653 (ptm) cc_final: 0.7145 (ppp) REVERT: F 295 ASP cc_start: 0.7242 (m-30) cc_final: 0.6757 (m-30) REVERT: F 301 LYS cc_start: 0.8264 (ptpt) cc_final: 0.7936 (pttm) REVERT: F 322 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7751 (mmt180) REVERT: F 323 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7679 (tm-30) REVERT: F 332 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6323 (pm20) REVERT: F 352 PHE cc_start: 0.8040 (m-80) cc_final: 0.7789 (m-10) REVERT: F 353 ASP cc_start: 0.7256 (t0) cc_final: 0.7009 (t0) REVERT: F 368 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7123 (tm-30) REVERT: F 414 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8708 (mmtm) REVERT: F 423 GLN cc_start: 0.8174 (tt0) cc_final: 0.7562 (tt0) REVERT: F 489 GLN cc_start: 0.8085 (mt0) cc_final: 0.7754 (tp-100) REVERT: F 490 HIS cc_start: 0.7039 (m90) cc_final: 0.6835 (m-70) REVERT: F 671 ARG cc_start: 0.6148 (tpt-90) cc_final: 0.5471 (tpt90) REVERT: F 673 LYS cc_start: 0.8065 (ptmm) cc_final: 0.7800 (pptt) REVERT: F 687 GLU cc_start: 0.4598 (OUTLIER) cc_final: 0.2205 (tt0) REVERT: F 735 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5517 (mp) REVERT: D 42 CYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5413 (m) outliers start: 115 outliers final: 67 residues processed: 785 average time/residue: 0.3767 time to fit residues: 436.5085 Evaluate side-chains 768 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 689 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 735 LEU Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 113 GLN C 134 ASN C 135 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 729 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 729 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22731 Z= 0.236 Angle : 0.708 13.047 30684 Z= 0.361 Chirality : 0.044 0.300 3385 Planarity : 0.005 0.053 3934 Dihedral : 4.607 27.524 3006 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.88 % Rotamer: Outliers : 4.33 % Allowed : 23.84 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2718 helix: 0.82 (0.15), residues: 1257 sheet: -0.99 (0.31), residues: 254 loop : -2.42 (0.16), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 233 HIS 0.021 0.001 HIS E 77 PHE 0.032 0.002 PHE B 537 TYR 0.024 0.002 TYR C 125 ARG 0.008 0.001 ARG C 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 712 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7840 (pt) REVERT: A 13 TYR cc_start: 0.7132 (t80) cc_final: 0.6716 (t80) REVERT: A 20 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8028 (mm110) REVERT: A 22 LYS cc_start: 0.8596 (ttmt) cc_final: 0.7860 (ttmt) REVERT: A 23 LEU cc_start: 0.8421 (mt) cc_final: 0.8145 (tp) REVERT: A 26 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 34 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8770 (p) REVERT: A 37 VAL cc_start: 0.8588 (t) cc_final: 0.8291 (m) REVERT: A 57 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7623 (ttp80) REVERT: A 59 MET cc_start: 0.7508 (ttt) cc_final: 0.6973 (ttp) REVERT: A 60 PHE cc_start: 0.8439 (m-80) cc_final: 0.7825 (m-10) REVERT: A 66 GLU cc_start: 0.7749 (pm20) cc_final: 0.7265 (mp0) REVERT: A 84 ILE cc_start: 0.8572 (tp) cc_final: 0.8218 (tt) REVERT: A 87 THR cc_start: 0.8528 (t) cc_final: 0.8116 (p) REVERT: A 103 GLN cc_start: 0.7921 (tp40) cc_final: 0.7657 (tp40) REVERT: A 106 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 112 GLN cc_start: 0.8220 (mm-40) cc_final: 0.8010 (tp40) REVERT: A 115 ASP cc_start: 0.7970 (p0) cc_final: 0.7288 (p0) REVERT: A 117 LEU cc_start: 0.8293 (mt) cc_final: 0.8035 (tp) REVERT: A 118 GLN cc_start: 0.8153 (tt0) cc_final: 0.7709 (tt0) REVERT: A 122 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 127 LYS cc_start: 0.8568 (tppt) cc_final: 0.8160 (mmmt) REVERT: A 147 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7400 (mt-10) REVERT: A 157 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 159 LYS cc_start: 0.7460 (mtmt) cc_final: 0.7112 (mtmm) REVERT: A 165 HIS cc_start: 0.6673 (m90) cc_final: 0.6310 (m90) REVERT: A 170 MET cc_start: 0.6720 (mmp) cc_final: 0.6289 (mmp) REVERT: A 191 GLU cc_start: 0.7334 (pp20) cc_final: 0.7019 (tm-30) REVERT: A 196 GLU cc_start: 0.7718 (pp20) cc_final: 0.6744 (pp20) REVERT: A 199 MET cc_start: 0.7880 (mmm) cc_final: 0.7579 (mmp) REVERT: A 209 ARG cc_start: 0.7502 (mtm180) cc_final: 0.6932 (mtm-85) REVERT: A 211 GLN cc_start: 0.8013 (pm20) cc_final: 0.7770 (pm20) REVERT: A 225 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.4974 (mt) REVERT: A 267 GLU cc_start: 0.7515 (tp30) cc_final: 0.7020 (tp30) REVERT: A 294 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8110 (mmmm) REVERT: A 297 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7815 (ptpt) REVERT: A 301 PRO cc_start: 0.7587 (Cg_exo) cc_final: 0.7378 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8377 (p) cc_final: 0.8157 (t) REVERT: A 356 GLN cc_start: 0.8222 (pp30) cc_final: 0.6867 (pp30) REVERT: A 357 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6581 (mm-40) REVERT: A 358 ASN cc_start: 0.7940 (t0) cc_final: 0.7626 (t0) REVERT: A 361 PHE cc_start: 0.7138 (m-80) cc_final: 0.6374 (m-80) REVERT: A 382 ILE cc_start: 0.7195 (mm) cc_final: 0.6917 (mm) REVERT: A 383 TYR cc_start: 0.5705 (m-80) cc_final: 0.5283 (m-80) REVERT: A 443 PHE cc_start: 0.8519 (t80) cc_final: 0.8132 (t80) REVERT: A 558 LEU cc_start: 0.6915 (tp) cc_final: 0.6546 (mt) REVERT: A 583 VAL cc_start: 0.6736 (OUTLIER) cc_final: 0.6307 (m) REVERT: A 586 LEU cc_start: 0.8388 (mt) cc_final: 0.7923 (mp) REVERT: E 23 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7307 (mp0) REVERT: C 28 LYS cc_start: 0.8162 (mmmm) cc_final: 0.7755 (tptp) REVERT: C 33 ILE cc_start: 0.8981 (mm) cc_final: 0.8689 (tt) REVERT: C 43 GLU cc_start: 0.7341 (tp30) cc_final: 0.6335 (tp30) REVERT: C 45 GLN cc_start: 0.7655 (mt0) cc_final: 0.7440 (tt0) REVERT: C 48 ASN cc_start: 0.8204 (t0) cc_final: 0.6576 (t0) REVERT: C 62 TYR cc_start: 0.7965 (t80) cc_final: 0.7738 (t80) REVERT: C 68 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8183 (mptt) REVERT: C 71 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 72 LYS cc_start: 0.8526 (tttt) cc_final: 0.8093 (tptm) REVERT: C 83 GLU cc_start: 0.7773 (tp30) cc_final: 0.7529 (tp30) REVERT: C 134 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7874 (t0) REVERT: C 153 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7301 (mmm-85) REVERT: C 163 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7912 (mm110) REVERT: C 167 ASP cc_start: 0.7443 (t0) cc_final: 0.6939 (t70) REVERT: C 206 GLU cc_start: 0.6169 (mp0) cc_final: 0.5743 (mp0) REVERT: C 222 GLN cc_start: 0.7561 (tp40) cc_final: 0.7179 (tm-30) REVERT: C 234 ILE cc_start: 0.8632 (mm) cc_final: 0.8365 (tp) REVERT: C 235 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8093 (mtmm) REVERT: C 238 GLU cc_start: 0.7308 (tp30) cc_final: 0.6743 (tm-30) REVERT: C 243 GLU cc_start: 0.8216 (pt0) cc_final: 0.7501 (pp20) REVERT: C 244 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7299 (tp30) REVERT: C 246 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 250 HIS cc_start: 0.7927 (t-90) cc_final: 0.7311 (t-90) REVERT: C 258 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7255 (mm-30) REVERT: C 262 LYS cc_start: 0.8132 (tmtm) cc_final: 0.7459 (ttpp) REVERT: C 270 SER cc_start: 0.8715 (m) cc_final: 0.8156 (t) REVERT: C 282 SER cc_start: 0.7804 (m) cc_final: 0.7392 (t) REVERT: C 288 LEU cc_start: 0.8864 (tp) cc_final: 0.8494 (tp) REVERT: C 292 LYS cc_start: 0.8489 (mmmm) cc_final: 0.7963 (mmtm) REVERT: C 301 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8103 (ptpp) REVERT: C 306 VAL cc_start: 0.8760 (t) cc_final: 0.8325 (p) REVERT: C 315 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7099 (tm-30) REVERT: C 346 LEU cc_start: 0.8288 (tp) cc_final: 0.8075 (tp) REVERT: C 353 ASP cc_start: 0.7979 (t0) cc_final: 0.7544 (t70) REVERT: C 368 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6614 (tm-30) REVERT: C 369 THR cc_start: 0.8106 (p) cc_final: 0.7734 (t) REVERT: C 394 ASP cc_start: 0.7919 (t0) cc_final: 0.7529 (t0) REVERT: C 395 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8220 (mmmm) REVERT: C 409 GLU cc_start: 0.8230 (pt0) cc_final: 0.7885 (pp20) REVERT: C 412 LEU cc_start: 0.8682 (mt) cc_final: 0.8419 (mm) REVERT: C 416 MET cc_start: 0.7266 (tpp) cc_final: 0.6944 (tpp) REVERT: C 418 LEU cc_start: 0.8773 (tt) cc_final: 0.8495 (tp) REVERT: C 423 GLN cc_start: 0.7784 (pm20) cc_final: 0.6601 (pt0) REVERT: C 424 GLU cc_start: 0.7437 (mp0) cc_final: 0.6714 (mp0) REVERT: C 431 TYR cc_start: 0.8347 (m-80) cc_final: 0.7627 (m-10) REVERT: C 438 ARG cc_start: 0.7877 (tpm170) cc_final: 0.7294 (tpm170) REVERT: C 473 MET cc_start: 0.7999 (mmt) cc_final: 0.7166 (mmt) REVERT: C 554 MET cc_start: 0.6906 (tpp) cc_final: 0.6440 (tpp) REVERT: C 603 MET cc_start: 0.7821 (ptt) cc_final: 0.7499 (ptm) REVERT: C 687 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5989 (pp20) REVERT: C 692 ARG cc_start: 0.8425 (tpp-160) cc_final: 0.8183 (mmp80) REVERT: B 19 GLU cc_start: 0.7560 (pp20) cc_final: 0.6960 (pp20) REVERT: B 24 PHE cc_start: 0.8424 (m-10) cc_final: 0.8137 (m-80) REVERT: B 29 LEU cc_start: 0.8217 (mp) cc_final: 0.7910 (mp) REVERT: B 32 ASP cc_start: 0.7938 (p0) cc_final: 0.7315 (p0) REVERT: B 46 LYS cc_start: 0.8869 (mttt) cc_final: 0.8417 (mttm) REVERT: B 55 TYR cc_start: 0.8682 (t80) cc_final: 0.7212 (t80) REVERT: B 57 ARG cc_start: 0.8444 (ptm160) cc_final: 0.8159 (ttm110) REVERT: B 69 GLN cc_start: 0.7921 (tt0) cc_final: 0.7659 (tt0) REVERT: B 72 VAL cc_start: 0.8871 (m) cc_final: 0.8397 (p) REVERT: B 85 ILE cc_start: 0.8659 (mt) cc_final: 0.8335 (tp) REVERT: B 106 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 112 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7262 (mm-40) REVERT: B 114 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6320 (mm-30) REVERT: B 115 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7090 (p0) REVERT: B 123 TYR cc_start: 0.7833 (t80) cc_final: 0.7174 (t80) REVERT: B 145 CYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8083 (m) REVERT: B 149 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7603 (tptm) REVERT: B 153 LYS cc_start: 0.8707 (tptm) cc_final: 0.7877 (ttmm) REVERT: B 154 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7442 (mtp85) REVERT: B 155 MET cc_start: 0.8048 (tpt) cc_final: 0.7491 (tpp) REVERT: B 166 GLN cc_start: 0.5454 (mp10) cc_final: 0.4452 (mp10) REVERT: B 170 MET cc_start: 0.7890 (mmm) cc_final: 0.7625 (mmm) REVERT: B 184 ASP cc_start: 0.7829 (t70) cc_final: 0.7396 (t0) REVERT: B 199 MET cc_start: 0.7629 (mmp) cc_final: 0.7356 (mmp) REVERT: B 203 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7021 (mm-30) REVERT: B 209 ARG cc_start: 0.8174 (mmt90) cc_final: 0.7962 (mmt90) REVERT: B 212 TYR cc_start: 0.7947 (m-10) cc_final: 0.7661 (m-80) REVERT: B 242 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7826 (mmtt) REVERT: B 263 MET cc_start: 0.6955 (mpp) cc_final: 0.6741 (mtm) REVERT: B 307 LYS cc_start: 0.8490 (mmtt) cc_final: 0.7984 (mmtm) REVERT: B 363 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8421 (mmtp) REVERT: B 381 TYR cc_start: 0.7602 (m-80) cc_final: 0.6844 (m-80) REVERT: B 383 TYR cc_start: 0.5516 (m-80) cc_final: 0.5096 (m-80) REVERT: B 429 ASP cc_start: 0.7937 (m-30) cc_final: 0.7224 (m-30) REVERT: B 430 CYS cc_start: 0.5459 (m) cc_final: 0.4653 (t) REVERT: B 443 PHE cc_start: 0.7677 (t80) cc_final: 0.7454 (t80) REVERT: B 454 MET cc_start: 0.7742 (tpp) cc_final: 0.7315 (tpp) REVERT: B 469 ASP cc_start: 0.7429 (t70) cc_final: 0.6751 (t0) REVERT: B 472 PHE cc_start: 0.5954 (m-80) cc_final: 0.5360 (m-80) REVERT: B 502 TYR cc_start: 0.6867 (t80) cc_final: 0.6185 (t80) REVERT: B 503 ASP cc_start: 0.7961 (t0) cc_final: 0.7679 (t0) REVERT: F 28 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7522 (mmmm) REVERT: F 46 ARG cc_start: 0.7448 (mtm110) cc_final: 0.7231 (mtm110) REVERT: F 58 TYR cc_start: 0.8204 (t80) cc_final: 0.7889 (t80) REVERT: F 62 TYR cc_start: 0.7927 (t80) cc_final: 0.7052 (t80) REVERT: F 63 THR cc_start: 0.7504 (t) cc_final: 0.7232 (p) REVERT: F 64 MET cc_start: 0.7527 (tpt) cc_final: 0.6825 (tpp) REVERT: F 68 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8378 (mttm) REVERT: F 71 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7003 (tm-30) REVERT: F 78 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7967 (ttm-80) REVERT: F 79 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6634 (tp30) REVERT: F 113 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7348 (tp40) REVERT: F 116 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (tpp) REVERT: F 125 TYR cc_start: 0.5418 (t80) cc_final: 0.5083 (t80) REVERT: F 126 MET cc_start: 0.8043 (tmt) cc_final: 0.7501 (tmm) REVERT: F 140 TYR cc_start: 0.8007 (t80) cc_final: 0.6885 (t80) REVERT: F 145 ILE cc_start: 0.8920 (mt) cc_final: 0.8565 (tt) REVERT: F 153 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7511 (mmt180) REVERT: F 154 TYR cc_start: 0.7236 (t80) cc_final: 0.5586 (t80) REVERT: F 158 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7360 (ttm-80) REVERT: F 163 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7179 (mm110) REVERT: F 167 ASP cc_start: 0.7279 (t0) cc_final: 0.6946 (t0) REVERT: F 180 ARG cc_start: 0.7731 (ptp-110) cc_final: 0.7272 (ptp-110) REVERT: F 183 ILE cc_start: 0.8879 (mm) cc_final: 0.8660 (mm) REVERT: F 191 MET cc_start: 0.6844 (mmm) cc_final: 0.6597 (tpp) REVERT: F 219 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6946 (tmm) REVERT: F 233 TYR cc_start: 0.7206 (t80) cc_final: 0.6970 (t80) REVERT: F 235 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8340 (mmmt) REVERT: F 238 GLU cc_start: 0.8194 (tp30) cc_final: 0.7462 (tp30) REVERT: F 240 ARG cc_start: 0.7913 (mmt180) cc_final: 0.7667 (tpp80) REVERT: F 243 GLU cc_start: 0.7648 (pp20) cc_final: 0.7156 (pp20) REVERT: F 246 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7179 (tp30) REVERT: F 249 MET cc_start: 0.7681 (ppp) cc_final: 0.7194 (tmm) REVERT: F 258 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7659 (mp0) REVERT: F 265 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7250 (mm-30) REVERT: F 270 SER cc_start: 0.8508 (m) cc_final: 0.7968 (t) REVERT: F 273 MET cc_start: 0.7234 (tpp) cc_final: 0.6412 (mmm) REVERT: F 274 LYS cc_start: 0.8081 (tppt) cc_final: 0.7562 (tmmt) REVERT: F 295 ASP cc_start: 0.7230 (m-30) cc_final: 0.6780 (m-30) REVERT: F 301 LYS cc_start: 0.8340 (ptpt) cc_final: 0.7998 (ptpp) REVERT: F 303 PHE cc_start: 0.7634 (m-80) cc_final: 0.7395 (m-80) REVERT: F 322 ARG cc_start: 0.8216 (mmt90) cc_final: 0.7720 (mmt180) REVERT: F 332 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: F 352 PHE cc_start: 0.8066 (m-80) cc_final: 0.7847 (m-10) REVERT: F 353 ASP cc_start: 0.7266 (t0) cc_final: 0.7066 (t0) REVERT: F 363 ASP cc_start: 0.7713 (t70) cc_final: 0.7411 (t0) REVERT: F 366 PHE cc_start: 0.6968 (m-80) cc_final: 0.6709 (m-10) REVERT: F 368 GLN cc_start: 0.7385 (tm-30) cc_final: 0.7082 (tm-30) REVERT: F 414 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8717 (mmtm) REVERT: F 423 GLN cc_start: 0.8121 (tt0) cc_final: 0.7516 (tt0) REVERT: F 489 GLN cc_start: 0.8064 (mt0) cc_final: 0.7776 (tp40) REVERT: F 554 MET cc_start: 0.6093 (mmm) cc_final: 0.5346 (tpp) REVERT: F 599 MET cc_start: 0.6205 (mtm) cc_final: 0.5712 (mmt) REVERT: F 671 ARG cc_start: 0.6224 (tpt-90) cc_final: 0.5839 (tpt-90) REVERT: F 673 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7806 (pptt) REVERT: F 687 GLU cc_start: 0.4611 (OUTLIER) cc_final: 0.2055 (tt0) REVERT: D 42 CYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5454 (m) REVERT: D 55 GLU cc_start: 0.4156 (mm-30) cc_final: 0.3941 (mm-30) outliers start: 107 outliers final: 69 residues processed: 772 average time/residue: 0.3725 time to fit residues: 427.3528 Evaluate side-chains 769 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 686 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.7980 chunk 236 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 263 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22731 Z= 0.239 Angle : 0.727 15.350 30684 Z= 0.371 Chirality : 0.045 0.222 3385 Planarity : 0.005 0.155 3934 Dihedral : 4.697 26.465 3006 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.35 % Favored : 90.58 % Rotamer: Outliers : 4.45 % Allowed : 24.24 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2718 helix: 0.73 (0.15), residues: 1256 sheet: -1.11 (0.30), residues: 266 loop : -2.47 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 233 HIS 0.020 0.002 HIS F 490 PHE 0.035 0.002 PHE B 537 TYR 0.023 0.002 TYR C 125 ARG 0.014 0.001 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 714 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8293 (tp) cc_final: 0.7883 (pt) REVERT: A 13 TYR cc_start: 0.7287 (t80) cc_final: 0.6899 (t80) REVERT: A 19 GLU cc_start: 0.7006 (pp20) cc_final: 0.6688 (pp20) REVERT: A 20 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8156 (mm110) REVERT: A 22 LYS cc_start: 0.8573 (ttmt) cc_final: 0.7854 (ttmt) REVERT: A 23 LEU cc_start: 0.8374 (mt) cc_final: 0.8080 (tp) REVERT: A 26 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 37 VAL cc_start: 0.8555 (t) cc_final: 0.8090 (m) REVERT: A 57 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7663 (ttp80) REVERT: A 59 MET cc_start: 0.7401 (ttt) cc_final: 0.6886 (ttp) REVERT: A 60 PHE cc_start: 0.8477 (m-80) cc_final: 0.7841 (m-10) REVERT: A 84 ILE cc_start: 0.8632 (tp) cc_final: 0.8242 (tt) REVERT: A 87 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8138 (p) REVERT: A 103 GLN cc_start: 0.7933 (tp40) cc_final: 0.7696 (tp40) REVERT: A 106 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 112 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8019 (tp40) REVERT: A 115 ASP cc_start: 0.7996 (p0) cc_final: 0.7339 (p0) REVERT: A 117 LEU cc_start: 0.8305 (mt) cc_final: 0.7890 (tt) REVERT: A 118 GLN cc_start: 0.8183 (tt0) cc_final: 0.7788 (tt0) REVERT: A 122 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 127 LYS cc_start: 0.8532 (tppt) cc_final: 0.8311 (mmmt) REVERT: A 147 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 149 LYS cc_start: 0.8180 (tttt) cc_final: 0.7889 (ttmt) REVERT: A 157 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6888 (mm-30) REVERT: A 160 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.3986 (t80) REVERT: A 170 MET cc_start: 0.6746 (mmp) cc_final: 0.6266 (mmp) REVERT: A 191 GLU cc_start: 0.7460 (pp20) cc_final: 0.7135 (tm-30) REVERT: A 196 GLU cc_start: 0.7859 (pp20) cc_final: 0.7060 (pp20) REVERT: A 199 MET cc_start: 0.8039 (mmm) cc_final: 0.7698 (mmp) REVERT: A 211 GLN cc_start: 0.7833 (pm20) cc_final: 0.7390 (pm20) REVERT: A 225 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5858 (mt) REVERT: A 267 GLU cc_start: 0.7529 (tp30) cc_final: 0.7267 (tp30) REVERT: A 268 MET cc_start: 0.6549 (mmm) cc_final: 0.5856 (tmm) REVERT: A 294 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8160 (mmmm) REVERT: A 297 LYS cc_start: 0.8189 (ptpt) cc_final: 0.7876 (ptpt) REVERT: A 352 TRP cc_start: 0.7707 (t60) cc_final: 0.7495 (t60) REVERT: A 361 PHE cc_start: 0.7233 (m-80) cc_final: 0.6357 (m-80) REVERT: A 382 ILE cc_start: 0.7161 (mm) cc_final: 0.6879 (mm) REVERT: A 383 TYR cc_start: 0.5758 (m-80) cc_final: 0.5469 (m-80) REVERT: A 443 PHE cc_start: 0.8489 (t80) cc_final: 0.8005 (t80) REVERT: A 558 LEU cc_start: 0.6898 (tp) cc_final: 0.6639 (mt) REVERT: E 23 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7263 (mp0) REVERT: C 28 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7769 (tptp) REVERT: C 33 ILE cc_start: 0.9045 (mm) cc_final: 0.8732 (mm) REVERT: C 43 GLU cc_start: 0.7392 (tp30) cc_final: 0.6367 (tp30) REVERT: C 45 GLN cc_start: 0.7748 (mt0) cc_final: 0.7503 (tt0) REVERT: C 48 ASN cc_start: 0.8169 (t0) cc_final: 0.6558 (t0) REVERT: C 62 TYR cc_start: 0.7964 (t80) cc_final: 0.7662 (t80) REVERT: C 64 MET cc_start: 0.7151 (tpt) cc_final: 0.6762 (tpp) REVERT: C 68 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8217 (mptt) REVERT: C 71 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 72 LYS cc_start: 0.8561 (tttt) cc_final: 0.8127 (tptm) REVERT: C 83 GLU cc_start: 0.7935 (tp30) cc_final: 0.7393 (tp30) REVERT: C 153 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7349 (mmm-85) REVERT: C 163 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7948 (mm110) REVERT: C 191 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.6984 (tmm) REVERT: C 206 GLU cc_start: 0.6180 (mp0) cc_final: 0.5628 (mp0) REVERT: C 222 GLN cc_start: 0.7494 (tp40) cc_final: 0.7178 (tm-30) REVERT: C 224 PHE cc_start: 0.6924 (m-10) cc_final: 0.6138 (m-80) REVERT: C 234 ILE cc_start: 0.8658 (mm) cc_final: 0.8316 (tp) REVERT: C 235 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8053 (mtmm) REVERT: C 238 GLU cc_start: 0.7315 (tp30) cc_final: 0.6797 (tm-30) REVERT: C 243 GLU cc_start: 0.8213 (pt0) cc_final: 0.7484 (pp20) REVERT: C 246 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 250 HIS cc_start: 0.7978 (t-90) cc_final: 0.7236 (t-90) REVERT: C 258 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7118 (mm-30) REVERT: C 262 LYS cc_start: 0.8146 (tmtm) cc_final: 0.7496 (ttpp) REVERT: C 270 SER cc_start: 0.8635 (m) cc_final: 0.8080 (t) REVERT: C 274 LYS cc_start: 0.8365 (tppt) cc_final: 0.8145 (tppt) REVERT: C 282 SER cc_start: 0.7771 (m) cc_final: 0.7528 (m) REVERT: C 288 LEU cc_start: 0.8845 (tp) cc_final: 0.8577 (tp) REVERT: C 292 LYS cc_start: 0.8452 (mmmm) cc_final: 0.7981 (mmtm) REVERT: C 301 LYS cc_start: 0.8363 (ptpt) cc_final: 0.8117 (ptpp) REVERT: C 306 VAL cc_start: 0.8711 (t) cc_final: 0.8296 (p) REVERT: C 315 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7059 (tm-30) REVERT: C 346 LEU cc_start: 0.8338 (tp) cc_final: 0.8082 (tp) REVERT: C 353 ASP cc_start: 0.7944 (t0) cc_final: 0.7582 (t0) REVERT: C 368 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6627 (tm-30) REVERT: C 369 THR cc_start: 0.8239 (p) cc_final: 0.7727 (t) REVERT: C 394 ASP cc_start: 0.7926 (t0) cc_final: 0.7552 (t0) REVERT: C 395 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8208 (mmmm) REVERT: C 409 GLU cc_start: 0.8275 (pt0) cc_final: 0.7942 (pp20) REVERT: C 412 LEU cc_start: 0.8692 (mt) cc_final: 0.8412 (mm) REVERT: C 413 ASP cc_start: 0.8478 (m-30) cc_final: 0.7860 (m-30) REVERT: C 416 MET cc_start: 0.7269 (tpp) cc_final: 0.7035 (tpp) REVERT: C 418 LEU cc_start: 0.8859 (tt) cc_final: 0.8563 (tp) REVERT: C 423 GLN cc_start: 0.7700 (pm20) cc_final: 0.6665 (pt0) REVERT: C 424 GLU cc_start: 0.7489 (mp0) cc_final: 0.6719 (mp0) REVERT: C 431 TYR cc_start: 0.8430 (m-80) cc_final: 0.7622 (m-10) REVERT: C 433 LYS cc_start: 0.7873 (pttp) cc_final: 0.7508 (ptmt) REVERT: C 438 ARG cc_start: 0.7902 (tpm170) cc_final: 0.7279 (tpm170) REVERT: C 554 MET cc_start: 0.6921 (tpp) cc_final: 0.6481 (tpp) REVERT: C 603 MET cc_start: 0.7853 (ptt) cc_final: 0.7509 (ptt) REVERT: C 692 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8170 (mmp80) REVERT: B 19 GLU cc_start: 0.7597 (pp20) cc_final: 0.6977 (pp20) REVERT: B 24 PHE cc_start: 0.8473 (m-10) cc_final: 0.8134 (m-80) REVERT: B 29 LEU cc_start: 0.8243 (mp) cc_final: 0.7916 (mp) REVERT: B 32 ASP cc_start: 0.7943 (p0) cc_final: 0.7518 (p0) REVERT: B 61 MET cc_start: 0.6873 (tmm) cc_final: 0.6288 (tmm) REVERT: B 69 GLN cc_start: 0.7883 (tt0) cc_final: 0.7661 (tt0) REVERT: B 72 VAL cc_start: 0.8877 (m) cc_final: 0.8436 (p) REVERT: B 85 ILE cc_start: 0.8647 (mt) cc_final: 0.8358 (tp) REVERT: B 106 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7796 (pt0) REVERT: B 112 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7031 (mm-40) REVERT: B 114 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6325 (mm-30) REVERT: B 123 TYR cc_start: 0.7853 (t80) cc_final: 0.7273 (t80) REVERT: B 127 LYS cc_start: 0.8244 (tptt) cc_final: 0.8016 (tptt) REVERT: B 129 ASN cc_start: 0.7993 (p0) cc_final: 0.6880 (p0) REVERT: B 149 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7578 (tptm) REVERT: B 154 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7499 (mtp85) REVERT: B 155 MET cc_start: 0.7992 (tpt) cc_final: 0.7514 (tpp) REVERT: B 166 GLN cc_start: 0.5526 (mp10) cc_final: 0.4799 (mp10) REVERT: B 170 MET cc_start: 0.7924 (mmm) cc_final: 0.7624 (mmm) REVERT: B 178 ILE cc_start: 0.8033 (tp) cc_final: 0.7810 (tp) REVERT: B 184 ASP cc_start: 0.7808 (t70) cc_final: 0.7423 (t0) REVERT: B 199 MET cc_start: 0.7680 (mmp) cc_final: 0.7410 (mmp) REVERT: B 209 ARG cc_start: 0.8246 (mmt90) cc_final: 0.8031 (mmt90) REVERT: B 212 TYR cc_start: 0.7890 (m-10) cc_final: 0.7520 (m-80) REVERT: B 215 SER cc_start: 0.8277 (m) cc_final: 0.7898 (p) REVERT: B 242 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7861 (mmtt) REVERT: B 294 LYS cc_start: 0.7540 (mmtm) cc_final: 0.7301 (mmtm) REVERT: B 307 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7894 (mmtm) REVERT: B 361 PHE cc_start: 0.7707 (t80) cc_final: 0.7444 (t80) REVERT: B 363 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8232 (mmmm) REVERT: B 381 TYR cc_start: 0.7580 (m-80) cc_final: 0.6810 (m-80) REVERT: B 383 TYR cc_start: 0.5527 (m-80) cc_final: 0.5127 (m-80) REVERT: B 429 ASP cc_start: 0.8029 (m-30) cc_final: 0.7299 (m-30) REVERT: B 443 PHE cc_start: 0.7701 (t80) cc_final: 0.7496 (t80) REVERT: B 454 MET cc_start: 0.7710 (tpp) cc_final: 0.7437 (tpp) REVERT: B 469 ASP cc_start: 0.7445 (t70) cc_final: 0.6917 (t70) REVERT: B 472 PHE cc_start: 0.5992 (m-80) cc_final: 0.5376 (m-80) REVERT: B 502 TYR cc_start: 0.6752 (t80) cc_final: 0.6154 (t80) REVERT: B 503 ASP cc_start: 0.8028 (t0) cc_final: 0.7818 (t0) REVERT: B 583 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7621 (t) REVERT: F 28 LYS cc_start: 0.7863 (mmmm) cc_final: 0.7537 (mmmm) REVERT: F 45 GLN cc_start: 0.8060 (tt0) cc_final: 0.7686 (tp-100) REVERT: F 53 SER cc_start: 0.7899 (t) cc_final: 0.6693 (t) REVERT: F 56 GLU cc_start: 0.7866 (mp0) cc_final: 0.6957 (pm20) REVERT: F 62 TYR cc_start: 0.7952 (t80) cc_final: 0.7027 (t80) REVERT: F 63 THR cc_start: 0.7569 (t) cc_final: 0.7321 (p) REVERT: F 64 MET cc_start: 0.7506 (tpt) cc_final: 0.7035 (tpt) REVERT: F 68 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8403 (mttm) REVERT: F 71 GLU cc_start: 0.7640 (tm-30) cc_final: 0.6997 (tm-30) REVERT: F 78 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7950 (ttm-80) REVERT: F 79 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6561 (tp30) REVERT: F 103 GLN cc_start: 0.8477 (tp40) cc_final: 0.8002 (tp40) REVERT: F 113 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7466 (tp40) REVERT: F 116 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8373 (mmm) REVERT: F 118 MET cc_start: 0.7205 (mtm) cc_final: 0.6969 (mtm) REVERT: F 125 TYR cc_start: 0.5480 (t80) cc_final: 0.5119 (t80) REVERT: F 126 MET cc_start: 0.8103 (tmt) cc_final: 0.7648 (tmm) REVERT: F 140 TYR cc_start: 0.7994 (t80) cc_final: 0.7004 (t80) REVERT: F 145 ILE cc_start: 0.8821 (mt) cc_final: 0.8417 (tp) REVERT: F 153 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7510 (mmt180) REVERT: F 154 TYR cc_start: 0.7234 (t80) cc_final: 0.5659 (t80) REVERT: F 158 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7402 (ttm-80) REVERT: F 163 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7239 (mm110) REVERT: F 167 ASP cc_start: 0.7346 (t0) cc_final: 0.6939 (t0) REVERT: F 168 MET cc_start: 0.7420 (ptp) cc_final: 0.7101 (ptp) REVERT: F 183 ILE cc_start: 0.8868 (mm) cc_final: 0.8567 (mm) REVERT: F 212 MET cc_start: 0.7231 (tmm) cc_final: 0.7025 (tmm) REVERT: F 233 TYR cc_start: 0.7619 (t80) cc_final: 0.7190 (t80) REVERT: F 235 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8318 (mmmt) REVERT: F 238 GLU cc_start: 0.8231 (tp30) cc_final: 0.7501 (tp30) REVERT: F 240 ARG cc_start: 0.7918 (mmt180) cc_final: 0.7707 (tpp80) REVERT: F 243 GLU cc_start: 0.7645 (pp20) cc_final: 0.7197 (pp20) REVERT: F 249 MET cc_start: 0.7679 (ppp) cc_final: 0.7270 (ppp) REVERT: F 258 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7754 (mp0) REVERT: F 265 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7216 (mm-30) REVERT: F 270 SER cc_start: 0.8469 (m) cc_final: 0.8072 (t) REVERT: F 272 HIS cc_start: 0.6604 (m170) cc_final: 0.6334 (m170) REVERT: F 273 MET cc_start: 0.7276 (tpp) cc_final: 0.6870 (tpp) REVERT: F 274 LYS cc_start: 0.8258 (tppt) cc_final: 0.7929 (tmmt) REVERT: F 287 MET cc_start: 0.7783 (ptm) cc_final: 0.7184 (ppp) REVERT: F 301 LYS cc_start: 0.8434 (ptpt) cc_final: 0.8131 (ptpp) REVERT: F 322 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7745 (mmt180) REVERT: F 332 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6348 (pm20) REVERT: F 352 PHE cc_start: 0.8132 (m-80) cc_final: 0.7874 (m-10) REVERT: F 353 ASP cc_start: 0.7273 (t0) cc_final: 0.7061 (t0) REVERT: F 363 ASP cc_start: 0.7845 (t70) cc_final: 0.7524 (t0) REVERT: F 366 PHE cc_start: 0.7014 (m-80) cc_final: 0.6710 (m-10) REVERT: F 368 GLN cc_start: 0.7350 (tm-30) cc_final: 0.7067 (tm-30) REVERT: F 369 THR cc_start: 0.8041 (p) cc_final: 0.7759 (t) REVERT: F 378 LEU cc_start: 0.4969 (OUTLIER) cc_final: 0.4132 (mt) REVERT: F 414 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8705 (mmtm) REVERT: F 423 GLN cc_start: 0.7834 (tt0) cc_final: 0.7191 (tt0) REVERT: F 489 GLN cc_start: 0.8055 (mt0) cc_final: 0.7730 (tp40) REVERT: F 671 ARG cc_start: 0.6306 (tpt-90) cc_final: 0.5953 (tpt-90) REVERT: F 673 LYS cc_start: 0.8080 (ptmm) cc_final: 0.7831 (pptt) REVERT: F 687 GLU cc_start: 0.4590 (OUTLIER) cc_final: 0.2206 (tt0) REVERT: D 42 CYS cc_start: 0.6059 (OUTLIER) cc_final: 0.5591 (m) outliers start: 110 outliers final: 69 residues processed: 775 average time/residue: 0.3669 time to fit residues: 423.5688 Evaluate side-chains 774 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 694 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 149 optimal weight: 0.1980 chunk 192 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 146 optimal weight: 0.0980 chunk 262 optimal weight: 1.9990 chunk 164 optimal weight: 0.0980 chunk 159 optimal weight: 0.3980 chunk 121 optimal weight: 0.0970 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 316 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22731 Z= 0.197 Angle : 0.729 13.665 30684 Z= 0.365 Chirality : 0.044 0.234 3385 Planarity : 0.005 0.081 3934 Dihedral : 4.580 25.816 3006 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.72 % Favored : 91.21 % Rotamer: Outliers : 4.01 % Allowed : 25.62 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2718 helix: 0.81 (0.15), residues: 1258 sheet: -1.05 (0.30), residues: 274 loop : -2.41 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 352 HIS 0.022 0.001 HIS F 490 PHE 0.048 0.002 PHE A 256 TYR 0.023 0.002 TYR A 402 ARG 0.014 0.001 ARG F 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 703 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8239 (tp) cc_final: 0.7850 (pt) REVERT: A 13 TYR cc_start: 0.7208 (t80) cc_final: 0.6766 (t80) REVERT: A 19 GLU cc_start: 0.6980 (pp20) cc_final: 0.6646 (pp20) REVERT: A 20 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8103 (mm110) REVERT: A 22 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8251 (tttp) REVERT: A 26 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7340 (mt-10) REVERT: A 57 ARG cc_start: 0.8059 (ptm160) cc_final: 0.7593 (ttp80) REVERT: A 59 MET cc_start: 0.7489 (ttt) cc_final: 0.7138 (ttp) REVERT: A 60 PHE cc_start: 0.8366 (m-80) cc_final: 0.7825 (m-10) REVERT: A 66 GLU cc_start: 0.7356 (mp0) cc_final: 0.6783 (mp0) REVERT: A 84 ILE cc_start: 0.8521 (tp) cc_final: 0.8156 (tt) REVERT: A 87 THR cc_start: 0.8498 (t) cc_final: 0.8106 (p) REVERT: A 103 GLN cc_start: 0.7942 (tp40) cc_final: 0.7665 (tp40) REVERT: A 106 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 115 ASP cc_start: 0.7916 (p0) cc_final: 0.7236 (p0) REVERT: A 117 LEU cc_start: 0.8239 (mt) cc_final: 0.8036 (tp) REVERT: A 122 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 128 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8540 (mp) REVERT: A 129 ASN cc_start: 0.6996 (p0) cc_final: 0.6697 (p0) REVERT: A 147 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 149 LYS cc_start: 0.8150 (tttt) cc_final: 0.7871 (ttmt) REVERT: A 157 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7020 (mm-30) REVERT: A 159 LYS cc_start: 0.7036 (mtmt) cc_final: 0.6337 (ptpp) REVERT: A 160 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4048 (t80) REVERT: A 165 HIS cc_start: 0.6822 (m90) cc_final: 0.6601 (m-70) REVERT: A 170 MET cc_start: 0.6542 (mmp) cc_final: 0.6269 (mmp) REVERT: A 191 GLU cc_start: 0.7419 (pp20) cc_final: 0.7133 (tm-30) REVERT: A 196 GLU cc_start: 0.7623 (pp20) cc_final: 0.6342 (pp20) REVERT: A 199 MET cc_start: 0.7966 (mmm) cc_final: 0.7543 (mmp) REVERT: A 211 GLN cc_start: 0.7762 (pm20) cc_final: 0.7298 (pm20) REVERT: A 219 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7944 (tp40) REVERT: A 267 GLU cc_start: 0.7506 (tp30) cc_final: 0.7013 (tp30) REVERT: A 271 PHE cc_start: 0.7495 (m-80) cc_final: 0.7131 (m-80) REVERT: A 291 GLN cc_start: 0.8017 (mp10) cc_final: 0.7647 (mp10) REVERT: A 294 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8093 (mmmm) REVERT: A 297 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7859 (ptpt) REVERT: A 352 TRP cc_start: 0.7609 (t60) cc_final: 0.7383 (t60) REVERT: A 357 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6591 (mm-40) REVERT: A 361 PHE cc_start: 0.7180 (m-80) cc_final: 0.6335 (m-80) REVERT: A 382 ILE cc_start: 0.7153 (mm) cc_final: 0.6728 (mm) REVERT: A 401 ARG cc_start: 0.6391 (tmm-80) cc_final: 0.6130 (tmm-80) REVERT: A 443 PHE cc_start: 0.8503 (t80) cc_final: 0.7978 (t80) REVERT: A 558 LEU cc_start: 0.6852 (tp) cc_final: 0.6571 (mt) REVERT: A 586 LEU cc_start: 0.8336 (mt) cc_final: 0.7835 (mp) REVERT: E 23 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7283 (mp0) REVERT: E 35 TRP cc_start: 0.3402 (m-10) cc_final: 0.3177 (m-10) REVERT: C 28 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7704 (tptp) REVERT: C 33 ILE cc_start: 0.9051 (mm) cc_final: 0.8751 (mm) REVERT: C 45 GLN cc_start: 0.7704 (mt0) cc_final: 0.7471 (tt0) REVERT: C 62 TYR cc_start: 0.7946 (t80) cc_final: 0.7698 (t80) REVERT: C 68 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8179 (mptt) REVERT: C 71 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7477 (tm-30) REVERT: C 72 LYS cc_start: 0.8507 (tttt) cc_final: 0.8066 (tptm) REVERT: C 83 GLU cc_start: 0.7749 (tp30) cc_final: 0.7503 (tp30) REVERT: C 153 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7534 (mmm-85) REVERT: C 163 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7947 (mm110) REVERT: C 191 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6895 (tmm) REVERT: C 206 GLU cc_start: 0.6153 (mp0) cc_final: 0.5600 (mp0) REVERT: C 222 GLN cc_start: 0.7521 (tp40) cc_final: 0.7014 (tm-30) REVERT: C 224 PHE cc_start: 0.6351 (m-10) cc_final: 0.5429 (m-10) REVERT: C 234 ILE cc_start: 0.8590 (mm) cc_final: 0.8160 (tp) REVERT: C 238 GLU cc_start: 0.7274 (tp30) cc_final: 0.6752 (tm-30) REVERT: C 246 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7345 (tm-30) REVERT: C 250 HIS cc_start: 0.7971 (t-90) cc_final: 0.7223 (t-90) REVERT: C 258 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7001 (mm-30) REVERT: C 262 LYS cc_start: 0.8009 (tmtm) cc_final: 0.7313 (ttpp) REVERT: C 270 SER cc_start: 0.8494 (m) cc_final: 0.8038 (t) REVERT: C 282 SER cc_start: 0.7595 (m) cc_final: 0.7369 (m) REVERT: C 288 LEU cc_start: 0.8811 (tp) cc_final: 0.8564 (tp) REVERT: C 292 LYS cc_start: 0.8398 (mmmm) cc_final: 0.7990 (mmtm) REVERT: C 301 LYS cc_start: 0.8364 (ptpt) cc_final: 0.8121 (ptpt) REVERT: C 306 VAL cc_start: 0.8719 (t) cc_final: 0.8375 (p) REVERT: C 315 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7089 (tm-30) REVERT: C 346 LEU cc_start: 0.8296 (tp) cc_final: 0.8048 (tp) REVERT: C 353 ASP cc_start: 0.7857 (t0) cc_final: 0.7553 (t0) REVERT: C 363 ASP cc_start: 0.8145 (t0) cc_final: 0.7911 (t70) REVERT: C 368 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6600 (tm-30) REVERT: C 369 THR cc_start: 0.8143 (p) cc_final: 0.7721 (t) REVERT: C 394 ASP cc_start: 0.7860 (t0) cc_final: 0.7434 (t0) REVERT: C 395 LYS cc_start: 0.8585 (mmtm) cc_final: 0.8214 (mmmm) REVERT: C 409 GLU cc_start: 0.8082 (pt0) cc_final: 0.7709 (pp20) REVERT: C 412 LEU cc_start: 0.8647 (mt) cc_final: 0.8373 (mm) REVERT: C 413 ASP cc_start: 0.8474 (m-30) cc_final: 0.7855 (m-30) REVERT: C 418 LEU cc_start: 0.8772 (tt) cc_final: 0.8496 (tp) REVERT: C 423 GLN cc_start: 0.7600 (pm20) cc_final: 0.6760 (pt0) REVERT: C 424 GLU cc_start: 0.7543 (mp0) cc_final: 0.6918 (mp0) REVERT: C 431 TYR cc_start: 0.8218 (m-80) cc_final: 0.7498 (m-10) REVERT: C 438 ARG cc_start: 0.7853 (tpm170) cc_final: 0.6970 (tpm170) REVERT: C 473 MET cc_start: 0.7981 (mmt) cc_final: 0.7226 (mmt) REVERT: C 554 MET cc_start: 0.6891 (tpp) cc_final: 0.6405 (tpp) REVERT: C 603 MET cc_start: 0.7781 (ptt) cc_final: 0.7470 (ptm) REVERT: C 692 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.8196 (mmp80) REVERT: B 19 GLU cc_start: 0.7417 (pp20) cc_final: 0.6819 (pp20) REVERT: B 21 LEU cc_start: 0.8611 (mt) cc_final: 0.8228 (mm) REVERT: B 24 PHE cc_start: 0.8463 (m-10) cc_final: 0.8115 (m-80) REVERT: B 29 LEU cc_start: 0.8131 (mp) cc_final: 0.7808 (mp) REVERT: B 61 MET cc_start: 0.6855 (tmm) cc_final: 0.6259 (tmm) REVERT: B 72 VAL cc_start: 0.8867 (m) cc_final: 0.8460 (p) REVERT: B 85 ILE cc_start: 0.8655 (mt) cc_final: 0.8424 (tp) REVERT: B 103 GLN cc_start: 0.7428 (pm20) cc_final: 0.7128 (pm20) REVERT: B 105 TYR cc_start: 0.7889 (t80) cc_final: 0.7665 (t80) REVERT: B 106 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7652 (pt0) REVERT: B 112 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7308 (mm-40) REVERT: B 114 GLU cc_start: 0.6580 (tm-30) cc_final: 0.6192 (mm-30) REVERT: B 115 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7007 (p0) REVERT: B 123 TYR cc_start: 0.7779 (t80) cc_final: 0.7105 (t80) REVERT: B 145 CYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7897 (m) REVERT: B 149 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7627 (tptp) REVERT: B 154 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7468 (mtp85) REVERT: B 155 MET cc_start: 0.7873 (tpt) cc_final: 0.7432 (tpp) REVERT: B 166 GLN cc_start: 0.5204 (mp10) cc_final: 0.4638 (mp10) REVERT: B 178 ILE cc_start: 0.7890 (tp) cc_final: 0.7534 (mm) REVERT: B 184 ASP cc_start: 0.7740 (t70) cc_final: 0.7068 (t0) REVERT: B 199 MET cc_start: 0.7618 (mmp) cc_final: 0.7343 (mmp) REVERT: B 209 ARG cc_start: 0.8131 (mmt90) cc_final: 0.7866 (mmt90) REVERT: B 212 TYR cc_start: 0.7862 (m-10) cc_final: 0.7524 (m-80) REVERT: B 215 SER cc_start: 0.8290 (m) cc_final: 0.7944 (p) REVERT: B 242 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7834 (mmtt) REVERT: B 263 MET cc_start: 0.7006 (mpp) cc_final: 0.6370 (mtp) REVERT: B 294 LYS cc_start: 0.7539 (mmtm) cc_final: 0.7272 (mmtm) REVERT: B 307 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7773 (mmtm) REVERT: B 363 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8149 (mmtp) REVERT: B 381 TYR cc_start: 0.7444 (m-80) cc_final: 0.6772 (m-80) REVERT: B 383 TYR cc_start: 0.5452 (m-80) cc_final: 0.5081 (m-80) REVERT: B 429 ASP cc_start: 0.7945 (m-30) cc_final: 0.7262 (m-30) REVERT: B 443 PHE cc_start: 0.7689 (t80) cc_final: 0.7454 (t80) REVERT: B 469 ASP cc_start: 0.7448 (t70) cc_final: 0.6840 (t70) REVERT: B 472 PHE cc_start: 0.5938 (m-80) cc_final: 0.5365 (m-80) REVERT: B 502 TYR cc_start: 0.6674 (t80) cc_final: 0.6062 (t80) REVERT: B 503 ASP cc_start: 0.8160 (t0) cc_final: 0.7792 (t0) REVERT: B 583 VAL cc_start: 0.7992 (p) cc_final: 0.7618 (t) REVERT: B 585 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8393 (mtpp) REVERT: F 28 LYS cc_start: 0.7865 (mmmm) cc_final: 0.7523 (mmmm) REVERT: F 45 GLN cc_start: 0.7976 (tt0) cc_final: 0.7509 (tp40) REVERT: F 53 SER cc_start: 0.7995 (t) cc_final: 0.7011 (t) REVERT: F 56 GLU cc_start: 0.7889 (mp0) cc_final: 0.6943 (pm20) REVERT: F 62 TYR cc_start: 0.7903 (t80) cc_final: 0.6984 (t80) REVERT: F 63 THR cc_start: 0.7474 (t) cc_final: 0.7166 (p) REVERT: F 64 MET cc_start: 0.7429 (tpt) cc_final: 0.6903 (tpt) REVERT: F 68 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8368 (mttm) REVERT: F 71 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6892 (tm-30) REVERT: F 78 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7928 (ttm-80) REVERT: F 79 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6532 (tp30) REVERT: F 103 GLN cc_start: 0.8473 (tp40) cc_final: 0.8023 (tp40) REVERT: F 113 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: F 116 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8283 (tpp) REVERT: F 118 MET cc_start: 0.7108 (mtm) cc_final: 0.6880 (mtm) REVERT: F 126 MET cc_start: 0.8103 (tmt) cc_final: 0.7622 (tmm) REVERT: F 140 TYR cc_start: 0.7936 (t80) cc_final: 0.6956 (t80) REVERT: F 145 ILE cc_start: 0.8775 (mt) cc_final: 0.8425 (tp) REVERT: F 153 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7354 (mmt180) REVERT: F 154 TYR cc_start: 0.7116 (t80) cc_final: 0.5563 (t80) REVERT: F 158 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7237 (ttm-80) REVERT: F 163 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7171 (mm110) REVERT: F 167 ASP cc_start: 0.7279 (t0) cc_final: 0.6866 (t0) REVERT: F 168 MET cc_start: 0.7227 (ptp) cc_final: 0.6969 (ptp) REVERT: F 183 ILE cc_start: 0.8811 (mm) cc_final: 0.8531 (mm) REVERT: F 233 TYR cc_start: 0.7550 (t80) cc_final: 0.7105 (t80) REVERT: F 235 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8102 (mmmm) REVERT: F 238 GLU cc_start: 0.8166 (tp30) cc_final: 0.7444 (tp30) REVERT: F 240 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7677 (tpp80) REVERT: F 243 GLU cc_start: 0.7584 (pp20) cc_final: 0.7236 (pp20) REVERT: F 249 MET cc_start: 0.7664 (ppp) cc_final: 0.7227 (ppp) REVERT: F 258 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7893 (mp0) REVERT: F 265 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7206 (mm-30) REVERT: F 270 SER cc_start: 0.8480 (m) cc_final: 0.8003 (t) REVERT: F 272 HIS cc_start: 0.6238 (m170) cc_final: 0.5949 (m170) REVERT: F 274 LYS cc_start: 0.7797 (tppt) cc_final: 0.7441 (tmmt) REVERT: F 287 MET cc_start: 0.7590 (ptm) cc_final: 0.7171 (ppp) REVERT: F 301 LYS cc_start: 0.8356 (ptpt) cc_final: 0.8057 (ptpp) REVERT: F 311 LYS cc_start: 0.7755 (tmmt) cc_final: 0.7278 (ttmm) REVERT: F 322 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7740 (mmt180) REVERT: F 332 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6315 (pm20) REVERT: F 363 ASP cc_start: 0.7737 (t70) cc_final: 0.7375 (t0) REVERT: F 366 PHE cc_start: 0.6830 (m-80) cc_final: 0.6630 (m-10) REVERT: F 368 GLN cc_start: 0.7272 (tm-30) cc_final: 0.7019 (tm-30) REVERT: F 369 THR cc_start: 0.7836 (p) cc_final: 0.7478 (t) REVERT: F 378 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.4748 (mt) REVERT: F 414 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8668 (mmtm) REVERT: F 423 GLN cc_start: 0.7670 (tt0) cc_final: 0.7128 (tt0) REVERT: F 489 GLN cc_start: 0.8034 (mt0) cc_final: 0.7675 (tp40) REVERT: F 671 ARG cc_start: 0.6181 (tpt-90) cc_final: 0.5841 (tpt-90) REVERT: F 673 LYS cc_start: 0.8048 (ptmm) cc_final: 0.7830 (pptt) REVERT: D 42 CYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5621 (m) outliers start: 99 outliers final: 68 residues processed: 751 average time/residue: 0.3855 time to fit residues: 432.8366 Evaluate side-chains 763 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 685 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 734 PHE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 156 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 206 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 316 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22731 Z= 0.248 Angle : 0.772 13.142 30684 Z= 0.392 Chirality : 0.046 0.264 3385 Planarity : 0.005 0.100 3934 Dihedral : 4.758 25.167 3006 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.35 % Favored : 90.54 % Rotamer: Outliers : 3.89 % Allowed : 26.35 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2718 helix: 0.61 (0.14), residues: 1264 sheet: -1.06 (0.31), residues: 268 loop : -2.45 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 27 HIS 0.022 0.002 HIS F 490 PHE 0.029 0.002 PHE C 419 TYR 0.033 0.002 TYR A 164 ARG 0.011 0.001 ARG F 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 697 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8268 (tp) cc_final: 0.7897 (pt) REVERT: A 13 TYR cc_start: 0.7343 (t80) cc_final: 0.6969 (t80) REVERT: A 19 GLU cc_start: 0.7063 (pp20) cc_final: 0.6668 (pp20) REVERT: A 20 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8158 (mm110) REVERT: A 22 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8267 (tttp) REVERT: A 26 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 57 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7669 (ttm-80) REVERT: A 59 MET cc_start: 0.7467 (ttt) cc_final: 0.6977 (ttt) REVERT: A 60 PHE cc_start: 0.8422 (m-80) cc_final: 0.8140 (m-10) REVERT: A 67 SER cc_start: 0.8454 (p) cc_final: 0.8183 (p) REVERT: A 84 ILE cc_start: 0.8615 (tp) cc_final: 0.8274 (tt) REVERT: A 87 THR cc_start: 0.8567 (t) cc_final: 0.8192 (p) REVERT: A 106 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 115 ASP cc_start: 0.7977 (p0) cc_final: 0.7334 (p0) REVERT: A 117 LEU cc_start: 0.8301 (mt) cc_final: 0.7903 (tt) REVERT: A 122 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 127 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8609 (mmtm) REVERT: A 129 ASN cc_start: 0.7494 (p0) cc_final: 0.7281 (p0) REVERT: A 147 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 149 LYS cc_start: 0.8168 (tttt) cc_final: 0.7887 (ttmt) REVERT: A 157 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6921 (mm-30) REVERT: A 159 LYS cc_start: 0.7254 (mtmt) cc_final: 0.6619 (ptpp) REVERT: A 160 PHE cc_start: 0.5432 (OUTLIER) cc_final: 0.4152 (t80) REVERT: A 170 MET cc_start: 0.6702 (mmp) cc_final: 0.6345 (mmp) REVERT: A 191 GLU cc_start: 0.7452 (pp20) cc_final: 0.7233 (tm-30) REVERT: A 196 GLU cc_start: 0.7589 (pp20) cc_final: 0.6999 (pp20) REVERT: A 199 MET cc_start: 0.8025 (mmm) cc_final: 0.7603 (mmp) REVERT: A 211 GLN cc_start: 0.7839 (pm20) cc_final: 0.7342 (pm20) REVERT: A 263 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5730 (mmp) REVERT: A 267 GLU cc_start: 0.7486 (tp30) cc_final: 0.6898 (tp30) REVERT: A 291 GLN cc_start: 0.8072 (mp10) cc_final: 0.7699 (mp10) REVERT: A 294 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8224 (mmmm) REVERT: A 297 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7864 (ptpt) REVERT: A 352 TRP cc_start: 0.7695 (t60) cc_final: 0.7446 (t60) REVERT: A 357 GLN cc_start: 0.7554 (mm-40) cc_final: 0.6773 (mm-40) REVERT: A 361 PHE cc_start: 0.7230 (m-80) cc_final: 0.6372 (m-80) REVERT: A 397 ARG cc_start: 0.7766 (ptp90) cc_final: 0.7438 (ptp90) REVERT: A 443 PHE cc_start: 0.8529 (t80) cc_final: 0.7978 (t80) REVERT: A 454 MET cc_start: 0.6697 (tpp) cc_final: 0.6248 (tpp) REVERT: A 586 LEU cc_start: 0.8362 (mt) cc_final: 0.7827 (mp) REVERT: E 23 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7311 (mp0) REVERT: E 48 HIS cc_start: 0.5209 (t-90) cc_final: 0.4712 (t-90) REVERT: C 28 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7798 (tptp) REVERT: C 33 ILE cc_start: 0.8998 (mm) cc_final: 0.8716 (tt) REVERT: C 35 ASP cc_start: 0.7398 (t0) cc_final: 0.7093 (m-30) REVERT: C 45 GLN cc_start: 0.7730 (mt0) cc_final: 0.7464 (tt0) REVERT: C 62 TYR cc_start: 0.7995 (t80) cc_final: 0.7706 (t80) REVERT: C 68 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8203 (mptt) REVERT: C 71 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7460 (tm-30) REVERT: C 72 LYS cc_start: 0.8496 (tttt) cc_final: 0.8079 (tptm) REVERT: C 83 GLU cc_start: 0.7933 (tp30) cc_final: 0.7411 (tp30) REVERT: C 153 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7402 (mmm-85) REVERT: C 163 GLN cc_start: 0.8538 (mm-40) cc_final: 0.7971 (mm110) REVERT: C 191 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7046 (tmm) REVERT: C 206 GLU cc_start: 0.6249 (mp0) cc_final: 0.5673 (mp0) REVERT: C 222 GLN cc_start: 0.7463 (tp40) cc_final: 0.7086 (tm-30) REVERT: C 236 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8162 (ptpp) REVERT: C 238 GLU cc_start: 0.7368 (tp30) cc_final: 0.6736 (tm-30) REVERT: C 246 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 247 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7762 (ttm170) REVERT: C 250 HIS cc_start: 0.7955 (t-90) cc_final: 0.7207 (t-90) REVERT: C 258 GLU cc_start: 0.7712 (mm-30) cc_final: 0.6988 (mp0) REVERT: C 262 LYS cc_start: 0.8035 (tmtm) cc_final: 0.7386 (ttmm) REVERT: C 270 SER cc_start: 0.8581 (m) cc_final: 0.8034 (t) REVERT: C 282 SER cc_start: 0.7795 (m) cc_final: 0.7557 (m) REVERT: C 292 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8112 (mmmm) REVERT: C 301 LYS cc_start: 0.8350 (ptpt) cc_final: 0.7869 (pttm) REVERT: C 306 VAL cc_start: 0.8738 (t) cc_final: 0.8369 (p) REVERT: C 314 CYS cc_start: 0.7487 (m) cc_final: 0.7252 (m) REVERT: C 346 LEU cc_start: 0.8348 (tp) cc_final: 0.8112 (tp) REVERT: C 353 ASP cc_start: 0.7901 (t0) cc_final: 0.7606 (t0) REVERT: C 368 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6566 (tm-30) REVERT: C 369 THR cc_start: 0.8218 (p) cc_final: 0.7660 (t) REVERT: C 394 ASP cc_start: 0.7840 (t0) cc_final: 0.7455 (t0) REVERT: C 409 GLU cc_start: 0.8276 (pt0) cc_final: 0.7964 (pp20) REVERT: C 412 LEU cc_start: 0.8683 (mt) cc_final: 0.8380 (mm) REVERT: C 413 ASP cc_start: 0.8483 (m-30) cc_final: 0.7874 (m-30) REVERT: C 418 LEU cc_start: 0.8823 (tt) cc_final: 0.8581 (tp) REVERT: C 423 GLN cc_start: 0.7617 (pm20) cc_final: 0.6746 (pt0) REVERT: C 424 GLU cc_start: 0.7503 (mp0) cc_final: 0.6704 (mp0) REVERT: C 431 TYR cc_start: 0.8423 (m-80) cc_final: 0.7596 (m-10) REVERT: C 554 MET cc_start: 0.6920 (tpp) cc_final: 0.6416 (tpp) REVERT: C 603 MET cc_start: 0.7828 (ptt) cc_final: 0.7388 (ptm) REVERT: B 19 GLU cc_start: 0.7617 (pp20) cc_final: 0.6972 (pp20) REVERT: B 24 PHE cc_start: 0.8482 (m-10) cc_final: 0.8116 (m-80) REVERT: B 29 LEU cc_start: 0.8230 (mp) cc_final: 0.7909 (mt) REVERT: B 46 LYS cc_start: 0.8697 (mttm) cc_final: 0.8399 (mttm) REVERT: B 72 VAL cc_start: 0.8761 (m) cc_final: 0.8430 (p) REVERT: B 85 ILE cc_start: 0.8649 (mt) cc_final: 0.8376 (tp) REVERT: B 105 TYR cc_start: 0.7943 (t80) cc_final: 0.7672 (t80) REVERT: B 106 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7741 (pt0) REVERT: B 112 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7102 (mm-40) REVERT: B 114 GLU cc_start: 0.6688 (tm-30) cc_final: 0.6277 (mm-30) REVERT: B 115 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.6953 (p0) REVERT: B 123 TYR cc_start: 0.7847 (t80) cc_final: 0.7245 (t80) REVERT: B 145 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8035 (m) REVERT: B 149 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7618 (tptp) REVERT: B 154 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7504 (mtp85) REVERT: B 155 MET cc_start: 0.8012 (tpt) cc_final: 0.7529 (tpp) REVERT: B 166 GLN cc_start: 0.5622 (mp10) cc_final: 0.4922 (mp10) REVERT: B 178 ILE cc_start: 0.7907 (tp) cc_final: 0.7573 (mm) REVERT: B 184 ASP cc_start: 0.7745 (t70) cc_final: 0.7318 (t0) REVERT: B 199 MET cc_start: 0.7708 (mmp) cc_final: 0.7434 (mmp) REVERT: B 209 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7574 (mmt90) REVERT: B 212 TYR cc_start: 0.7673 (m-10) cc_final: 0.7387 (m-80) REVERT: B 215 SER cc_start: 0.8274 (m) cc_final: 0.7915 (p) REVERT: B 242 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7827 (mmtt) REVERT: B 263 MET cc_start: 0.7060 (mpp) cc_final: 0.6349 (mtp) REVERT: B 294 LYS cc_start: 0.7512 (mmtm) cc_final: 0.7281 (mmtm) REVERT: B 297 LYS cc_start: 0.7785 (ptpp) cc_final: 0.7406 (ptpp) REVERT: B 301 PRO cc_start: 0.7402 (Cg_exo) cc_final: 0.7113 (Cg_endo) REVERT: B 307 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7787 (mmtm) REVERT: B 363 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8185 (mmmm) REVERT: B 381 TYR cc_start: 0.7517 (m-80) cc_final: 0.6883 (m-80) REVERT: B 383 TYR cc_start: 0.5615 (m-80) cc_final: 0.5193 (m-80) REVERT: B 429 ASP cc_start: 0.7978 (m-30) cc_final: 0.6906 (m-30) REVERT: B 469 ASP cc_start: 0.7471 (t70) cc_final: 0.6892 (t70) REVERT: B 502 TYR cc_start: 0.6642 (t80) cc_final: 0.6217 (t80) REVERT: B 503 ASP cc_start: 0.8188 (t0) cc_final: 0.7701 (t0) REVERT: B 529 VAL cc_start: 0.6916 (t) cc_final: 0.6160 (m) REVERT: B 583 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7653 (t) REVERT: F 28 LYS cc_start: 0.7868 (mmmm) cc_final: 0.7528 (mmmm) REVERT: F 53 SER cc_start: 0.8071 (t) cc_final: 0.7410 (t) REVERT: F 56 GLU cc_start: 0.7916 (mp0) cc_final: 0.7228 (mp0) REVERT: F 62 TYR cc_start: 0.7979 (t80) cc_final: 0.7016 (t80) REVERT: F 63 THR cc_start: 0.7583 (t) cc_final: 0.7307 (p) REVERT: F 64 MET cc_start: 0.7500 (tpt) cc_final: 0.7021 (tpt) REVERT: F 68 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8422 (mttm) REVERT: F 71 GLU cc_start: 0.7619 (tm-30) cc_final: 0.6974 (tm-30) REVERT: F 78 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7960 (ttm-80) REVERT: F 79 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6666 (tp30) REVERT: F 103 GLN cc_start: 0.8515 (tp40) cc_final: 0.8051 (tp40) REVERT: F 113 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7492 (tp40) REVERT: F 116 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8311 (tpp) REVERT: F 118 MET cc_start: 0.7217 (mtm) cc_final: 0.6942 (mtm) REVERT: F 124 MET cc_start: 0.4311 (tmm) cc_final: 0.3581 (tmm) REVERT: F 126 MET cc_start: 0.8042 (tmt) cc_final: 0.7641 (tmm) REVERT: F 140 TYR cc_start: 0.7990 (t80) cc_final: 0.7082 (t80) REVERT: F 145 ILE cc_start: 0.8847 (mt) cc_final: 0.8587 (mm) REVERT: F 153 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7494 (mmt180) REVERT: F 154 TYR cc_start: 0.7198 (t80) cc_final: 0.5725 (t80) REVERT: F 158 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7126 (ttm-80) REVERT: F 163 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7228 (mm110) REVERT: F 167 ASP cc_start: 0.7332 (t0) cc_final: 0.6933 (t0) REVERT: F 168 MET cc_start: 0.7591 (ptp) cc_final: 0.7193 (ptp) REVERT: F 183 ILE cc_start: 0.8847 (mm) cc_final: 0.8593 (mm) REVERT: F 206 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6967 (tm-30) REVERT: F 233 TYR cc_start: 0.7864 (t80) cc_final: 0.7344 (t80) REVERT: F 238 GLU cc_start: 0.8202 (tp30) cc_final: 0.7497 (tp30) REVERT: F 240 ARG cc_start: 0.7962 (mmt180) cc_final: 0.7747 (tpp80) REVERT: F 243 GLU cc_start: 0.7627 (pp20) cc_final: 0.7240 (pp20) REVERT: F 249 MET cc_start: 0.7599 (ppp) cc_final: 0.7167 (ppp) REVERT: F 258 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7914 (mp0) REVERT: F 265 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7212 (mm-30) REVERT: F 270 SER cc_start: 0.8571 (m) cc_final: 0.8033 (t) REVERT: F 272 HIS cc_start: 0.6022 (m170) cc_final: 0.5722 (m170) REVERT: F 295 ASP cc_start: 0.7285 (m-30) cc_final: 0.6732 (m-30) REVERT: F 296 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6489 (mm) REVERT: F 301 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8127 (ptpp) REVERT: F 303 PHE cc_start: 0.7877 (m-80) cc_final: 0.7525 (t80) REVERT: F 322 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7705 (mmt180) REVERT: F 332 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: F 368 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7067 (tm-30) REVERT: F 369 THR cc_start: 0.7912 (p) cc_final: 0.7637 (t) REVERT: F 414 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8691 (mmtm) REVERT: F 423 GLN cc_start: 0.7892 (tt0) cc_final: 0.7521 (pt0) REVERT: F 489 GLN cc_start: 0.8054 (mt0) cc_final: 0.7710 (tp-100) REVERT: F 539 TYR cc_start: 0.6540 (m-80) cc_final: 0.6179 (m-80) REVERT: F 671 ARG cc_start: 0.6289 (tpt-90) cc_final: 0.6010 (tpt-90) REVERT: F 673 LYS cc_start: 0.8070 (ptmm) cc_final: 0.7822 (pptt) REVERT: D 42 CYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5792 (m) REVERT: D 55 GLU cc_start: 0.4064 (mm-30) cc_final: 0.3764 (mp0) outliers start: 96 outliers final: 65 residues processed: 745 average time/residue: 0.3647 time to fit residues: 402.3598 Evaluate side-chains 760 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 684 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 599 MET Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 229 optimal weight: 0.0170 chunk 244 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 106 optimal weight: 0.0370 chunk 191 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 243 optimal weight: 0.2980 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN F 60 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22731 Z= 0.212 Angle : 0.793 15.398 30684 Z= 0.396 Chirality : 0.045 0.248 3385 Planarity : 0.005 0.100 3934 Dihedral : 4.732 26.921 3006 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.50 % Favored : 91.43 % Rotamer: Outliers : 4.09 % Allowed : 27.40 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2718 helix: 0.62 (0.14), residues: 1259 sheet: -1.01 (0.31), residues: 276 loop : -2.42 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 27 HIS 0.020 0.001 HIS F 490 PHE 0.027 0.002 PHE B 537 TYR 0.025 0.002 TYR F 125 ARG 0.013 0.001 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 686 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8193 (tp) cc_final: 0.7834 (pt) REVERT: A 13 TYR cc_start: 0.7288 (t80) cc_final: 0.6881 (t80) REVERT: A 19 GLU cc_start: 0.7046 (pp20) cc_final: 0.6749 (pp20) REVERT: A 20 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8129 (mm110) REVERT: A 22 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7785 (ttmt) REVERT: A 23 LEU cc_start: 0.8336 (mt) cc_final: 0.8086 (tp) REVERT: A 26 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7295 (mt-10) REVERT: A 57 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7655 (ttp80) REVERT: A 59 MET cc_start: 0.7463 (ttt) cc_final: 0.6867 (ttt) REVERT: A 60 PHE cc_start: 0.8388 (m-80) cc_final: 0.8072 (m-10) REVERT: A 66 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 69 GLN cc_start: 0.8287 (tp40) cc_final: 0.8077 (tp-100) REVERT: A 84 ILE cc_start: 0.8559 (tp) cc_final: 0.8304 (tt) REVERT: A 87 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 106 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 115 ASP cc_start: 0.7872 (p0) cc_final: 0.7234 (p0) REVERT: A 117 LEU cc_start: 0.8230 (mt) cc_final: 0.7849 (tt) REVERT: A 122 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 127 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8595 (mmtm) REVERT: A 147 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 149 LYS cc_start: 0.8134 (tttt) cc_final: 0.7829 (ttmt) REVERT: A 150 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7778 (mm-40) REVERT: A 157 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 159 LYS cc_start: 0.7130 (mtmt) cc_final: 0.6452 (ptpp) REVERT: A 160 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.4034 (t80) REVERT: A 170 MET cc_start: 0.6551 (mmp) cc_final: 0.6265 (mmp) REVERT: A 199 MET cc_start: 0.7958 (mmm) cc_final: 0.7563 (mmp) REVERT: A 211 GLN cc_start: 0.7781 (pm20) cc_final: 0.7440 (pm20) REVERT: A 219 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7948 (tp40) REVERT: A 267 GLU cc_start: 0.7588 (tp30) cc_final: 0.6884 (tp30) REVERT: A 291 GLN cc_start: 0.7995 (mp10) cc_final: 0.7747 (mp10) REVERT: A 294 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8087 (mmmm) REVERT: A 297 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7794 (ptpt) REVERT: A 357 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6646 (mm-40) REVERT: A 361 PHE cc_start: 0.7216 (m-80) cc_final: 0.6350 (m-80) REVERT: A 397 ARG cc_start: 0.7703 (ptp90) cc_final: 0.7341 (ptp90) REVERT: A 443 PHE cc_start: 0.8528 (t80) cc_final: 0.7992 (t80) REVERT: A 454 MET cc_start: 0.6496 (tpp) cc_final: 0.5994 (tpp) REVERT: A 558 LEU cc_start: 0.6871 (tp) cc_final: 0.6524 (mt) REVERT: E 23 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7238 (mp0) REVERT: E 35 TRP cc_start: 0.3448 (m-10) cc_final: 0.3134 (m-10) REVERT: E 48 HIS cc_start: 0.5117 (t-90) cc_final: 0.4640 (t-90) REVERT: C 28 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7756 (tptp) REVERT: C 33 ILE cc_start: 0.8997 (mm) cc_final: 0.8675 (tt) REVERT: C 45 GLN cc_start: 0.7693 (mt0) cc_final: 0.7466 (tt0) REVERT: C 55 GLU cc_start: 0.7447 (mp0) cc_final: 0.6981 (mp0) REVERT: C 62 TYR cc_start: 0.7935 (t80) cc_final: 0.7641 (t80) REVERT: C 68 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8157 (mptt) REVERT: C 71 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7442 (tm-30) REVERT: C 72 LYS cc_start: 0.8460 (tttt) cc_final: 0.7954 (tptp) REVERT: C 83 GLU cc_start: 0.7758 (tp30) cc_final: 0.7394 (tp30) REVERT: C 153 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7427 (mmm-85) REVERT: C 163 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7847 (mm110) REVERT: C 191 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.6986 (tmm) REVERT: C 206 GLU cc_start: 0.6209 (mp0) cc_final: 0.5681 (mp0) REVERT: C 222 GLN cc_start: 0.7531 (tp40) cc_final: 0.7049 (tm-30) REVERT: C 234 ILE cc_start: 0.8560 (mm) cc_final: 0.8037 (tp) REVERT: C 235 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7620 (ptpt) REVERT: C 238 GLU cc_start: 0.7337 (tp30) cc_final: 0.6500 (tm-30) REVERT: C 246 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7342 (tm-30) REVERT: C 247 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7674 (ttm110) REVERT: C 250 HIS cc_start: 0.7929 (t-90) cc_final: 0.7190 (t-90) REVERT: C 258 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6886 (mp0) REVERT: C 262 LYS cc_start: 0.8010 (tmtm) cc_final: 0.7319 (ttpp) REVERT: C 270 SER cc_start: 0.8522 (m) cc_final: 0.7986 (t) REVERT: C 274 LYS cc_start: 0.8430 (tppt) cc_final: 0.8148 (tppt) REVERT: C 282 SER cc_start: 0.7588 (m) cc_final: 0.7322 (m) REVERT: C 292 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8207 (mmtt) REVERT: C 301 LYS cc_start: 0.8388 (ptpt) cc_final: 0.8151 (ptpp) REVERT: C 306 VAL cc_start: 0.8769 (t) cc_final: 0.8379 (p) REVERT: C 314 CYS cc_start: 0.7453 (m) cc_final: 0.7213 (m) REVERT: C 346 LEU cc_start: 0.8327 (tp) cc_final: 0.8123 (tp) REVERT: C 351 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7956 (tmm-80) REVERT: C 353 ASP cc_start: 0.7913 (t0) cc_final: 0.7582 (t0) REVERT: C 368 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6582 (tm-30) REVERT: C 369 THR cc_start: 0.8093 (p) cc_final: 0.7329 (t) REVERT: C 394 ASP cc_start: 0.7848 (t0) cc_final: 0.7458 (t0) REVERT: C 395 LYS cc_start: 0.8585 (mmtm) cc_final: 0.8192 (mmmm) REVERT: C 409 GLU cc_start: 0.8237 (pt0) cc_final: 0.7913 (pp20) REVERT: C 412 LEU cc_start: 0.8651 (mt) cc_final: 0.8350 (mm) REVERT: C 413 ASP cc_start: 0.8482 (m-30) cc_final: 0.7866 (m-30) REVERT: C 418 LEU cc_start: 0.8766 (tt) cc_final: 0.8508 (tp) REVERT: C 423 GLN cc_start: 0.7639 (pm20) cc_final: 0.6838 (pt0) REVERT: C 424 GLU cc_start: 0.7529 (mp0) cc_final: 0.6906 (mp0) REVERT: C 431 TYR cc_start: 0.8207 (m-80) cc_final: 0.7443 (m-80) REVERT: C 438 ARG cc_start: 0.7901 (tpm170) cc_final: 0.7023 (tpm170) REVERT: C 473 MET cc_start: 0.7658 (mmt) cc_final: 0.6796 (tpp) REVERT: C 554 MET cc_start: 0.6884 (tpp) cc_final: 0.6371 (tpp) REVERT: C 603 MET cc_start: 0.7749 (ptt) cc_final: 0.7351 (ptm) REVERT: C 692 ARG cc_start: 0.8564 (mmp80) cc_final: 0.8307 (mmp80) REVERT: B 19 GLU cc_start: 0.7428 (pp20) cc_final: 0.6940 (pp20) REVERT: B 24 PHE cc_start: 0.8488 (m-10) cc_final: 0.8155 (m-80) REVERT: B 29 LEU cc_start: 0.8104 (mp) cc_final: 0.7789 (mt) REVERT: B 66 GLU cc_start: 0.7910 (mp0) cc_final: 0.7707 (pm20) REVERT: B 72 VAL cc_start: 0.8808 (m) cc_final: 0.8479 (p) REVERT: B 85 ILE cc_start: 0.8692 (mt) cc_final: 0.8463 (tp) REVERT: B 88 TYR cc_start: 0.8749 (t80) cc_final: 0.7667 (t80) REVERT: B 105 TYR cc_start: 0.7852 (t80) cc_final: 0.7529 (t80) REVERT: B 106 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7783 (pt0) REVERT: B 112 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7118 (mm-40) REVERT: B 114 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6170 (mm-30) REVERT: B 115 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7065 (p0) REVERT: B 123 TYR cc_start: 0.7802 (t80) cc_final: 0.7168 (t80) REVERT: B 148 LEU cc_start: 0.8289 (tp) cc_final: 0.8050 (tp) REVERT: B 149 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7622 (tptp) REVERT: B 153 LYS cc_start: 0.8651 (tptm) cc_final: 0.7910 (ttmm) REVERT: B 154 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7410 (mtp85) REVERT: B 155 MET cc_start: 0.7914 (tpt) cc_final: 0.7445 (tpp) REVERT: B 166 GLN cc_start: 0.5353 (mp10) cc_final: 0.4745 (mp10) REVERT: B 170 MET cc_start: 0.7545 (mmm) cc_final: 0.7296 (mmm) REVERT: B 178 ILE cc_start: 0.7851 (tp) cc_final: 0.7520 (mm) REVERT: B 184 ASP cc_start: 0.7720 (t70) cc_final: 0.7035 (t0) REVERT: B 199 MET cc_start: 0.7601 (mmp) cc_final: 0.7279 (mmm) REVERT: B 209 ARG cc_start: 0.8141 (mmt90) cc_final: 0.7659 (mmt90) REVERT: B 212 TYR cc_start: 0.7751 (m-10) cc_final: 0.7469 (m-80) REVERT: B 215 SER cc_start: 0.8228 (m) cc_final: 0.7868 (p) REVERT: B 242 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7790 (mmtt) REVERT: B 263 MET cc_start: 0.6978 (mpp) cc_final: 0.6337 (mtp) REVERT: B 297 LYS cc_start: 0.7729 (ptpp) cc_final: 0.7423 (ptpp) REVERT: B 301 PRO cc_start: 0.7365 (Cg_exo) cc_final: 0.7085 (Cg_endo) REVERT: B 307 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7707 (mmtm) REVERT: B 363 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8093 (mmtp) REVERT: B 381 TYR cc_start: 0.7426 (m-80) cc_final: 0.6827 (m-80) REVERT: B 383 TYR cc_start: 0.5506 (m-80) cc_final: 0.5115 (m-80) REVERT: B 429 ASP cc_start: 0.8120 (m-30) cc_final: 0.7084 (m-30) REVERT: B 469 ASP cc_start: 0.7405 (t70) cc_final: 0.7002 (t70) REVERT: B 470 LYS cc_start: 0.7107 (tttp) cc_final: 0.6596 (ttmm) REVERT: B 502 TYR cc_start: 0.6540 (t80) cc_final: 0.6299 (t80) REVERT: B 503 ASP cc_start: 0.8087 (t0) cc_final: 0.7648 (t0) REVERT: B 583 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7633 (t) REVERT: F 28 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7488 (mmmm) REVERT: F 53 SER cc_start: 0.8028 (t) cc_final: 0.7385 (t) REVERT: F 55 GLU cc_start: 0.7596 (tp30) cc_final: 0.7391 (tp30) REVERT: F 56 GLU cc_start: 0.7971 (mp0) cc_final: 0.7305 (mp0) REVERT: F 60 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7800 (m-40) REVERT: F 62 TYR cc_start: 0.7951 (t80) cc_final: 0.7002 (t80) REVERT: F 63 THR cc_start: 0.7505 (t) cc_final: 0.7213 (p) REVERT: F 64 MET cc_start: 0.7490 (tpt) cc_final: 0.6810 (tpp) REVERT: F 68 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8390 (mttm) REVERT: F 71 GLU cc_start: 0.7600 (tm-30) cc_final: 0.6948 (tm-30) REVERT: F 78 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7956 (ttm-80) REVERT: F 79 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6618 (tp30) REVERT: F 103 GLN cc_start: 0.8489 (tp40) cc_final: 0.8029 (tp40) REVERT: F 113 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: F 116 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8301 (tpp) REVERT: F 117 VAL cc_start: 0.8339 (t) cc_final: 0.7965 (p) REVERT: F 118 MET cc_start: 0.7088 (mtm) cc_final: 0.6775 (mtm) REVERT: F 124 MET cc_start: 0.4242 (tmm) cc_final: 0.3517 (tmm) REVERT: F 126 MET cc_start: 0.8039 (tmt) cc_final: 0.7646 (tmm) REVERT: F 140 TYR cc_start: 0.7937 (t80) cc_final: 0.7001 (t80) REVERT: F 145 ILE cc_start: 0.8802 (mt) cc_final: 0.8395 (tp) REVERT: F 153 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7457 (mmt180) REVERT: F 154 TYR cc_start: 0.7099 (t80) cc_final: 0.5738 (t80) REVERT: F 158 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7368 (ttm-80) REVERT: F 163 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7177 (mm110) REVERT: F 167 ASP cc_start: 0.7285 (t0) cc_final: 0.6932 (t0) REVERT: F 191 MET cc_start: 0.6762 (tmm) cc_final: 0.6412 (tpp) REVERT: F 238 GLU cc_start: 0.8189 (tp30) cc_final: 0.7448 (tp30) REVERT: F 240 ARG cc_start: 0.7965 (mmt180) cc_final: 0.7737 (tpp80) REVERT: F 243 GLU cc_start: 0.7599 (pp20) cc_final: 0.7268 (pp20) REVERT: F 265 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7212 (mm-30) REVERT: F 270 SER cc_start: 0.8506 (m) cc_final: 0.7977 (t) REVERT: F 287 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7160 (ppp) REVERT: F 295 ASP cc_start: 0.7342 (m-30) cc_final: 0.6822 (m-30) REVERT: F 301 LYS cc_start: 0.8347 (ptpt) cc_final: 0.8095 (ptpp) REVERT: F 311 LYS cc_start: 0.7615 (tmmt) cc_final: 0.7218 (ttmm) REVERT: F 322 ARG cc_start: 0.8163 (mmt90) cc_final: 0.7760 (mmt180) REVERT: F 332 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: F 352 PHE cc_start: 0.7768 (m-10) cc_final: 0.7544 (m-10) REVERT: F 360 PHE cc_start: 0.7948 (m-80) cc_final: 0.7553 (m-80) REVERT: F 366 PHE cc_start: 0.6857 (m-80) cc_final: 0.6650 (m-10) REVERT: F 368 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6989 (tm-30) REVERT: F 369 THR cc_start: 0.7906 (p) cc_final: 0.7593 (t) REVERT: F 414 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8703 (mmtm) REVERT: F 423 GLN cc_start: 0.8063 (tt0) cc_final: 0.7701 (pt0) REVERT: F 489 GLN cc_start: 0.8027 (mt0) cc_final: 0.7669 (tp-100) REVERT: F 554 MET cc_start: 0.6388 (mmm) cc_final: 0.5739 (tpp) REVERT: F 671 ARG cc_start: 0.6177 (tpt-90) cc_final: 0.5849 (tpt-90) REVERT: F 673 LYS cc_start: 0.8051 (ptmm) cc_final: 0.7827 (pptt) REVERT: D 42 CYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5529 (m) REVERT: D 55 GLU cc_start: 0.3899 (mm-30) cc_final: 0.3653 (mp0) outliers start: 101 outliers final: 69 residues processed: 733 average time/residue: 0.3706 time to fit residues: 402.1098 Evaluate side-chains 749 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 666 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 734 PHE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 157 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 249 optimal weight: 0.0980 chunk 215 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 166 optimal weight: 0.8980 chunk 132 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22731 Z= 0.227 Angle : 0.816 15.659 30684 Z= 0.409 Chirality : 0.046 0.295 3385 Planarity : 0.005 0.074 3934 Dihedral : 4.756 27.589 3006 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.68 % Favored : 91.24 % Rotamer: Outliers : 3.60 % Allowed : 27.72 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2718 helix: 0.57 (0.14), residues: 1259 sheet: -1.07 (0.30), residues: 276 loop : -2.43 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 513 HIS 0.023 0.001 HIS F 490 PHE 0.029 0.002 PHE B 537 TYR 0.027 0.002 TYR A 164 ARG 0.014 0.001 ARG C 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 692 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8204 (tp) cc_final: 0.7900 (pt) REVERT: A 13 TYR cc_start: 0.7353 (t80) cc_final: 0.6925 (t80) REVERT: A 19 GLU cc_start: 0.6979 (pp20) cc_final: 0.6635 (pp20) REVERT: A 20 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8079 (mm110) REVERT: A 22 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7726 (ttmt) REVERT: A 23 LEU cc_start: 0.8427 (mt) cc_final: 0.7981 (tp) REVERT: A 26 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 57 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7692 (ttp80) REVERT: A 59 MET cc_start: 0.7470 (ttt) cc_final: 0.6917 (ttt) REVERT: A 60 PHE cc_start: 0.8397 (m-80) cc_final: 0.8086 (m-10) REVERT: A 66 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: A 84 ILE cc_start: 0.8537 (tp) cc_final: 0.8147 (tt) REVERT: A 87 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8123 (p) REVERT: A 106 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7213 (tm-30) REVERT: A 115 ASP cc_start: 0.7960 (p0) cc_final: 0.7328 (p0) REVERT: A 122 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 147 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 157 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7006 (mm-30) REVERT: A 159 LYS cc_start: 0.7141 (mtmt) cc_final: 0.6864 (ptpt) REVERT: A 160 PHE cc_start: 0.5102 (OUTLIER) cc_final: 0.4005 (t80) REVERT: A 170 MET cc_start: 0.6589 (mmp) cc_final: 0.6269 (mmp) REVERT: A 179 ASP cc_start: 0.7667 (t0) cc_final: 0.7224 (t70) REVERT: A 199 MET cc_start: 0.7997 (mmm) cc_final: 0.7569 (mmp) REVERT: A 211 GLN cc_start: 0.7797 (pm20) cc_final: 0.7401 (pm20) REVERT: A 219 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7950 (tp40) REVERT: A 263 MET cc_start: 0.5706 (mmp) cc_final: 0.5324 (mmp) REVERT: A 268 MET cc_start: 0.7172 (tpp) cc_final: 0.6408 (tpp) REVERT: A 291 GLN cc_start: 0.7965 (mp10) cc_final: 0.7636 (mp10) REVERT: A 294 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8083 (mmmm) REVERT: A 297 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7838 (ptpp) REVERT: A 357 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6638 (mm-40) REVERT: A 361 PHE cc_start: 0.7255 (m-80) cc_final: 0.6373 (m-80) REVERT: A 397 ARG cc_start: 0.7767 (ptp90) cc_final: 0.7422 (ptp90) REVERT: A 443 PHE cc_start: 0.8532 (t80) cc_final: 0.8075 (t80) REVERT: A 454 MET cc_start: 0.6494 (tpp) cc_final: 0.6008 (tpp) REVERT: A 510 LYS cc_start: 0.7039 (pttt) cc_final: 0.6747 (tttt) REVERT: A 558 LEU cc_start: 0.6905 (tp) cc_final: 0.6639 (mt) REVERT: E 23 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7237 (mp0) REVERT: E 35 TRP cc_start: 0.3517 (m-10) cc_final: 0.3141 (m-10) REVERT: E 48 HIS cc_start: 0.5175 (t-90) cc_final: 0.4719 (t-90) REVERT: C 28 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7789 (tptp) REVERT: C 33 ILE cc_start: 0.9006 (mm) cc_final: 0.8678 (tt) REVERT: C 45 GLN cc_start: 0.7730 (mt0) cc_final: 0.7480 (tt0) REVERT: C 55 GLU cc_start: 0.7429 (mp0) cc_final: 0.6998 (mp0) REVERT: C 62 TYR cc_start: 0.7970 (t80) cc_final: 0.7679 (t80) REVERT: C 68 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8358 (mptt) REVERT: C 71 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 72 LYS cc_start: 0.8464 (tttt) cc_final: 0.7966 (tptp) REVERT: C 83 GLU cc_start: 0.7746 (tp30) cc_final: 0.7399 (tp30) REVERT: C 153 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7263 (mmm-85) REVERT: C 163 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7712 (mm110) REVERT: C 167 ASP cc_start: 0.7575 (t0) cc_final: 0.7108 (t70) REVERT: C 168 MET cc_start: 0.7748 (ptp) cc_final: 0.7508 (ptp) REVERT: C 191 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7021 (tmm) REVERT: C 192 ILE cc_start: 0.8343 (mt) cc_final: 0.8069 (tp) REVERT: C 206 GLU cc_start: 0.6212 (mp0) cc_final: 0.5656 (mp0) REVERT: C 222 GLN cc_start: 0.7638 (tp40) cc_final: 0.6983 (tm-30) REVERT: C 238 GLU cc_start: 0.7345 (tp30) cc_final: 0.6467 (tm-30) REVERT: C 246 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 250 HIS cc_start: 0.7917 (t-90) cc_final: 0.7211 (t-90) REVERT: C 258 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6908 (mp0) REVERT: C 262 LYS cc_start: 0.8027 (tmtm) cc_final: 0.7354 (ttpp) REVERT: C 270 SER cc_start: 0.8535 (m) cc_final: 0.7979 (t) REVERT: C 274 LYS cc_start: 0.8415 (tppt) cc_final: 0.7855 (tppt) REVERT: C 282 SER cc_start: 0.7644 (m) cc_final: 0.7415 (m) REVERT: C 288 LEU cc_start: 0.8808 (tp) cc_final: 0.8595 (tp) REVERT: C 292 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8178 (mmtt) REVERT: C 301 LYS cc_start: 0.8369 (ptpt) cc_final: 0.8109 (ptpp) REVERT: C 306 VAL cc_start: 0.8742 (t) cc_final: 0.8349 (p) REVERT: C 314 CYS cc_start: 0.7486 (m) cc_final: 0.7188 (m) REVERT: C 346 LEU cc_start: 0.8302 (tp) cc_final: 0.8063 (tp) REVERT: C 353 ASP cc_start: 0.7809 (t0) cc_final: 0.7488 (t0) REVERT: C 368 GLN cc_start: 0.7287 (tm-30) cc_final: 0.6608 (tm-30) REVERT: C 369 THR cc_start: 0.8125 (p) cc_final: 0.7364 (t) REVERT: C 394 ASP cc_start: 0.7868 (t0) cc_final: 0.7476 (t0) REVERT: C 395 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8243 (mmmm) REVERT: C 409 GLU cc_start: 0.8229 (pt0) cc_final: 0.7913 (pp20) REVERT: C 412 LEU cc_start: 0.8667 (mt) cc_final: 0.8371 (mm) REVERT: C 413 ASP cc_start: 0.8482 (m-30) cc_final: 0.7870 (m-30) REVERT: C 418 LEU cc_start: 0.8766 (tt) cc_final: 0.8500 (tp) REVERT: C 423 GLN cc_start: 0.7607 (pm20) cc_final: 0.6846 (pt0) REVERT: C 424 GLU cc_start: 0.7473 (mp0) cc_final: 0.6683 (mp0) REVERT: C 431 TYR cc_start: 0.8209 (m-80) cc_final: 0.7401 (m-80) REVERT: C 473 MET cc_start: 0.7511 (mmt) cc_final: 0.6561 (tpp) REVERT: C 477 MET cc_start: 0.7773 (tmm) cc_final: 0.7408 (tmm) REVERT: C 554 MET cc_start: 0.6893 (tpp) cc_final: 0.6339 (tpp) REVERT: C 603 MET cc_start: 0.7834 (ptt) cc_final: 0.7407 (ptm) REVERT: C 692 ARG cc_start: 0.8558 (mmp80) cc_final: 0.8282 (mmp80) REVERT: B 19 GLU cc_start: 0.7435 (pp20) cc_final: 0.6959 (pp20) REVERT: B 24 PHE cc_start: 0.8487 (m-10) cc_final: 0.8169 (m-80) REVERT: B 29 LEU cc_start: 0.8130 (mp) cc_final: 0.7877 (mp) REVERT: B 46 LYS cc_start: 0.8630 (mttm) cc_final: 0.8364 (mttm) REVERT: B 61 MET cc_start: 0.6783 (tmm) cc_final: 0.6224 (tmm) REVERT: B 72 VAL cc_start: 0.8801 (m) cc_final: 0.8517 (p) REVERT: B 106 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7640 (pt0) REVERT: B 112 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7128 (mm-40) REVERT: B 114 GLU cc_start: 0.6609 (tm-30) cc_final: 0.6275 (mm-30) REVERT: B 123 TYR cc_start: 0.7718 (t80) cc_final: 0.7156 (t80) REVERT: B 149 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7568 (tptp) REVERT: B 154 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7430 (mtp85) REVERT: B 155 MET cc_start: 0.7975 (tpt) cc_final: 0.7502 (tpp) REVERT: B 166 GLN cc_start: 0.5466 (mp10) cc_final: 0.4819 (mp10) REVERT: B 170 MET cc_start: 0.7604 (mmm) cc_final: 0.7393 (mmm) REVERT: B 178 ILE cc_start: 0.7830 (tp) cc_final: 0.7479 (mm) REVERT: B 184 ASP cc_start: 0.7738 (t70) cc_final: 0.7079 (t0) REVERT: B 199 MET cc_start: 0.7626 (mmp) cc_final: 0.7327 (mmm) REVERT: B 203 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 209 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7647 (mmt90) REVERT: B 212 TYR cc_start: 0.7765 (m-10) cc_final: 0.7479 (m-80) REVERT: B 215 SER cc_start: 0.8294 (m) cc_final: 0.7938 (p) REVERT: B 242 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7753 (mmtt) REVERT: B 263 MET cc_start: 0.6979 (mpp) cc_final: 0.6294 (mtp) REVERT: B 301 PRO cc_start: 0.7447 (Cg_exo) cc_final: 0.7186 (Cg_endo) REVERT: B 307 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7721 (mmtm) REVERT: B 363 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8106 (mmtp) REVERT: B 381 TYR cc_start: 0.7458 (m-80) cc_final: 0.6906 (m-80) REVERT: B 383 TYR cc_start: 0.5532 (m-80) cc_final: 0.5122 (m-80) REVERT: B 429 ASP cc_start: 0.8188 (m-30) cc_final: 0.7123 (m-30) REVERT: B 430 CYS cc_start: 0.5260 (m) cc_final: 0.4552 (t) REVERT: B 502 TYR cc_start: 0.6571 (t80) cc_final: 0.6243 (t80) REVERT: B 503 ASP cc_start: 0.8076 (t0) cc_final: 0.7570 (t0) REVERT: B 583 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7641 (t) REVERT: F 28 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7495 (mmmm) REVERT: F 45 GLN cc_start: 0.7997 (tt0) cc_final: 0.7784 (tp-100) REVERT: F 53 SER cc_start: 0.8096 (t) cc_final: 0.7605 (t) REVERT: F 56 GLU cc_start: 0.7957 (mp0) cc_final: 0.7278 (mp0) REVERT: F 60 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7835 (m-40) REVERT: F 62 TYR cc_start: 0.7983 (t80) cc_final: 0.7087 (t80) REVERT: F 63 THR cc_start: 0.7532 (t) cc_final: 0.7289 (p) REVERT: F 64 MET cc_start: 0.7518 (tpt) cc_final: 0.6815 (tpp) REVERT: F 68 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8412 (mttm) REVERT: F 71 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6956 (tm-30) REVERT: F 78 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7981 (ttm-80) REVERT: F 79 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6610 (tp30) REVERT: F 92 ASP cc_start: 0.7278 (t0) cc_final: 0.7073 (t0) REVERT: F 103 GLN cc_start: 0.8503 (tp40) cc_final: 0.8028 (tp40) REVERT: F 113 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7374 (tp40) REVERT: F 116 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: F 117 VAL cc_start: 0.8351 (t) cc_final: 0.7936 (p) REVERT: F 124 MET cc_start: 0.4283 (tmm) cc_final: 0.3552 (tmm) REVERT: F 140 TYR cc_start: 0.7936 (t80) cc_final: 0.7035 (t80) REVERT: F 145 ILE cc_start: 0.8814 (mt) cc_final: 0.8570 (mm) REVERT: F 153 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7472 (mmt180) REVERT: F 154 TYR cc_start: 0.7106 (t80) cc_final: 0.5817 (t80) REVERT: F 158 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7263 (ttm-80) REVERT: F 163 GLN cc_start: 0.7325 (mm-40) cc_final: 0.6997 (mm110) REVERT: F 167 ASP cc_start: 0.7346 (t0) cc_final: 0.7009 (t0) REVERT: F 191 MET cc_start: 0.6843 (tmm) cc_final: 0.6456 (tpp) REVERT: F 235 LYS cc_start: 0.8297 (mmtp) cc_final: 0.7872 (mppt) REVERT: F 238 GLU cc_start: 0.8174 (tp30) cc_final: 0.7440 (tp30) REVERT: F 240 ARG cc_start: 0.7981 (mmt180) cc_final: 0.7752 (tpp80) REVERT: F 243 GLU cc_start: 0.7652 (pp20) cc_final: 0.7422 (pp20) REVERT: F 249 MET cc_start: 0.7509 (ppp) cc_final: 0.7077 (ppp) REVERT: F 265 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7214 (mm-30) REVERT: F 270 SER cc_start: 0.8572 (m) cc_final: 0.7965 (t) REVERT: F 295 ASP cc_start: 0.7303 (m-30) cc_final: 0.6769 (m-30) REVERT: F 301 LYS cc_start: 0.8329 (ptpt) cc_final: 0.8090 (ptpp) REVERT: F 322 ARG cc_start: 0.8161 (mmt90) cc_final: 0.7792 (mmt180) REVERT: F 332 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: F 346 LEU cc_start: 0.7704 (tp) cc_final: 0.7410 (pp) REVERT: F 360 PHE cc_start: 0.7954 (m-80) cc_final: 0.7545 (m-80) REVERT: F 378 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4462 (mt) REVERT: F 414 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8661 (mmtm) REVERT: F 423 GLN cc_start: 0.8031 (tt0) cc_final: 0.7715 (pt0) REVERT: F 489 GLN cc_start: 0.8041 (mt0) cc_final: 0.7675 (tp-100) REVERT: F 554 MET cc_start: 0.6404 (mmm) cc_final: 0.5735 (tpp) REVERT: F 671 ARG cc_start: 0.6177 (tpt-90) cc_final: 0.5862 (tpt-90) REVERT: F 673 LYS cc_start: 0.8057 (ptmm) cc_final: 0.7834 (pptt) REVERT: D 42 CYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5864 (m) REVERT: D 55 GLU cc_start: 0.4189 (mm-30) cc_final: 0.3895 (mp0) outliers start: 89 outliers final: 66 residues processed: 732 average time/residue: 0.3785 time to fit residues: 408.5474 Evaluate side-chains 757 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 680 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.5980 chunk 229 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 198 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 chunk 90 optimal weight: 0.0670 chunk 221 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.167931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.141559 restraints weight = 48997.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.145977 restraints weight = 26276.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.148877 restraints weight = 16069.601| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22731 Z= 0.230 Angle : 0.822 12.876 30684 Z= 0.411 Chirality : 0.046 0.311 3385 Planarity : 0.005 0.079 3934 Dihedral : 4.752 29.217 3006 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.83 % Favored : 91.10 % Rotamer: Outliers : 3.48 % Allowed : 27.64 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2718 helix: 0.55 (0.14), residues: 1260 sheet: -0.99 (0.31), residues: 270 loop : -2.43 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.003 TRP C 513 HIS 0.024 0.001 HIS F 490 PHE 0.029 0.002 PHE B 537 TYR 0.028 0.002 TYR A 164 ARG 0.015 0.001 ARG F 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7049.97 seconds wall clock time: 124 minutes 34.84 seconds (7474.84 seconds total)