Starting phenix.real_space_refine on Thu May 22 03:46:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gq6_34199/05_2025/8gq6_34199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gq6_34199/05_2025/8gq6_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/cci-nas-00/data/ceres_data/8gq6_34199/05_2025/8gq6_34199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gq6_34199/05_2025/8gq6_34199.map" model { file = "/net/cci-nas-00/data/ceres_data/8gq6_34199/05_2025/8gq6_34199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gq6_34199/05_2025/8gq6_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-5687/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: 12.16, per 1000 atoms: 0.55 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: 5.21 Conformation dependent library (CDL) restraints added in 2.9 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: 2.67 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: 8.06 Time building geometry restraints manager: 5.98 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: 4.150 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 52.420 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.970 ------------------------------------------------------------------------------- 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 22753 Z= 0.131 Angle : 0.539 10.746 30696 Z= 0.313 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 Details of bonding type rmsd hydrogen bonds : bond 0.16614 ( 1102) hydrogen bonds : angle 6.08964 ( 3228) metal coordination : bond 0.00887 ( 22) metal coordination : angle 3.79914 ( 12) covalent geometry : bond 0.00210 (22731) covalent geometry : angle 0.53432 (30684) *********************** 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 to be fit. rotamer outliers: 8 poor density : 867 time to evaluate : 2.486 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: 0.3920 time to fit residues: 497.5561 Evaluate side-chains 725 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 723 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.169872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.143351 restraints weight = 50072.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.147847 restraints weight = 26712.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.150729 restraints weight = 16149.341| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 22753 Z= 0.194 Angle : 0.674 10.189 30696 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 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 1102) hydrogen bonds : angle 5.07970 ( 3228) metal coordination : bond 0.01146 ( 22) metal coordination : angle 5.04226 ( 12) covalent geometry : bond 0.00397 (22731) covalent geometry : angle 0.66718 (30684) *********************** 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 to be fit. rotamer outliers: 91 poor density : 771 time to evaluate : 2.362 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: 0.7973 (mt-10) cc_final: 0.7599 (pp20) REVERT: A 20 GLN cc_start: 0.8773 (mm-40) cc_final: 0.7935 (mm110) REVERT: A 22 LYS cc_start: 0.8580 (ttmt) cc_final: 0.7769 (ttmt) REVERT: A 26 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 34 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8583 (m) REVERT: A 42 PHE cc_start: 0.8902 (m-80) cc_final: 0.8595 (m-80) REVERT: A 59 MET cc_start: 0.7730 (ttt) cc_final: 0.7366 (ttt) REVERT: A 60 PHE cc_start: 0.8499 (m-80) cc_final: 0.7751 (m-10) REVERT: A 66 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7221 (pt0) REVERT: A 68 LYS cc_start: 0.8619 (tptp) cc_final: 0.8156 (tptp) REVERT: A 75 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7593 (ptp-170) REVERT: A 83 GLN cc_start: 0.8477 (tp40) cc_final: 0.8228 (tp40) REVERT: A 84 ILE cc_start: 0.8640 (tp) cc_final: 0.8313 (tt) REVERT: A 87 THR cc_start: 0.8500 (t) cc_final: 0.8008 (p) REVERT: A 90 TYR cc_start: 0.7842 (m-80) cc_final: 0.7352 (m-80) REVERT: A 112 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7759 (mm-40) REVERT: A 117 LEU cc_start: 0.8283 (mt) cc_final: 0.7950 (tt) REVERT: A 121 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8279 (ttp80) REVERT: A 122 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 127 LYS cc_start: 0.8485 (tppt) cc_final: 0.8134 (mmmm) REVERT: A 159 LYS cc_start: 0.7567 (mtmt) cc_final: 0.7060 (mtmm) REVERT: A 165 HIS cc_start: 0.6525 (m90) cc_final: 0.6218 (m90) REVERT: A 170 MET cc_start: 0.6899 (mmp) cc_final: 0.6489 (mmp) REVERT: A 191 GLU cc_start: 0.7470 (pp20) cc_final: 0.7059 (tm-30) REVERT: A 196 GLU cc_start: 0.7659 (pp20) cc_final: 0.7210 (pp20) REVERT: A 225 LEU cc_start: 0.5413 (mt) cc_final: 0.5125 (mt) REVERT: A 267 GLU cc_start: 0.7525 (tp30) cc_final: 0.7128 (tp30) REVERT: A 269 MET cc_start: 0.6822 (mmp) cc_final: 0.6242 (mmp) REVERT: A 288 TYR cc_start: 0.7362 (t80) cc_final: 0.6963 (t80) REVERT: A 293 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 294 LYS cc_start: 0.8325 (mmmm) cc_final: 0.7895 (mmmm) REVERT: A 296 TYR cc_start: 0.7038 (m-80) cc_final: 0.6568 (m-80) REVERT: A 297 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7931 (ptpt) REVERT: A 301 PRO cc_start: 0.7444 (Cg_exo) cc_final: 0.7201 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8281 (p) cc_final: 0.7876 (t) REVERT: A 352 TRP cc_start: 0.7919 (t60) cc_final: 0.7582 (t60) REVERT: A 353 PHE cc_start: 0.8058 (t80) cc_final: 0.7499 (t80) REVERT: A 354 ASP cc_start: 0.6542 (t0) cc_final: 0.5306 (t70) REVERT: A 361 PHE cc_start: 0.7264 (m-80) cc_final: 0.6455 (m-80) REVERT: A 366 MET cc_start: 0.7375 (mtp) cc_final: 0.7138 (mtp) REVERT: A 408 GLU cc_start: 0.7473 (pm20) cc_final: 0.6884 (pm20) REVERT: A 443 PHE cc_start: 0.8530 (t80) cc_final: 0.8214 (t80) REVERT: A 511 MET cc_start: 0.6524 (tpt) cc_final: 0.6193 (tpp) REVERT: E 23 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6547 (mp0) REVERT: E 25 LYS cc_start: 0.5409 (mmpt) cc_final: 0.5182 (mmpt) REVERT: E 48 HIS cc_start: 0.5048 (t-90) cc_final: 0.4611 (t-90) REVERT: C 28 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7611 (tptp) REVERT: C 33 ILE cc_start: 0.8958 (mm) cc_final: 0.8615 (tt) REVERT: C 43 GLU cc_start: 0.7488 (tp30) cc_final: 0.6619 (tp30) REVERT: C 48 ASN cc_start: 0.8164 (t0) cc_final: 0.7093 (t0) REVERT: C 62 TYR cc_start: 0.8017 (t80) cc_final: 0.7566 (t80) REVERT: C 68 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8346 (mptt) REVERT: C 71 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 72 LYS cc_start: 0.8432 (tttt) cc_final: 0.7797 (tptm) REVERT: C 83 GLU cc_start: 0.7630 (tp30) cc_final: 0.7142 (tp30) REVERT: C 86 ILE cc_start: 0.7936 (mt) cc_final: 0.7723 (mm) REVERT: C 91 GLU cc_start: 0.7368 (tp30) cc_final: 0.7063 (mm-30) REVERT: C 125 TYR cc_start: 0.4591 (t80) cc_final: 0.4314 (t80) REVERT: C 153 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7620 (mmm160) REVERT: C 163 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7679 (mm110) REVERT: C 188 GLN cc_start: 0.7860 (tp40) cc_final: 0.7645 (tp40) REVERT: C 204 ASP cc_start: 0.7242 (t0) cc_final: 0.6908 (t0) REVERT: C 206 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6574 (mp0) REVERT: C 215 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: C 217 PHE cc_start: 0.7940 (m-80) cc_final: 0.7540 (m-10) REVERT: C 220 GLU cc_start: 0.7426 (tp30) cc_final: 0.6927 (tp30) REVERT: C 222 GLN cc_start: 0.7763 (tp40) cc_final: 0.7375 (tm-30) REVERT: C 224 PHE cc_start: 0.7048 (m-80) cc_final: 0.5765 (m-80) REVERT: C 235 LYS cc_start: 0.8427 (mmmt) cc_final: 0.7918 (mtmm) REVERT: C 238 GLU cc_start: 0.7441 (tp30) cc_final: 0.6739 (tm-30) REVERT: C 243 GLU cc_start: 0.8316 (pt0) cc_final: 0.7519 (pp20) REVERT: C 246 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 250 HIS cc_start: 0.7895 (t-90) cc_final: 0.7224 (t-90) REVERT: C 258 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7021 (mm-30) REVERT: C 262 LYS cc_start: 0.7906 (tmtm) cc_final: 0.7356 (ttpp) REVERT: C 282 SER cc_start: 0.7570 (OUTLIER) cc_final: 0.6951 (p) REVERT: C 292 LYS cc_start: 0.8575 (mmmm) cc_final: 0.7915 (mmtm) REVERT: C 301 LYS cc_start: 0.8391 (ptpt) cc_final: 0.8098 (ptpt) REVERT: C 306 VAL cc_start: 0.8584 (t) cc_final: 0.8208 (p) REVERT: C 321 LEU cc_start: 0.8585 (mt) cc_final: 0.8349 (mt) REVERT: C 346 LEU cc_start: 0.8126 (tp) cc_final: 0.7849 (tp) REVERT: C 353 ASP cc_start: 0.7919 (t0) cc_final: 0.7668 (t0) REVERT: C 360 PHE cc_start: 0.8240 (m-10) cc_final: 0.7788 (m-10) REVERT: C 368 GLN cc_start: 0.7349 (tm-30) cc_final: 0.6718 (tm-30) REVERT: C 369 THR cc_start: 0.8145 (p) cc_final: 0.7663 (t) REVERT: C 394 ASP cc_start: 0.7981 (t0) cc_final: 0.7636 (t0) REVERT: C 395 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8592 (mmmt) REVERT: C 409 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7277 (pt0) REVERT: C 412 LEU cc_start: 0.8702 (mt) cc_final: 0.8147 (pp) REVERT: C 413 ASP cc_start: 0.8323 (m-30) cc_final: 0.7603 (m-30) REVERT: C 418 LEU cc_start: 0.8748 (tt) cc_final: 0.8413 (tp) REVERT: C 424 GLU cc_start: 0.7339 (mp0) cc_final: 0.6976 (mp0) REVERT: C 429 GLU cc_start: 0.7959 (tp30) cc_final: 0.7756 (tp30) REVERT: C 431 TYR cc_start: 0.8023 (m-80) cc_final: 0.7218 (m-10) REVERT: C 438 ARG cc_start: 0.7855 (tpm170) cc_final: 0.7192 (tpm170) REVERT: C 441 LEU cc_start: 0.8223 (mt) cc_final: 0.7929 (mt) REVERT: C 457 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8693 (mmmt) REVERT: C 479 ILE cc_start: 0.7706 (mm) cc_final: 0.7414 (mt) REVERT: C 554 MET cc_start: 0.6615 (tpp) cc_final: 0.6217 (tpp) REVERT: C 603 MET cc_start: 0.7264 (tmm) cc_final: 0.6855 (tmm) REVERT: C 692 ARG cc_start: 0.8481 (tpp-160) cc_final: 0.8233 (mmp80) REVERT: B 19 GLU cc_start: 0.7645 (pp20) cc_final: 0.7025 (pp20) REVERT: B 20 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8327 (mm-40) REVERT: B 24 PHE cc_start: 0.8557 (m-10) cc_final: 0.8228 (m-80) REVERT: B 25 TYR cc_start: 0.8700 (t80) cc_final: 0.8422 (t80) REVERT: B 29 LEU cc_start: 0.8305 (mp) cc_final: 0.8046 (mp) REVERT: B 32 ASP cc_start: 0.8042 (p0) cc_final: 0.7703 (p0) REVERT: B 45 HIS cc_start: 0.8289 (m90) cc_final: 0.7975 (m170) REVERT: B 46 LYS cc_start: 0.8733 (mttt) cc_final: 0.8398 (mtpp) REVERT: B 60 PHE cc_start: 0.8566 (m-10) cc_final: 0.8351 (m-10) REVERT: B 61 MET cc_start: 0.7115 (tmm) cc_final: 0.6701 (tmm) REVERT: B 69 GLN cc_start: 0.7900 (tt0) cc_final: 0.7685 (tt0) REVERT: B 72 VAL cc_start: 0.8740 (m) cc_final: 0.8389 (p) REVERT: B 75 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7503 (ptp-110) REVERT: B 85 ILE cc_start: 0.8690 (mt) cc_final: 0.8412 (tp) REVERT: B 86 ILE cc_start: 0.8524 (mt) cc_final: 0.8313 (mm) REVERT: B 103 GLN cc_start: 0.7564 (pm20) cc_final: 0.7032 (pm20) REVERT: B 105 TYR cc_start: 0.8057 (t80) cc_final: 0.7664 (t80) REVERT: B 106 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 112 GLN cc_start: 0.7613 (mm-40) cc_final: 0.6079 (mm110) REVERT: B 114 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6253 (mm-30) REVERT: B 123 TYR cc_start: 0.7567 (t80) cc_final: 0.6875 (t80) REVERT: B 127 LYS cc_start: 0.7973 (tptt) cc_final: 0.7674 (tptt) REVERT: B 132 ASN cc_start: 0.7846 (p0) cc_final: 0.7436 (p0) REVERT: B 136 LEU cc_start: 0.8279 (mt) cc_final: 0.7936 (mm) REVERT: B 149 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7794 (tptp) REVERT: B 155 MET cc_start: 0.7960 (tpt) cc_final: 0.7213 (tpp) REVERT: B 166 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7267 (mp10) REVERT: B 167 ASP cc_start: 0.7519 (p0) cc_final: 0.7092 (p0) REVERT: B 170 MET cc_start: 0.7921 (mmm) cc_final: 0.7645 (mmm) REVERT: B 184 ASP cc_start: 0.8038 (t70) cc_final: 0.7514 (t0) REVERT: B 195 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7382 (ttt180) REVERT: B 199 MET cc_start: 0.7661 (mmp) cc_final: 0.7389 (mmp) REVERT: B 203 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7147 (mm-30) REVERT: B 212 TYR cc_start: 0.7961 (m-10) cc_final: 0.7574 (m-80) REVERT: B 242 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7879 (mmtt) REVERT: B 267 GLU cc_start: 0.6981 (tp30) cc_final: 0.6627 (tp30) REVERT: B 269 MET cc_start: 0.5607 (mmp) cc_final: 0.5148 (mmp) REVERT: B 290 PRO cc_start: 0.8383 (Cg_exo) cc_final: 0.7963 (Cg_endo) REVERT: B 307 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8304 (mmtm) REVERT: B 363 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8224 (mmtp) REVERT: B 381 TYR cc_start: 0.7758 (m-80) cc_final: 0.6916 (m-80) REVERT: B 383 TYR cc_start: 0.5720 (m-80) cc_final: 0.5127 (m-80) REVERT: B 429 ASP cc_start: 0.7935 (m-30) cc_final: 0.7355 (m-30) REVERT: B 430 CYS cc_start: 0.5620 (m) cc_final: 0.5258 (t) REVERT: B 436 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6319 (tt) REVERT: B 443 PHE cc_start: 0.7516 (t80) cc_final: 0.7315 (t80) REVERT: B 469 ASP cc_start: 0.7378 (t70) cc_final: 0.6584 (t0) REVERT: B 470 LYS cc_start: 0.7065 (mttm) cc_final: 0.6567 (mtpp) REVERT: B 502 TYR cc_start: 0.6749 (t80) cc_final: 0.6129 (t80) REVERT: B 507 ASN cc_start: 0.8218 (t0) cc_final: 0.7773 (t0) REVERT: B 529 VAL cc_start: 0.6152 (t) cc_final: 0.5360 (m) REVERT: B 553 GLN cc_start: 0.6264 (tt0) cc_final: 0.6026 (tm-30) REVERT: F 28 LYS cc_start: 0.7778 (mmmm) cc_final: 0.7447 (mmmm) REVERT: F 30 VAL cc_start: 0.7178 (m) cc_final: 0.6937 (p) REVERT: F 35 ASP cc_start: 0.7472 (t0) cc_final: 0.7177 (t70) REVERT: F 62 TYR cc_start: 0.8045 (t80) cc_final: 0.7691 (t80) REVERT: F 64 MET cc_start: 0.7463 (tpt) cc_final: 0.7105 (tpt) REVERT: F 66 LEU cc_start: 0.7524 (tp) cc_final: 0.7247 (tp) REVERT: F 68 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8392 (mttm) REVERT: F 78 ARG cc_start: 0.8280 (ttm170) cc_final: 0.8029 (ttm-80) REVERT: F 79 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6844 (tp30) REVERT: F 113 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7659 (tp40) REVERT: F 126 MET cc_start: 0.8209 (tmt) cc_final: 0.7799 (tmm) REVERT: F 128 ARG cc_start: 0.6473 (mtm-85) cc_final: 0.5309 (mtm-85) REVERT: F 139 VAL cc_start: 0.7407 (m) cc_final: 0.6713 (t) REVERT: F 140 TYR cc_start: 0.7964 (t80) cc_final: 0.6969 (t80) REVERT: F 145 ILE cc_start: 0.8756 (mt) cc_final: 0.8524 (mm) REVERT: F 153 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7433 (mtt180) REVERT: F 160 HIS cc_start: 0.8146 (t-90) cc_final: 0.7877 (t-90) REVERT: F 167 ASP cc_start: 0.7040 (t0) cc_final: 0.6688 (t0) REVERT: F 168 MET cc_start: 0.7251 (ptp) cc_final: 0.6721 (ptp) REVERT: F 208 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8282 (Cg_endo) REVERT: F 216 PHE cc_start: 0.7512 (t80) cc_final: 0.7154 (t80) REVERT: F 233 TYR cc_start: 0.7573 (t80) cc_final: 0.7156 (t80) REVERT: F 235 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8402 (mmmt) REVERT: F 240 ARG cc_start: 0.7977 (mmt180) cc_final: 0.7637 (tpp80) REVERT: F 241 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8537 (tp) REVERT: F 243 GLU cc_start: 0.7637 (pp20) cc_final: 0.7148 (pp20) REVERT: F 246 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7322 (tp30) REVERT: F 249 MET cc_start: 0.7843 (ppp) cc_final: 0.7414 (ppp) REVERT: F 258 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7818 (mm-30) REVERT: F 265 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7196 (mm-30) REVERT: F 270 SER cc_start: 0.8496 (m) cc_final: 0.8046 (t) REVERT: F 274 LYS cc_start: 0.8119 (tppt) cc_final: 0.7505 (tmmt) REVERT: F 287 MET cc_start: 0.7835 (ptm) cc_final: 0.7420 (ppp) REVERT: F 295 ASP cc_start: 0.7376 (m-30) cc_final: 0.6839 (m-30) REVERT: F 301 LYS cc_start: 0.8367 (ptpt) cc_final: 0.8136 (ttpp) REVERT: F 303 PHE cc_start: 0.7919 (m-80) cc_final: 0.7298 (m-80) REVERT: F 311 LYS cc_start: 0.7871 (tmmt) cc_final: 0.7457 (ttmm) REVERT: F 319 SER cc_start: 0.8635 (t) cc_final: 0.8132 (p) REVERT: F 322 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7774 (mmt-90) REVERT: F 323 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7588 (tm-30) REVERT: F 332 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: F 414 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8661 (mmtm) REVERT: F 423 GLN cc_start: 0.8031 (tt0) cc_final: 0.7611 (tt0) REVERT: F 457 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8003 (mmtt) REVERT: F 461 GLU cc_start: 0.6600 (tp30) cc_final: 0.5914 (tp30) REVERT: F 484 MET cc_start: 0.3096 (mtp) cc_final: 0.2893 (mtp) REVERT: F 489 GLN cc_start: 0.7964 (mt0) cc_final: 0.7715 (tp-100) REVERT: F 490 HIS cc_start: 0.6821 (m90) cc_final: 0.6510 (m-70) REVERT: F 506 ARG cc_start: 0.5653 (mtm-85) cc_final: 0.5376 (mtm-85) REVERT: F 539 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: F 673 LYS cc_start: 0.7982 (ptmm) cc_final: 0.7723 (pptt) REVERT: F 725 GLU cc_start: 0.8115 (tt0) cc_final: 0.7857 (mt-10) REVERT: D 98 ASN cc_start: 0.7120 (p0) cc_final: 0.6901 (p0) outliers start: 91 outliers final: 39 residues processed: 826 average time/residue: 0.3852 time to fit residues: 468.4406 Evaluate side-chains 758 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 711 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 183 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 60 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN F 729 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.165436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.139452 restraints weight = 49452.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.143723 restraints weight = 26646.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.146475 restraints weight = 16271.957| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.937 22753 Z= 0.489 Angle : 0.727 11.086 30696 Z= 0.380 Chirality : 0.045 0.219 3385 Planarity : 0.005 0.063 3934 Dihedral : 4.721 31.993 3008 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.50 % Favored : 91.43 % Rotamer: Outliers : 4.41 % Allowed : 20.07 % Favored : 75.52 % 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: -1.18 (0.16), residues: 2718 helix: 0.72 (0.15), residues: 1273 sheet: -1.04 (0.30), residues: 274 loop : -2.51 (0.16), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 233 HIS 0.010 0.002 HIS B 158 PHE 0.028 0.002 PHE B 56 TYR 0.022 0.002 TYR C 432 ARG 0.007 0.001 ARG F 266 Details of bonding type rmsd hydrogen bonds : bond 0.05140 ( 1102) hydrogen bonds : angle 5.11074 ( 3228) metal coordination : bond 0.41322 ( 22) metal coordination : angle 5.15763 ( 12) covalent geometry : bond 0.00473 (22731) covalent geometry : angle 0.72040 (30684) *********************** 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 863 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 754 time to evaluate : 2.668 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: A 9 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7810 (pt) REVERT: A 19 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7642 (pp20) REVERT: A 20 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8061 (mm110) REVERT: A 22 LYS cc_start: 0.8614 (ttmt) cc_final: 0.7844 (ttmt) REVERT: A 26 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 34 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8654 (p) REVERT: A 42 PHE cc_start: 0.8927 (m-80) cc_final: 0.8651 (m-80) REVERT: A 57 ARG cc_start: 0.8281 (ptm160) cc_final: 0.7833 (ttp80) REVERT: A 59 MET cc_start: 0.7707 (ttt) cc_final: 0.7344 (ttt) REVERT: A 60 PHE cc_start: 0.8530 (m-80) cc_final: 0.7744 (m-10) REVERT: A 66 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7133 (pt0) REVERT: A 68 LYS cc_start: 0.8569 (tptp) cc_final: 0.8120 (tptp) REVERT: A 84 ILE cc_start: 0.8727 (tp) cc_final: 0.8352 (tt) REVERT: A 87 THR cc_start: 0.8574 (t) cc_final: 0.8165 (p) REVERT: A 88 TYR cc_start: 0.8555 (t80) cc_final: 0.7842 (t80) REVERT: A 90 TYR cc_start: 0.8078 (m-80) cc_final: 0.7385 (m-80) REVERT: A 106 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 109 CYS cc_start: 0.8232 (t) cc_final: 0.6860 (t) REVERT: A 112 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7947 (tp40) REVERT: A 115 ASP cc_start: 0.8105 (p0) cc_final: 0.7445 (p0) REVERT: A 117 LEU cc_start: 0.8363 (mt) cc_final: 0.7976 (tt) REVERT: A 118 GLN cc_start: 0.8279 (tt0) cc_final: 0.7837 (tt0) REVERT: A 122 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7596 (mm-30) REVERT: A 147 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 155 MET cc_start: 0.7422 (tpp) cc_final: 0.7122 (tpp) REVERT: A 157 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 159 LYS cc_start: 0.7749 (mtmt) cc_final: 0.6975 (mtmm) REVERT: A 170 MET cc_start: 0.7018 (mmp) cc_final: 0.6657 (mmp) REVERT: A 191 GLU cc_start: 0.7483 (pp20) cc_final: 0.7091 (tm-30) REVERT: A 195 ARG cc_start: 0.8332 (tmm160) cc_final: 0.8094 (ttm170) REVERT: A 196 GLU cc_start: 0.7846 (pp20) cc_final: 0.7310 (pp20) REVERT: A 199 MET cc_start: 0.7924 (mmm) cc_final: 0.7571 (mmp) REVERT: A 209 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7435 (mtm180) REVERT: A 211 GLN cc_start: 0.7740 (pm20) cc_final: 0.7393 (pm20) REVERT: A 228 VAL cc_start: 0.5365 (OUTLIER) cc_final: 0.5133 (p) REVERT: A 267 GLU cc_start: 0.7405 (tp30) cc_final: 0.7177 (tp30) REVERT: A 268 MET cc_start: 0.7359 (mtt) cc_final: 0.5696 (mtt) REVERT: A 294 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8158 (mmmm) REVERT: A 297 LYS cc_start: 0.8270 (ptpt) cc_final: 0.8023 (ptpt) REVERT: A 301 PRO cc_start: 0.7440 (Cg_exo) cc_final: 0.7188 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8329 (p) cc_final: 0.7930 (t) REVERT: A 352 TRP cc_start: 0.8101 (t60) cc_final: 0.7634 (t60) REVERT: A 353 PHE cc_start: 0.7947 (t80) cc_final: 0.7587 (t80) REVERT: A 358 ASN cc_start: 0.8220 (t0) cc_final: 0.8004 (t0) REVERT: A 361 PHE cc_start: 0.7218 (m-80) cc_final: 0.6254 (m-80) REVERT: A 382 ILE cc_start: 0.7223 (mm) cc_final: 0.6869 (pt) REVERT: A 383 TYR cc_start: 0.5972 (m-80) cc_final: 0.5497 (m-80) REVERT: A 439 MET cc_start: 0.5599 (ptt) cc_final: 0.5275 (ptt) REVERT: A 443 PHE cc_start: 0.8506 (t80) cc_final: 0.8193 (t80) REVERT: A 454 MET cc_start: 0.7098 (tpp) cc_final: 0.6757 (tpp) REVERT: A 502 TYR cc_start: 0.5866 (t80) cc_final: 0.4163 (t80) REVERT: A 558 LEU cc_start: 0.7020 (tp) cc_final: 0.6585 (mt) REVERT: E 23 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6979 (mp0) REVERT: C 28 LYS cc_start: 0.8160 (mmmm) cc_final: 0.7750 (tptp) REVERT: C 33 ILE cc_start: 0.9041 (mm) cc_final: 0.8715 (mm) REVERT: C 43 GLU cc_start: 0.7486 (tp30) cc_final: 0.6517 (tp30) REVERT: C 45 GLN cc_start: 0.7834 (mt0) cc_final: 0.7533 (tt0) REVERT: C 48 ASN cc_start: 0.8129 (t0) cc_final: 0.7314 (t0) REVERT: C 56 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6893 (mm-30) REVERT: C 62 TYR cc_start: 0.8091 (t80) cc_final: 0.7577 (t80) REVERT: C 64 MET cc_start: 0.7537 (tpt) cc_final: 0.7286 (tpp) REVERT: C 68 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8162 (mptt) REVERT: C 71 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 72 LYS cc_start: 0.8496 (tttt) cc_final: 0.8115 (tptm) REVERT: C 83 GLU cc_start: 0.7776 (tp30) cc_final: 0.7113 (tp30) REVERT: C 124 MET cc_start: 0.3079 (tmm) cc_final: 0.2804 (tmm) REVERT: C 125 TYR cc_start: 0.4887 (t80) cc_final: 0.4646 (t80) REVERT: C 126 MET cc_start: 0.8100 (tmm) cc_final: 0.7894 (tmm) REVERT: C 153 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7479 (mmm-85) REVERT: C 163 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7895 (mm110) REVERT: C 188 GLN cc_start: 0.8150 (tp40) cc_final: 0.7725 (tp40) REVERT: C 204 ASP cc_start: 0.7328 (t0) cc_final: 0.7045 (t0) REVERT: C 206 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6201 (mp0) REVERT: C 215 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: C 220 GLU cc_start: 0.7425 (tp30) cc_final: 0.6968 (tp30) REVERT: C 222 GLN cc_start: 0.7544 (tp40) cc_final: 0.7217 (tm-30) REVERT: C 224 PHE cc_start: 0.6914 (m-80) cc_final: 0.6299 (m-10) REVERT: C 235 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8098 (mtmm) REVERT: C 238 GLU cc_start: 0.7478 (tp30) cc_final: 0.6887 (tm-30) REVERT: C 246 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7531 (tm-30) REVERT: C 247 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7938 (ttm170) REVERT: C 248 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8055 (p) REVERT: C 250 HIS cc_start: 0.7870 (t-90) cc_final: 0.7262 (t-90) REVERT: C 258 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7246 (mm-30) REVERT: C 259 PRO cc_start: 0.8245 (Cg_exo) cc_final: 0.8040 (Cg_endo) REVERT: C 262 LYS cc_start: 0.8117 (tmtm) cc_final: 0.7435 (ttpp) REVERT: C 265 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7264 (mm-30) REVERT: C 274 LYS cc_start: 0.8333 (tppt) cc_final: 0.8069 (tppt) REVERT: C 282 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7661 (t) REVERT: C 288 LEU cc_start: 0.9097 (tp) cc_final: 0.8642 (tp) REVERT: C 292 LYS cc_start: 0.8426 (mmmm) cc_final: 0.7948 (mmtm) REVERT: C 299 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7514 (ttm) REVERT: C 301 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8122 (ptpp) REVERT: C 306 VAL cc_start: 0.8625 (t) cc_final: 0.8284 (p) REVERT: C 315 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7261 (mm-30) REVERT: C 346 LEU cc_start: 0.8267 (tp) cc_final: 0.8035 (tp) REVERT: C 353 ASP cc_start: 0.8058 (t0) cc_final: 0.7765 (t0) REVERT: C 354 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7741 (ttp-110) REVERT: C 368 GLN cc_start: 0.7446 (tm-30) cc_final: 0.6746 (tm-30) REVERT: C 369 THR cc_start: 0.8122 (p) cc_final: 0.7809 (t) REVERT: C 373 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.6069 (t0) REVERT: C 383 ARG cc_start: 0.7373 (ptp-170) cc_final: 0.7149 (ptp90) REVERT: C 394 ASP cc_start: 0.7960 (t0) cc_final: 0.7634 (t0) REVERT: C 395 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8292 (mmmm) REVERT: C 409 GLU cc_start: 0.7995 (mt-10) cc_final: 0.6964 (mm-30) REVERT: C 412 LEU cc_start: 0.8766 (mt) cc_final: 0.8360 (pp) REVERT: C 413 ASP cc_start: 0.8442 (m-30) cc_final: 0.8191 (m-30) REVERT: C 418 LEU cc_start: 0.8798 (tt) cc_final: 0.8519 (tp) REVERT: C 423 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6552 (pt0) REVERT: C 424 GLU cc_start: 0.7337 (mp0) cc_final: 0.6526 (mp0) REVERT: C 431 TYR cc_start: 0.8237 (m-80) cc_final: 0.7649 (m-80) REVERT: C 438 ARG cc_start: 0.7887 (tpm170) cc_final: 0.7389 (tpm170) REVERT: C 441 LEU cc_start: 0.8363 (mt) cc_final: 0.8096 (mt) REVERT: C 454 MET cc_start: 0.8117 (tmm) cc_final: 0.7814 (tmm) REVERT: C 457 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8755 (mmtp) REVERT: C 473 MET cc_start: 0.7902 (mmt) cc_final: 0.6986 (mmt) REVERT: C 554 MET cc_start: 0.6557 (tpp) cc_final: 0.6224 (tpp) REVERT: C 603 MET cc_start: 0.7358 (tmm) cc_final: 0.6866 (tmm) REVERT: C 685 ASP cc_start: 0.8035 (t0) cc_final: 0.7775 (t0) REVERT: C 687 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6237 (pt0) REVERT: C 692 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.8192 (mmp80) REVERT: B 19 GLU cc_start: 0.7697 (pp20) cc_final: 0.7088 (pp20) REVERT: B 20 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8355 (mm-40) REVERT: B 24 PHE cc_start: 0.8487 (m-10) cc_final: 0.8200 (m-80) REVERT: B 29 LEU cc_start: 0.8368 (mp) cc_final: 0.8008 (mp) REVERT: B 32 ASP cc_start: 0.8032 (p0) cc_final: 0.7573 (p0) REVERT: B 46 LYS cc_start: 0.8778 (mttt) cc_final: 0.8540 (mttm) REVERT: B 55 TYR cc_start: 0.8559 (t80) cc_final: 0.7361 (t80) REVERT: B 57 ARG cc_start: 0.8566 (ptm160) cc_final: 0.8261 (ttm110) REVERT: B 61 MET cc_start: 0.7148 (tmm) cc_final: 0.6669 (tmm) REVERT: B 69 GLN cc_start: 0.7889 (tt0) cc_final: 0.7606 (tt0) REVERT: B 72 VAL cc_start: 0.8909 (m) cc_final: 0.8481 (p) REVERT: B 75 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7514 (ptp-110) REVERT: B 76 ASN cc_start: 0.8754 (m-40) cc_final: 0.8551 (m-40) REVERT: B 85 ILE cc_start: 0.8724 (mt) cc_final: 0.8427 (tp) REVERT: B 103 GLN cc_start: 0.7610 (pm20) cc_final: 0.7216 (pm20) REVERT: B 106 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 112 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7521 (mm110) REVERT: B 118 GLN cc_start: 0.8306 (tp-100) cc_final: 0.8004 (tp-100) REVERT: B 123 TYR cc_start: 0.7834 (t80) cc_final: 0.7158 (t80) REVERT: B 127 LYS cc_start: 0.8062 (tptt) cc_final: 0.7842 (tptt) REVERT: B 132 ASN cc_start: 0.8099 (p0) cc_final: 0.7860 (p0) REVERT: B 136 LEU cc_start: 0.8196 (mt) cc_final: 0.7939 (mm) REVERT: B 149 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7701 (tptm) REVERT: B 153 LYS cc_start: 0.8627 (tptm) cc_final: 0.7844 (ttmm) REVERT: B 154 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7519 (mtp85) REVERT: B 155 MET cc_start: 0.8039 (tpt) cc_final: 0.7358 (tpp) REVERT: B 167 ASP cc_start: 0.7618 (p0) cc_final: 0.7206 (p0) REVERT: B 170 MET cc_start: 0.7961 (mmm) cc_final: 0.7672 (mmm) REVERT: B 184 ASP cc_start: 0.8083 (t70) cc_final: 0.7636 (t0) REVERT: B 192 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 199 MET cc_start: 0.7728 (mmp) cc_final: 0.7433 (mmp) REVERT: B 212 TYR cc_start: 0.8004 (m-10) cc_final: 0.7733 (m-80) REVERT: B 215 SER cc_start: 0.8269 (m) cc_final: 0.7870 (p) REVERT: B 242 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7908 (mmtt) REVERT: B 245 VAL cc_start: 0.7036 (t) cc_final: 0.6758 (p) REVERT: B 269 MET cc_start: 0.5625 (mmp) cc_final: 0.5142 (mmp) REVERT: B 307 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8286 (mmtt) REVERT: B 363 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8477 (mmmm) REVERT: B 381 TYR cc_start: 0.7664 (m-80) cc_final: 0.6823 (m-80) REVERT: B 383 TYR cc_start: 0.5676 (m-80) cc_final: 0.5187 (m-80) REVERT: B 429 ASP cc_start: 0.8150 (m-30) cc_final: 0.7285 (m-30) REVERT: B 469 ASP cc_start: 0.7420 (t70) cc_final: 0.6554 (t0) REVERT: B 502 TYR cc_start: 0.6761 (t80) cc_final: 0.6170 (t80) REVERT: B 553 GLN cc_start: 0.6302 (tt0) cc_final: 0.5921 (tm-30) REVERT: F 28 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7518 (mmmm) REVERT: F 58 TYR cc_start: 0.8256 (t80) cc_final: 0.7940 (t80) REVERT: F 62 TYR cc_start: 0.8098 (t80) cc_final: 0.7266 (t80) REVERT: F 63 THR cc_start: 0.7625 (t) cc_final: 0.7288 (p) REVERT: F 64 MET cc_start: 0.7610 (tpt) cc_final: 0.7174 (tpt) REVERT: F 68 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8458 (mttm) REVERT: F 71 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7121 (tm-30) REVERT: F 78 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7930 (ttm-80) REVERT: F 79 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6739 (tp30) REVERT: F 88 LYS cc_start: 0.8545 (tptp) cc_final: 0.8340 (tptm) REVERT: F 113 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7602 (tp40) REVERT: F 114 THR cc_start: 0.8180 (m) cc_final: 0.7948 (t) REVERT: F 116 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8190 (tpp) REVERT: F 118 MET cc_start: 0.7676 (mtm) cc_final: 0.7305 (mtm) REVERT: F 125 TYR cc_start: 0.5733 (t80) cc_final: 0.5424 (t80) REVERT: F 126 MET cc_start: 0.8268 (tmt) cc_final: 0.7781 (tmm) REVERT: F 140 TYR cc_start: 0.8079 (t80) cc_final: 0.7212 (t80) REVERT: F 145 ILE cc_start: 0.8840 (mt) cc_final: 0.8573 (tt) REVERT: F 153 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7593 (mtt180) REVERT: F 154 TYR cc_start: 0.7365 (t80) cc_final: 0.5702 (t80) REVERT: F 158 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7724 (ttm-80) REVERT: F 167 ASP cc_start: 0.7246 (t0) cc_final: 0.6876 (t0) REVERT: F 168 MET cc_start: 0.7432 (ptp) cc_final: 0.7016 (ptp) REVERT: F 172 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7891 (tm-30) REVERT: F 188 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7831 (mm-40) REVERT: F 205 PHE cc_start: 0.8523 (t80) cc_final: 0.8200 (t80) REVERT: F 233 TYR cc_start: 0.7705 (t80) cc_final: 0.7113 (t80) REVERT: F 235 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8284 (mmmm) REVERT: F 240 ARG cc_start: 0.7968 (mmt180) cc_final: 0.7664 (tpp80) REVERT: F 243 GLU cc_start: 0.7595 (pp20) cc_final: 0.7073 (pp20) REVERT: F 246 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7289 (tp30) REVERT: F 249 MET cc_start: 0.7768 (ppp) cc_final: 0.7322 (ppp) REVERT: F 258 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7804 (mp0) REVERT: F 265 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7209 (mm-30) REVERT: F 270 SER cc_start: 0.8605 (m) cc_final: 0.8103 (t) REVERT: F 272 HIS cc_start: 0.6052 (m-70) cc_final: 0.5034 (m170) REVERT: F 274 LYS cc_start: 0.8215 (tppt) cc_final: 0.7762 (tmmt) REVERT: F 276 ILE cc_start: 0.7524 (tp) cc_final: 0.6986 (mt) REVERT: F 287 MET cc_start: 0.7789 (ptm) cc_final: 0.7168 (ppp) REVERT: F 295 ASP cc_start: 0.7346 (m-30) cc_final: 0.6851 (m-30) REVERT: F 301 LYS cc_start: 0.8346 (ptpt) cc_final: 0.8022 (ptpp) REVERT: F 303 PHE cc_start: 0.8029 (m-80) cc_final: 0.7287 (m-80) REVERT: F 322 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7740 (mmt-90) REVERT: F 332 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: F 353 ASP cc_start: 0.7449 (t0) cc_final: 0.7219 (t0) REVERT: F 368 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7323 (tm-30) REVERT: F 423 GLN cc_start: 0.8187 (tt0) cc_final: 0.7743 (tt0) REVERT: F 457 LYS cc_start: 0.8534 (mmmt) cc_final: 0.7891 (mmtm) REVERT: F 484 MET cc_start: 0.3174 (mtp) cc_final: 0.2902 (mtp) REVERT: F 506 ARG cc_start: 0.5955 (mtm-85) cc_final: 0.5391 (mtm-85) REVERT: F 671 ARG cc_start: 0.6192 (tpt90) cc_final: 0.5843 (tpt-90) REVERT: F 673 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7800 (pptt) REVERT: F 687 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.2333 (tt0) REVERT: F 735 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5608 (mp) REVERT: D 42 CYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5862 (m) outliers start: 109 outliers final: 49 residues processed: 813 average time/residue: 0.3682 time to fit residues: 445.7007 Evaluate side-chains 781 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 716 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 228 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 397 ARG 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 129 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 273 MET 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 373 ASP Chi-restraints excluded: chain C residue 423 GLN 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 721 VAL Chi-restraints excluded: chain C residue 723 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 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 357 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 550 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 199 SER 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 594 VAL Chi-restraints excluded: chain F residue 600 THR 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 D residue 22 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 241 optimal weight: 0.0570 chunk 1 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 chunk 60 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 190 optimal weight: 0.0050 chunk 150 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.3912 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 100 ASN C 113 GLN C 134 ASN ** C 286 HIS ** 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** ** B 437 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.167680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141027 restraints weight = 49826.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.145551 restraints weight = 26533.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.148365 restraints weight = 16091.678| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22753 Z= 0.154 Angle : 0.687 14.434 30696 Z= 0.350 Chirality : 0.043 0.300 3385 Planarity : 0.005 0.065 3934 Dihedral : 4.606 28.555 3006 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.79 % Favored : 91.13 % Rotamer: Outliers : 4.41 % Allowed : 22.78 % Favored : 72.80 % 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: 1263 sheet: -0.90 (0.31), residues: 263 loop : -2.43 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 27 HIS 0.026 0.002 HIS E 77 PHE 0.029 0.002 PHE C 419 TYR 0.022 0.002 TYR C 125 ARG 0.008 0.001 ARG C 266 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 1102) hydrogen bonds : angle 4.95246 ( 3228) metal coordination : bond 0.01805 ( 22) metal coordination : angle 4.20423 ( 12) covalent geometry : bond 0.00329 (22731) covalent geometry : angle 0.68204 (30684) *********************** 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 833 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 724 time to evaluate : 2.362 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: A 9 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7794 (pt) REVERT: A 13 TYR cc_start: 0.7175 (t80) cc_final: 0.6782 (t80) REVERT: A 19 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7567 (pp20) REVERT: A 20 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8039 (mm110) REVERT: A 22 LYS cc_start: 0.8531 (ttmt) cc_final: 0.7777 (ttmt) REVERT: A 26 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 27 GLN cc_start: 0.8248 (mt0) cc_final: 0.7957 (mt0) REVERT: A 42 PHE cc_start: 0.8890 (m-80) cc_final: 0.8665 (m-80) REVERT: A 57 ARG cc_start: 0.8244 (ptm160) cc_final: 0.7766 (ttp80) REVERT: A 60 PHE cc_start: 0.8530 (m-80) cc_final: 0.8195 (m-10) REVERT: A 68 LYS cc_start: 0.8445 (tptp) cc_final: 0.8093 (tptp) REVERT: A 77 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8381 (m) REVERT: A 84 ILE cc_start: 0.8677 (tp) cc_final: 0.8277 (tt) REVERT: A 87 THR cc_start: 0.8567 (t) cc_final: 0.8134 (p) REVERT: A 88 TYR cc_start: 0.8545 (t80) cc_final: 0.7550 (t80) REVERT: A 90 TYR cc_start: 0.7955 (m-80) cc_final: 0.7279 (m-80) REVERT: A 102 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6940 (mm-30) REVERT: A 106 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 112 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7788 (mm-40) REVERT: A 115 ASP cc_start: 0.8038 (p0) cc_final: 0.7208 (p0) REVERT: A 118 GLN cc_start: 0.8231 (tt0) cc_final: 0.7731 (tt0) REVERT: A 122 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 123 TYR cc_start: 0.8262 (t80) cc_final: 0.7801 (t80) REVERT: A 127 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8203 (mmtm) REVERT: A 147 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 155 MET cc_start: 0.7431 (tpp) cc_final: 0.7017 (tpp) REVERT: A 157 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7111 (mm-30) REVERT: A 170 MET cc_start: 0.6826 (mmp) cc_final: 0.6339 (mmp) REVERT: A 191 GLU cc_start: 0.7480 (pp20) cc_final: 0.7036 (tm-30) REVERT: A 195 ARG cc_start: 0.8272 (tmm160) cc_final: 0.8037 (ttm170) REVERT: A 196 GLU cc_start: 0.7793 (pp20) cc_final: 0.6903 (pp20) REVERT: A 199 MET cc_start: 0.7960 (mmm) cc_final: 0.7621 (mmp) REVERT: A 209 ARG cc_start: 0.7542 (mtm180) cc_final: 0.6810 (mtm-85) REVERT: A 211 GLN cc_start: 0.7746 (pm20) cc_final: 0.7328 (pm20) REVERT: A 228 VAL cc_start: 0.5271 (OUTLIER) cc_final: 0.5027 (p) REVERT: A 267 GLU cc_start: 0.7446 (tp30) cc_final: 0.7002 (tp30) REVERT: A 294 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8154 (mmmm) REVERT: A 297 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7880 (ptpt) REVERT: A 301 PRO cc_start: 0.7425 (Cg_exo) cc_final: 0.6887 (Cg_endo) REVERT: A 352 TRP cc_start: 0.7957 (t60) cc_final: 0.7191 (t60) REVERT: A 354 ASP cc_start: 0.6708 (t0) cc_final: 0.5606 (t0) REVERT: A 357 GLN cc_start: 0.7660 (mm-40) cc_final: 0.6765 (mm-40) REVERT: A 358 ASN cc_start: 0.8186 (t0) cc_final: 0.7978 (t0) REVERT: A 360 TRP cc_start: 0.7917 (m100) cc_final: 0.5924 (m100) REVERT: A 361 PHE cc_start: 0.7207 (m-80) cc_final: 0.6231 (m-80) REVERT: A 382 ILE cc_start: 0.7281 (mm) cc_final: 0.7056 (mm) REVERT: A 383 TYR cc_start: 0.5850 (m-80) cc_final: 0.5453 (m-80) REVERT: A 397 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7241 (ptt-90) REVERT: A 434 MET cc_start: 0.2476 (tpt) cc_final: 0.1961 (tpt) REVERT: A 443 PHE cc_start: 0.8463 (t80) cc_final: 0.8183 (t80) REVERT: A 447 ASP cc_start: 0.7273 (t0) cc_final: 0.7044 (t70) REVERT: A 454 MET cc_start: 0.7356 (tpp) cc_final: 0.7032 (tpp) REVERT: A 502 TYR cc_start: 0.5582 (t80) cc_final: 0.4848 (t80) REVERT: A 558 LEU cc_start: 0.6927 (tp) cc_final: 0.6558 (mt) REVERT: A 583 VAL cc_start: 0.6558 (OUTLIER) cc_final: 0.6211 (m) REVERT: E 23 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7196 (mp0) REVERT: C 28 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7693 (tptp) REVERT: C 33 ILE cc_start: 0.9028 (mm) cc_final: 0.8681 (tt) REVERT: C 43 GLU cc_start: 0.7419 (tp30) cc_final: 0.6550 (tp30) REVERT: C 45 GLN cc_start: 0.7664 (mt0) cc_final: 0.7271 (tt0) REVERT: C 48 ASN cc_start: 0.8193 (t0) cc_final: 0.7284 (t0) REVERT: C 62 TYR cc_start: 0.8047 (t80) cc_final: 0.7661 (t80) REVERT: C 64 MET cc_start: 0.7426 (tpt) cc_final: 0.7173 (tpp) REVERT: C 68 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8253 (mptt) REVERT: C 71 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 72 LYS cc_start: 0.8481 (tttt) cc_final: 0.8034 (tptm) REVERT: C 83 GLU cc_start: 0.7675 (tp30) cc_final: 0.7210 (tp30) REVERT: C 124 MET cc_start: 0.2737 (tmm) cc_final: 0.2379 (tmm) REVERT: C 125 TYR cc_start: 0.5016 (t80) cc_final: 0.4778 (t80) REVERT: C 134 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8025 (t0) REVERT: C 153 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7476 (mmm-85) REVERT: C 163 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7887 (mm110) REVERT: C 188 GLN cc_start: 0.8133 (tp40) cc_final: 0.7710 (tp40) REVERT: C 204 ASP cc_start: 0.7276 (t0) cc_final: 0.6981 (t0) REVERT: C 205 PHE cc_start: 0.7778 (t80) cc_final: 0.7482 (t80) REVERT: C 206 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6333 (mp0) REVERT: C 220 GLU cc_start: 0.7475 (tp30) cc_final: 0.6999 (tp30) REVERT: C 222 GLN cc_start: 0.7581 (tp40) cc_final: 0.7240 (tm-30) REVERT: C 224 PHE cc_start: 0.7058 (m-80) cc_final: 0.6083 (m-10) REVERT: C 235 LYS cc_start: 0.8433 (mmmt) cc_final: 0.7812 (mtmm) REVERT: C 238 GLU cc_start: 0.7508 (tp30) cc_final: 0.6796 (tm-30) REVERT: C 243 GLU cc_start: 0.8339 (pt0) cc_final: 0.7580 (pp20) REVERT: C 244 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7377 (tp30) REVERT: C 246 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 247 ARG cc_start: 0.8234 (ttm110) cc_final: 0.8025 (ttm110) REVERT: C 248 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8093 (p) REVERT: C 250 HIS cc_start: 0.7955 (t-90) cc_final: 0.7188 (t-90) REVERT: C 258 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7242 (mm-30) REVERT: C 259 PRO cc_start: 0.8277 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: C 262 LYS cc_start: 0.8023 (tmtm) cc_final: 0.7393 (ttpp) REVERT: C 274 LYS cc_start: 0.8298 (tppt) cc_final: 0.7965 (tppt) REVERT: C 282 SER cc_start: 0.7826 (m) cc_final: 0.7447 (t) REVERT: C 288 LEU cc_start: 0.8914 (tp) cc_final: 0.8666 (tp) REVERT: C 292 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8081 (mmtm) REVERT: C 294 GLU cc_start: 0.7440 (pm20) cc_final: 0.7225 (pm20) REVERT: C 295 ASP cc_start: 0.7690 (t0) cc_final: 0.7429 (t0) REVERT: C 301 LYS cc_start: 0.8358 (ptpt) cc_final: 0.8012 (ptpp) REVERT: C 306 VAL cc_start: 0.8647 (t) cc_final: 0.8386 (p) REVERT: C 346 LEU cc_start: 0.8272 (tp) cc_final: 0.8044 (tp) REVERT: C 353 ASP cc_start: 0.8044 (t0) cc_final: 0.7719 (t0) REVERT: C 354 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7663 (ttp-110) REVERT: C 368 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6677 (tm-30) REVERT: C 369 THR cc_start: 0.8041 (p) cc_final: 0.7755 (t) REVERT: C 373 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6064 (t0) REVERT: C 394 ASP cc_start: 0.7993 (t0) cc_final: 0.7613 (t0) REVERT: C 395 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8229 (mmmm) REVERT: C 409 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7311 (mm-30) REVERT: C 412 LEU cc_start: 0.8723 (mt) cc_final: 0.8459 (mm) REVERT: C 413 ASP cc_start: 0.8606 (m-30) cc_final: 0.8294 (m-30) REVERT: C 416 MET cc_start: 0.7209 (tpp) cc_final: 0.6776 (tpp) REVERT: C 418 LEU cc_start: 0.8810 (tt) cc_final: 0.8544 (tp) REVERT: C 423 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6779 (pt0) REVERT: C 431 TYR cc_start: 0.8197 (m-80) cc_final: 0.7466 (m-80) REVERT: C 438 ARG cc_start: 0.7793 (tpm170) cc_final: 0.7250 (tpm170) REVERT: C 441 LEU cc_start: 0.8305 (mt) cc_final: 0.8021 (mt) REVERT: C 457 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8751 (mmtp) REVERT: C 473 MET cc_start: 0.7878 (mmt) cc_final: 0.6933 (mmt) REVERT: C 484 MET cc_start: 0.2960 (OUTLIER) cc_final: 0.2425 (tpt) REVERT: C 554 MET cc_start: 0.6615 (tpp) cc_final: 0.6247 (tpp) REVERT: C 603 MET cc_start: 0.7318 (tmm) cc_final: 0.6905 (tmm) REVERT: C 685 ASP cc_start: 0.8095 (t0) cc_final: 0.7817 (t0) REVERT: C 687 GLU cc_start: 0.6560 (pp20) cc_final: 0.6301 (pt0) REVERT: C 692 ARG cc_start: 0.8434 (tpp-160) cc_final: 0.8220 (mmp80) REVERT: B 19 GLU cc_start: 0.7595 (pp20) cc_final: 0.6952 (pp20) REVERT: B 24 PHE cc_start: 0.8511 (m-10) cc_final: 0.8211 (m-80) REVERT: B 25 TYR cc_start: 0.8728 (t80) cc_final: 0.8515 (t80) REVERT: B 29 LEU cc_start: 0.8293 (mp) cc_final: 0.7942 (mp) REVERT: B 32 ASP cc_start: 0.8010 (p0) cc_final: 0.7575 (p0) REVERT: B 46 LYS cc_start: 0.8734 (mttt) cc_final: 0.8508 (mttm) REVERT: B 57 ARG cc_start: 0.8544 (ptm160) cc_final: 0.8291 (ttm110) REVERT: B 69 GLN cc_start: 0.7867 (tt0) cc_final: 0.7602 (tt0) REVERT: B 72 VAL cc_start: 0.8881 (m) cc_final: 0.8389 (p) REVERT: B 85 ILE cc_start: 0.8682 (mt) cc_final: 0.8372 (tp) REVERT: B 88 TYR cc_start: 0.8792 (t80) cc_final: 0.7934 (t80) REVERT: B 105 TYR cc_start: 0.8055 (t80) cc_final: 0.7813 (t80) REVERT: B 106 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7633 (mt-10) REVERT: B 112 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7489 (mm-40) REVERT: B 115 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7055 (p0) REVERT: B 123 TYR cc_start: 0.7824 (t80) cc_final: 0.7196 (t80) REVERT: B 132 ASN cc_start: 0.7994 (p0) cc_final: 0.7678 (p0) REVERT: B 136 LEU cc_start: 0.8190 (mt) cc_final: 0.7885 (mm) REVERT: B 149 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7690 (tptm) REVERT: B 153 LYS cc_start: 0.8560 (tptm) cc_final: 0.7819 (ttmm) REVERT: B 154 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7609 (mtp85) REVERT: B 155 MET cc_start: 0.7955 (tpt) cc_final: 0.7448 (tpp) REVERT: B 166 GLN cc_start: 0.5357 (mp10) cc_final: 0.5011 (mp10) REVERT: B 170 MET cc_start: 0.7853 (mmm) cc_final: 0.7594 (mmm) REVERT: B 184 ASP cc_start: 0.8082 (t70) cc_final: 0.7663 (t0) REVERT: B 195 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7367 (ttp-170) REVERT: B 199 MET cc_start: 0.7786 (mmp) cc_final: 0.7387 (mmp) REVERT: B 203 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6779 (mm-30) REVERT: B 209 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7747 (mmt90) REVERT: B 212 TYR cc_start: 0.7976 (m-10) cc_final: 0.7648 (m-80) REVERT: B 242 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7824 (mmtt) REVERT: B 268 MET cc_start: 0.7229 (mmm) cc_final: 0.7004 (mmm) REVERT: B 307 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8036 (mmtm) REVERT: B 360 TRP cc_start: 0.7851 (m100) cc_final: 0.5972 (m100) REVERT: B 361 PHE cc_start: 0.7676 (t80) cc_final: 0.7367 (t80) REVERT: B 363 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8314 (mmtp) REVERT: B 381 TYR cc_start: 0.7524 (m-80) cc_final: 0.6821 (m-80) REVERT: B 383 TYR cc_start: 0.5643 (m-80) cc_final: 0.5203 (m-80) REVERT: B 429 ASP cc_start: 0.8011 (m-30) cc_final: 0.7133 (m-30) REVERT: B 430 CYS cc_start: 0.5527 (m) cc_final: 0.4701 (t) REVERT: B 452 MET cc_start: 0.6307 (mpp) cc_final: 0.6076 (mpp) REVERT: B 469 ASP cc_start: 0.7521 (t70) cc_final: 0.6868 (t70) REVERT: B 502 TYR cc_start: 0.6766 (t80) cc_final: 0.6311 (t80) REVERT: B 503 ASP cc_start: 0.8286 (t0) cc_final: 0.8068 (t0) REVERT: B 537 PHE cc_start: 0.6405 (t80) cc_final: 0.6151 (t80) REVERT: F 28 LYS cc_start: 0.7850 (mmmm) cc_final: 0.7536 (mmmm) REVERT: F 56 GLU cc_start: 0.7959 (mp0) cc_final: 0.7596 (mp0) REVERT: F 62 TYR cc_start: 0.8059 (t80) cc_final: 0.7212 (t80) REVERT: F 63 THR cc_start: 0.7526 (t) cc_final: 0.7217 (p) REVERT: F 64 MET cc_start: 0.7557 (tpt) cc_final: 0.7134 (tpt) REVERT: F 68 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8436 (mttm) REVERT: F 71 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7119 (tm-30) REVERT: F 78 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7943 (ttm-80) REVERT: F 79 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6716 (tp30) REVERT: F 113 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7478 (tp40) REVERT: F 116 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8237 (tpp) REVERT: F 118 MET cc_start: 0.7613 (mtm) cc_final: 0.7220 (mtm) REVERT: F 125 TYR cc_start: 0.5673 (t80) cc_final: 0.5304 (t80) REVERT: F 126 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7904 (tmm) REVERT: F 140 TYR cc_start: 0.8031 (t80) cc_final: 0.6954 (t80) REVERT: F 145 ILE cc_start: 0.8813 (mt) cc_final: 0.8546 (tt) REVERT: F 154 TYR cc_start: 0.7208 (t80) cc_final: 0.5554 (t80) REVERT: F 158 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7564 (ttm-80) REVERT: F 160 HIS cc_start: 0.8274 (t-90) cc_final: 0.8070 (t-90) REVERT: F 167 ASP cc_start: 0.7225 (t0) cc_final: 0.6833 (t0) REVERT: F 168 MET cc_start: 0.7442 (ptp) cc_final: 0.7069 (ptp) REVERT: F 173 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7740 (mtp180) REVERT: F 188 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7783 (mm-40) REVERT: F 203 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7309 (tm-30) REVERT: F 205 PHE cc_start: 0.8445 (t80) cc_final: 0.8173 (t80) REVERT: F 233 TYR cc_start: 0.7590 (t80) cc_final: 0.7143 (t80) REVERT: F 235 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8407 (mmtp) REVERT: F 238 GLU cc_start: 0.8031 (tp30) cc_final: 0.7671 (tp30) REVERT: F 240 ARG cc_start: 0.7883 (mmt180) cc_final: 0.7626 (tpp80) REVERT: F 243 GLU cc_start: 0.7651 (pp20) cc_final: 0.7148 (pp20) REVERT: F 246 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7304 (tp30) REVERT: F 249 MET cc_start: 0.7792 (ppp) cc_final: 0.7389 (ppp) REVERT: F 258 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7873 (mp0) REVERT: F 265 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7250 (mm-30) REVERT: F 270 SER cc_start: 0.8564 (m) cc_final: 0.8090 (t) REVERT: F 272 HIS cc_start: 0.6318 (m-70) cc_final: 0.5799 (m170) REVERT: F 274 LYS cc_start: 0.8265 (tppt) cc_final: 0.7735 (tmmt) REVERT: F 276 ILE cc_start: 0.7512 (tp) cc_final: 0.7234 (tt) REVERT: F 287 MET cc_start: 0.7715 (ptm) cc_final: 0.7290 (ppp) REVERT: F 295 ASP cc_start: 0.7355 (m-30) cc_final: 0.6904 (m-30) REVERT: F 301 LYS cc_start: 0.8206 (ptpt) cc_final: 0.7946 (ptpp) REVERT: F 303 PHE cc_start: 0.8041 (m-80) cc_final: 0.7317 (m-80) REVERT: F 322 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7607 (mmt180) REVERT: F 323 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7594 (tm-30) REVERT: F 332 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6214 (pm20) REVERT: F 352 PHE cc_start: 0.8031 (m-80) cc_final: 0.7741 (m-10) REVERT: F 353 ASP cc_start: 0.7443 (t0) cc_final: 0.7167 (t0) REVERT: F 368 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7263 (tm-30) REVERT: F 423 GLN cc_start: 0.8152 (tt0) cc_final: 0.7597 (tt0) REVERT: F 554 MET cc_start: 0.6728 (mmm) cc_final: 0.6220 (mmm) REVERT: F 671 ARG cc_start: 0.6148 (tpt90) cc_final: 0.3723 (tpt90) REVERT: F 673 LYS cc_start: 0.8001 (ptmm) cc_final: 0.7638 (pptt) REVERT: F 734 PHE cc_start: 0.7213 (p90) cc_final: 0.6992 (p90) REVERT: D 42 CYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5822 (m) outliers start: 109 outliers final: 62 residues processed: 784 average time/residue: 0.3706 time to fit residues: 430.0650 Evaluate side-chains 780 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 702 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 228 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 296 TYR 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 397 ARG 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 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 134 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 423 GLN 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 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 68 LYS 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 550 VAL 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 126 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 264 VAL 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 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 701 HIS Chi-restraints excluded: chain F residue 725 GLU 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 116 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 223 optimal weight: 0.1980 chunk 193 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 234 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.166898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.140583 restraints weight = 49361.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.144920 restraints weight = 26725.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.147741 restraints weight = 16390.306| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22753 Z= 0.166 Angle : 0.693 13.227 30696 Z= 0.354 Chirality : 0.044 0.300 3385 Planarity : 0.005 0.059 3934 Dihedral : 4.625 26.556 3006 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.31 % Favored : 90.62 % Rotamer: Outliers : 4.45 % Allowed : 23.67 % Favored : 71.87 % 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: -1.11 (0.16), residues: 2718 helix: 0.78 (0.15), residues: 1262 sheet: -0.93 (0.30), residues: 268 loop : -2.45 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 561 HIS 0.021 0.001 HIS F 490 PHE 0.025 0.002 PHE B 537 TYR 0.022 0.002 TYR C 125 ARG 0.010 0.001 ARG F 383 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 1102) hydrogen bonds : angle 4.95521 ( 3228) metal coordination : bond 0.01787 ( 22) metal coordination : angle 4.18702 ( 12) covalent geometry : bond 0.00346 (22731) covalent geometry : angle 0.68813 (30684) *********************** 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 844 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 734 time to evaluate : 2.590 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: A 9 ILE cc_start: 0.8261 (tp) cc_final: 0.7841 (pt) REVERT: A 13 TYR cc_start: 0.7234 (t80) cc_final: 0.6807 (t80) REVERT: A 19 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7566 (pp20) REVERT: A 20 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8046 (mm110) REVERT: A 22 LYS cc_start: 0.8545 (ttmt) cc_final: 0.7788 (ttmt) REVERT: A 26 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 37 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8225 (m) REVERT: A 57 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7720 (ttp80) REVERT: A 59 MET cc_start: 0.7842 (ttt) cc_final: 0.7584 (ttp) REVERT: A 60 PHE cc_start: 0.8460 (m-80) cc_final: 0.8016 (m-10) REVERT: A 68 LYS cc_start: 0.8372 (tptp) cc_final: 0.8092 (tptp) REVERT: A 84 ILE cc_start: 0.8676 (tp) cc_final: 0.8277 (tt) REVERT: A 87 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8229 (p) REVERT: A 88 TYR cc_start: 0.8506 (t80) cc_final: 0.7463 (t80) REVERT: A 90 TYR cc_start: 0.7969 (m-80) cc_final: 0.7333 (m-80) REVERT: A 102 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 106 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 110 PHE cc_start: 0.8543 (t80) cc_final: 0.8239 (t80) REVERT: A 112 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7757 (mm-40) REVERT: A 115 ASP cc_start: 0.8005 (p0) cc_final: 0.7171 (p0) REVERT: A 118 GLN cc_start: 0.8251 (tt0) cc_final: 0.7751 (tt0) REVERT: A 122 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 127 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8159 (mmmt) REVERT: A 129 ASN cc_start: 0.7717 (p0) cc_final: 0.7136 (p0) REVERT: A 131 GLU cc_start: 0.7400 (pm20) cc_final: 0.7157 (pm20) REVERT: A 139 PHE cc_start: 0.8629 (t80) cc_final: 0.7900 (t80) REVERT: A 147 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 157 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6977 (mm-30) REVERT: A 160 PHE cc_start: 0.5598 (OUTLIER) cc_final: 0.4099 (t80) REVERT: A 170 MET cc_start: 0.6844 (mmp) cc_final: 0.6381 (mmp) REVERT: A 191 GLU cc_start: 0.7488 (pp20) cc_final: 0.7143 (tm-30) REVERT: A 196 GLU cc_start: 0.7699 (pp20) cc_final: 0.7007 (pp20) REVERT: A 199 MET cc_start: 0.7999 (mmm) cc_final: 0.7608 (mmp) REVERT: A 209 ARG cc_start: 0.7560 (mtm180) cc_final: 0.7186 (mtm180) REVERT: A 211 GLN cc_start: 0.7831 (pm20) cc_final: 0.7494 (pm20) REVERT: A 225 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5476 (mt) REVERT: A 267 GLU cc_start: 0.7454 (tp30) cc_final: 0.6991 (tp30) REVERT: A 294 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8116 (mmmm) REVERT: A 297 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7817 (ptpt) REVERT: A 301 PRO cc_start: 0.7559 (Cg_exo) cc_final: 0.7334 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8344 (p) cc_final: 0.8126 (t) REVERT: A 352 TRP cc_start: 0.7924 (t60) cc_final: 0.7253 (t60) REVERT: A 353 PHE cc_start: 0.7744 (t80) cc_final: 0.7463 (t80) REVERT: A 357 GLN cc_start: 0.7606 (mm-40) cc_final: 0.6749 (mm-40) REVERT: A 358 ASN cc_start: 0.8164 (t0) cc_final: 0.7943 (t0) REVERT: A 361 PHE cc_start: 0.7256 (m-80) cc_final: 0.6217 (m-80) REVERT: A 382 ILE cc_start: 0.7247 (mm) cc_final: 0.6980 (mm) REVERT: A 383 TYR cc_start: 0.5787 (m-80) cc_final: 0.5386 (m-80) REVERT: A 397 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7148 (ptt-90) REVERT: A 443 PHE cc_start: 0.8395 (t80) cc_final: 0.8160 (t80) REVERT: A 502 TYR cc_start: 0.5831 (t80) cc_final: 0.4970 (t80) REVERT: A 536 VAL cc_start: 0.7638 (m) cc_final: 0.7362 (p) REVERT: A 558 LEU cc_start: 0.6947 (tp) cc_final: 0.6679 (mt) REVERT: A 583 VAL cc_start: 0.6543 (OUTLIER) cc_final: 0.6168 (m) REVERT: A 586 LEU cc_start: 0.8533 (mt) cc_final: 0.8011 (mp) REVERT: E 23 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7216 (mp0) REVERT: E 35 TRP cc_start: 0.2854 (m-10) cc_final: 0.2585 (m-10) REVERT: C 28 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7736 (tptp) REVERT: C 33 ILE cc_start: 0.9104 (mm) cc_final: 0.8769 (mm) REVERT: C 43 GLU cc_start: 0.7401 (tp30) cc_final: 0.6604 (tp30) REVERT: C 45 GLN cc_start: 0.7816 (mt0) cc_final: 0.7532 (tt0) REVERT: C 48 ASN cc_start: 0.8149 (t0) cc_final: 0.7328 (t0) REVERT: C 62 TYR cc_start: 0.7994 (t80) cc_final: 0.7721 (t80) REVERT: C 64 MET cc_start: 0.7439 (tpt) cc_final: 0.7065 (tpp) REVERT: C 68 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8259 (mptt) REVERT: C 71 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 72 LYS cc_start: 0.8463 (tttt) cc_final: 0.8032 (tptm) REVERT: C 83 GLU cc_start: 0.7698 (tp30) cc_final: 0.7259 (tp30) REVERT: C 124 MET cc_start: 0.3058 (tmm) cc_final: 0.2611 (tmm) REVERT: C 125 TYR cc_start: 0.5014 (t80) cc_final: 0.4721 (t80) REVERT: C 153 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7489 (mmm-85) REVERT: C 163 GLN cc_start: 0.8475 (mm-40) cc_final: 0.7904 (mm110) REVERT: C 168 MET cc_start: 0.7831 (ptp) cc_final: 0.7623 (ptm) REVERT: C 188 GLN cc_start: 0.8125 (tp40) cc_final: 0.7711 (tp40) REVERT: C 199 SER cc_start: 0.8597 (t) cc_final: 0.8278 (p) REVERT: C 204 ASP cc_start: 0.7250 (t0) cc_final: 0.7043 (t0) REVERT: C 205 PHE cc_start: 0.7804 (t80) cc_final: 0.7531 (t80) REVERT: C 206 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6306 (mp0) REVERT: C 222 GLN cc_start: 0.7580 (tp40) cc_final: 0.7187 (tm-30) REVERT: C 234 ILE cc_start: 0.8627 (mm) cc_final: 0.8333 (tp) REVERT: C 235 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7952 (mtmm) REVERT: C 238 GLU cc_start: 0.7456 (tp30) cc_final: 0.6790 (tm-30) REVERT: C 243 GLU cc_start: 0.8309 (pt0) cc_final: 0.7550 (pp20) REVERT: C 246 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 247 ARG cc_start: 0.8246 (ttm110) cc_final: 0.8002 (ttm110) REVERT: C 248 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8147 (p) REVERT: C 250 HIS cc_start: 0.7994 (t-90) cc_final: 0.7308 (t-90) REVERT: C 258 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7080 (mm-30) REVERT: C 259 PRO cc_start: 0.8371 (Cg_exo) cc_final: 0.8103 (Cg_endo) REVERT: C 262 LYS cc_start: 0.8071 (tmtm) cc_final: 0.7425 (ttpp) REVERT: C 274 LYS cc_start: 0.8410 (tppt) cc_final: 0.7844 (tppt) REVERT: C 282 SER cc_start: 0.7758 (m) cc_final: 0.7483 (m) REVERT: C 288 LEU cc_start: 0.8850 (tp) cc_final: 0.8638 (tp) REVERT: C 292 LYS cc_start: 0.8504 (mmmm) cc_final: 0.7896 (mmtm) REVERT: C 295 ASP cc_start: 0.7623 (t0) cc_final: 0.7232 (t0) REVERT: C 301 LYS cc_start: 0.8322 (ptpt) cc_final: 0.7931 (ptpp) REVERT: C 306 VAL cc_start: 0.8682 (t) cc_final: 0.8354 (p) REVERT: C 314 CYS cc_start: 0.7542 (m) cc_final: 0.7191 (m) REVERT: C 346 LEU cc_start: 0.8303 (tp) cc_final: 0.8059 (tp) REVERT: C 353 ASP cc_start: 0.8045 (t0) cc_final: 0.7730 (t0) REVERT: C 354 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7620 (ttp-110) REVERT: C 368 GLN cc_start: 0.7401 (tm-30) cc_final: 0.6677 (tm-30) REVERT: C 369 THR cc_start: 0.8202 (p) cc_final: 0.7756 (t) REVERT: C 373 ASP cc_start: 0.6421 (OUTLIER) cc_final: 0.6091 (t0) REVERT: C 386 GLU cc_start: 0.8381 (mp0) cc_final: 0.6598 (mp0) REVERT: C 394 ASP cc_start: 0.7931 (t0) cc_final: 0.7559 (t0) REVERT: C 395 LYS cc_start: 0.8562 (mmtm) cc_final: 0.8185 (mmmm) REVERT: C 409 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7290 (mm-30) REVERT: C 412 LEU cc_start: 0.8716 (mt) cc_final: 0.8449 (mm) REVERT: C 413 ASP cc_start: 0.8595 (m-30) cc_final: 0.8148 (m-30) REVERT: C 416 MET cc_start: 0.7199 (tpp) cc_final: 0.6992 (tpp) REVERT: C 418 LEU cc_start: 0.8796 (tt) cc_final: 0.8533 (tp) REVERT: C 423 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6817 (pt0) REVERT: C 431 TYR cc_start: 0.8294 (m-80) cc_final: 0.6652 (m-10) REVERT: C 438 ARG cc_start: 0.7815 (tpm170) cc_final: 0.7192 (tpm170) REVERT: C 441 LEU cc_start: 0.8320 (mt) cc_final: 0.7883 (mt) REVERT: C 457 LYS cc_start: 0.8935 (mmmt) cc_final: 0.8508 (mmmm) REVERT: C 473 MET cc_start: 0.7865 (mmt) cc_final: 0.6966 (mmt) REVERT: C 477 MET cc_start: 0.7554 (tmm) cc_final: 0.7308 (tmm) REVERT: C 534 ILE cc_start: 0.8223 (mt) cc_final: 0.8020 (mt) REVERT: C 554 MET cc_start: 0.6639 (tpp) cc_final: 0.6248 (tpp) REVERT: C 603 MET cc_start: 0.7337 (tmm) cc_final: 0.6842 (tmm) REVERT: C 687 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5802 (pp20) REVERT: C 688 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: C 692 ARG cc_start: 0.8448 (tpp-160) cc_final: 0.8161 (mmp80) REVERT: B 19 GLU cc_start: 0.7592 (pp20) cc_final: 0.6956 (pp20) REVERT: B 24 PHE cc_start: 0.8518 (m-10) cc_final: 0.8188 (m-80) REVERT: B 25 TYR cc_start: 0.8708 (t80) cc_final: 0.8468 (t80) REVERT: B 29 LEU cc_start: 0.8283 (mp) cc_final: 0.7979 (mp) REVERT: B 32 ASP cc_start: 0.8010 (p0) cc_final: 0.7573 (p0) REVERT: B 57 ARG cc_start: 0.8505 (ptm160) cc_final: 0.8284 (ttm110) REVERT: B 69 GLN cc_start: 0.7807 (tt0) cc_final: 0.7563 (tt0) REVERT: B 72 VAL cc_start: 0.8877 (m) cc_final: 0.8365 (p) REVERT: B 85 ILE cc_start: 0.8694 (mt) cc_final: 0.8359 (tp) REVERT: B 88 TYR cc_start: 0.8751 (t80) cc_final: 0.7895 (t80) REVERT: B 106 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7753 (mt-10) REVERT: B 112 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7030 (mm-40) REVERT: B 115 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7032 (p0) REVERT: B 123 TYR cc_start: 0.7876 (t80) cc_final: 0.7281 (t80) REVERT: B 132 ASN cc_start: 0.8120 (p0) cc_final: 0.7895 (p0) REVERT: B 149 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7699 (tptp) REVERT: B 155 MET cc_start: 0.7976 (tpt) cc_final: 0.7465 (tpp) REVERT: B 166 GLN cc_start: 0.5762 (mp10) cc_final: 0.5373 (mp10) REVERT: B 170 MET cc_start: 0.7888 (mmm) cc_final: 0.7608 (mmm) REVERT: B 184 ASP cc_start: 0.8019 (t70) cc_final: 0.7630 (t0) REVERT: B 195 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7534 (ttt180) REVERT: B 199 MET cc_start: 0.7785 (mmp) cc_final: 0.7400 (mmp) REVERT: B 209 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7521 (mmt90) REVERT: B 212 TYR cc_start: 0.7987 (m-10) cc_final: 0.7645 (m-80) REVERT: B 215 SER cc_start: 0.8209 (m) cc_final: 0.7804 (p) REVERT: B 242 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7862 (mmtt) REVERT: B 294 LYS cc_start: 0.7417 (mmtm) cc_final: 0.7172 (mmtm) REVERT: B 307 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7997 (mmtm) REVERT: B 360 TRP cc_start: 0.7774 (m100) cc_final: 0.5891 (m100) REVERT: B 363 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8324 (mmtp) REVERT: B 381 TYR cc_start: 0.7543 (m-80) cc_final: 0.6712 (m-80) REVERT: B 383 TYR cc_start: 0.5592 (m-80) cc_final: 0.5187 (m-80) REVERT: B 429 ASP cc_start: 0.8035 (m-30) cc_final: 0.7170 (m-30) REVERT: B 430 CYS cc_start: 0.5476 (m) cc_final: 0.4698 (t) REVERT: B 452 MET cc_start: 0.6369 (mpp) cc_final: 0.5861 (mpp) REVERT: B 469 ASP cc_start: 0.7378 (t70) cc_final: 0.6857 (t70) REVERT: B 502 TYR cc_start: 0.6676 (t80) cc_final: 0.6271 (t80) REVERT: B 537 PHE cc_start: 0.6458 (t80) cc_final: 0.6125 (t80) REVERT: B 538 MET cc_start: 0.6890 (mmm) cc_final: 0.6640 (ptp) REVERT: B 583 VAL cc_start: 0.7953 (p) cc_final: 0.7611 (t) REVERT: F 28 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7565 (mmmm) REVERT: F 46 ARG cc_start: 0.7410 (mtm110) cc_final: 0.6945 (mtm110) REVERT: F 47 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7698 (mmmm) REVERT: F 56 GLU cc_start: 0.7890 (mp0) cc_final: 0.7347 (pm20) REVERT: F 62 TYR cc_start: 0.8071 (t80) cc_final: 0.7069 (t80) REVERT: F 63 THR cc_start: 0.7564 (t) cc_final: 0.7230 (p) REVERT: F 64 MET cc_start: 0.7586 (tpt) cc_final: 0.7081 (tpt) REVERT: F 68 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8420 (mttm) REVERT: F 71 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7039 (tm-30) REVERT: F 78 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7926 (ttm-80) REVERT: F 79 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6689 (tp30) REVERT: F 103 GLN cc_start: 0.8555 (tp40) cc_final: 0.8026 (tp40) REVERT: F 113 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: F 116 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8220 (tpp) REVERT: F 118 MET cc_start: 0.7420 (mtm) cc_final: 0.7159 (mtm) REVERT: F 125 TYR cc_start: 0.4443 (t80) cc_final: 0.4241 (t80) REVERT: F 126 MET cc_start: 0.8148 (tmt) cc_final: 0.7454 (tmm) REVERT: F 140 TYR cc_start: 0.8026 (t80) cc_final: 0.6983 (t80) REVERT: F 145 ILE cc_start: 0.8812 (mt) cc_final: 0.8568 (tt) REVERT: F 150 GLN cc_start: 0.7720 (mm110) cc_final: 0.7313 (mm-40) REVERT: F 154 TYR cc_start: 0.7207 (t80) cc_final: 0.5640 (t80) REVERT: F 163 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7228 (mm110) REVERT: F 167 ASP cc_start: 0.7302 (t0) cc_final: 0.6950 (t0) REVERT: F 168 MET cc_start: 0.7507 (ptp) cc_final: 0.7011 (ptp) REVERT: F 180 ARG cc_start: 0.7738 (ptp-110) cc_final: 0.7479 (ptp-110) REVERT: F 188 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7896 (mm-40) REVERT: F 205 PHE cc_start: 0.8553 (t80) cc_final: 0.8096 (t80) REVERT: F 233 TYR cc_start: 0.7625 (t80) cc_final: 0.7220 (t80) REVERT: F 235 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8415 (mmtp) REVERT: F 238 GLU cc_start: 0.8173 (tp30) cc_final: 0.7671 (tp30) REVERT: F 240 ARG cc_start: 0.7866 (mmt180) cc_final: 0.7638 (tpp80) REVERT: F 243 GLU cc_start: 0.7668 (pp20) cc_final: 0.7209 (pp20) REVERT: F 246 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7280 (tp30) REVERT: F 249 MET cc_start: 0.7791 (ppp) cc_final: 0.7362 (ppp) REVERT: F 257 GLU cc_start: 0.7337 (pp20) cc_final: 0.7099 (pp20) REVERT: F 258 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7656 (mp0) REVERT: F 265 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7190 (mm-30) REVERT: F 270 SER cc_start: 0.8558 (m) cc_final: 0.8055 (t) REVERT: F 272 HIS cc_start: 0.6409 (m-70) cc_final: 0.5863 (m170) REVERT: F 274 LYS cc_start: 0.8378 (tppt) cc_final: 0.7865 (tmmt) REVERT: F 276 ILE cc_start: 0.7579 (tp) cc_final: 0.7265 (tt) REVERT: F 287 MET cc_start: 0.7620 (ptm) cc_final: 0.7032 (ppp) REVERT: F 301 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7867 (ptpp) REVERT: F 303 PHE cc_start: 0.7986 (m-80) cc_final: 0.7331 (m-80) REVERT: F 322 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7695 (mmt180) REVERT: F 332 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6346 (pm20) REVERT: F 352 PHE cc_start: 0.7994 (m-80) cc_final: 0.7748 (m-10) REVERT: F 353 ASP cc_start: 0.7339 (t0) cc_final: 0.7087 (t0) REVERT: F 368 GLN cc_start: 0.7455 (tm-30) cc_final: 0.7167 (tm-30) REVERT: F 414 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8755 (mmtm) REVERT: F 423 GLN cc_start: 0.8119 (tt0) cc_final: 0.7570 (tt0) REVERT: F 457 LYS cc_start: 0.8456 (mmmt) cc_final: 0.7881 (mmtt) REVERT: F 484 MET cc_start: 0.2771 (mtp) cc_final: 0.2049 (mtp) REVERT: F 554 MET cc_start: 0.6662 (mmm) cc_final: 0.6117 (mmm) REVERT: F 671 ARG cc_start: 0.6122 (tpt90) cc_final: 0.5853 (tpt90) REVERT: F 673 LYS cc_start: 0.8047 (ptmm) cc_final: 0.7781 (pptt) REVERT: F 734 PHE cc_start: 0.7230 (p90) cc_final: 0.6882 (p90) REVERT: F 735 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5561 (mp) REVERT: D 42 CYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5833 (m) outliers start: 110 outliers final: 69 residues processed: 794 average time/residue: 0.3762 time to fit residues: 445.7781 Evaluate side-chains 795 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 710 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 397 ARG 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 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 423 GLN 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 717 MET 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 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 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU 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 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 165 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 199 SER 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 701 HIS Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 735 LEU 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 20 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 190 optimal weight: 0.0570 chunk 170 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 203 optimal weight: 0.2980 chunk 214 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 229 optimal weight: 0.5980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** 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 729 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.167616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.141150 restraints weight = 49051.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.145566 restraints weight = 26276.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.148352 restraints weight = 16023.170| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22753 Z= 0.142 Angle : 0.686 13.477 30696 Z= 0.347 Chirality : 0.043 0.181 3385 Planarity : 0.004 0.053 3934 Dihedral : 4.562 24.817 3006 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.69 % Rotamer: Outliers : 4.65 % Allowed : 24.36 % Favored : 70.98 % 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: -1.04 (0.16), residues: 2718 helix: 0.85 (0.15), residues: 1263 sheet: -0.96 (0.30), residues: 273 loop : -2.42 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 561 HIS 0.021 0.001 HIS F 490 PHE 0.031 0.002 PHE C 419 TYR 0.022 0.002 TYR C 125 ARG 0.009 0.001 ARG F 266 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 1102) hydrogen bonds : angle 4.90237 ( 3228) metal coordination : bond 0.01521 ( 22) metal coordination : angle 3.88784 ( 12) covalent geometry : bond 0.00305 (22731) covalent geometry : angle 0.68213 (30684) *********************** 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 847 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 732 time to evaluate : 2.439 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: 0.8255 (tp) cc_final: 0.7848 (pt) REVERT: A 13 TYR cc_start: 0.7251 (t80) cc_final: 0.6751 (t80) REVERT: A 19 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7505 (pp20) REVERT: A 20 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8029 (mm110) REVERT: A 26 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 37 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8026 (m) REVERT: A 57 ARG cc_start: 0.8183 (ptm160) cc_final: 0.7705 (ttp80) REVERT: A 66 GLU cc_start: 0.7355 (mp0) cc_final: 0.6928 (mp0) REVERT: A 68 LYS cc_start: 0.8187 (tptp) cc_final: 0.7933 (tptp) REVERT: A 84 ILE cc_start: 0.8594 (tp) cc_final: 0.8192 (tt) REVERT: A 87 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 88 TYR cc_start: 0.8508 (t80) cc_final: 0.7408 (t80) REVERT: A 90 TYR cc_start: 0.7904 (m-80) cc_final: 0.7573 (m-80) REVERT: A 102 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 106 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7303 (tm-30) REVERT: A 109 CYS cc_start: 0.8245 (t) cc_final: 0.6556 (t) REVERT: A 115 ASP cc_start: 0.7986 (p0) cc_final: 0.7062 (p0) REVERT: A 118 GLN cc_start: 0.8241 (tt0) cc_final: 0.7733 (tt0) REVERT: A 122 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 123 TYR cc_start: 0.8243 (t80) cc_final: 0.8030 (t80) REVERT: A 127 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8412 (mmtm) REVERT: A 129 ASN cc_start: 0.7633 (p0) cc_final: 0.7413 (p0) REVERT: A 147 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 149 LYS cc_start: 0.8131 (tttt) cc_final: 0.7804 (ttmt) REVERT: A 157 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 160 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4349 (t80) REVERT: A 170 MET cc_start: 0.6798 (mmp) cc_final: 0.6368 (mmp) REVERT: A 191 GLU cc_start: 0.7484 (pp20) cc_final: 0.7147 (tm-30) REVERT: A 196 GLU cc_start: 0.7696 (pp20) cc_final: 0.6540 (pp20) REVERT: A 199 MET cc_start: 0.8027 (mmm) cc_final: 0.7605 (mmp) REVERT: A 209 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6718 (mtm-85) REVERT: A 211 GLN cc_start: 0.7834 (pm20) cc_final: 0.7481 (pm20) REVERT: A 225 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5322 (mt) REVERT: A 268 MET cc_start: 0.7004 (mmm) cc_final: 0.6044 (tpt) REVERT: A 294 LYS cc_start: 0.8518 (mmmm) cc_final: 0.8105 (mmmm) REVERT: A 297 LYS cc_start: 0.8145 (ptpt) cc_final: 0.7853 (ptpt) REVERT: A 301 PRO cc_start: 0.7463 (Cg_exo) cc_final: 0.6936 (Cg_endo) REVERT: A 352 TRP cc_start: 0.7944 (t60) cc_final: 0.7456 (t60) REVERT: A 357 GLN cc_start: 0.7545 (mm-40) cc_final: 0.6722 (mm-40) REVERT: A 360 TRP cc_start: 0.7996 (m100) cc_final: 0.5806 (m100) REVERT: A 361 PHE cc_start: 0.7250 (m-80) cc_final: 0.6205 (m-80) REVERT: A 383 TYR cc_start: 0.5827 (m-80) cc_final: 0.5602 (m-80) REVERT: A 397 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7157 (ptt-90) REVERT: A 405 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7802 (mm-30) REVERT: A 430 CYS cc_start: 0.7159 (p) cc_final: 0.6758 (p) REVERT: A 502 TYR cc_start: 0.5992 (t80) cc_final: 0.5141 (t80) REVERT: A 536 VAL cc_start: 0.7657 (m) cc_final: 0.7426 (p) REVERT: A 558 LEU cc_start: 0.6926 (tp) cc_final: 0.6600 (mt) REVERT: E 23 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7256 (mp0) REVERT: E 35 TRP cc_start: 0.3129 (m-10) cc_final: 0.2905 (m-10) REVERT: C 28 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7701 (tptp) REVERT: C 33 ILE cc_start: 0.9105 (mm) cc_final: 0.8823 (mm) REVERT: C 45 GLN cc_start: 0.7770 (mt0) cc_final: 0.7471 (tt0) REVERT: C 62 TYR cc_start: 0.7953 (t80) cc_final: 0.7469 (t80) REVERT: C 68 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8236 (mptt) REVERT: C 71 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 72 LYS cc_start: 0.8450 (tttt) cc_final: 0.8013 (tptm) REVERT: C 83 GLU cc_start: 0.7708 (tp30) cc_final: 0.7247 (tp30) REVERT: C 86 ILE cc_start: 0.7978 (mt) cc_final: 0.7686 (mm) REVERT: C 124 MET cc_start: 0.3219 (tmm) cc_final: 0.2787 (tmm) REVERT: C 125 TYR cc_start: 0.5112 (t80) cc_final: 0.4822 (t80) REVERT: C 153 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7456 (mmm-85) REVERT: C 163 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7707 (mm110) REVERT: C 188 GLN cc_start: 0.8118 (tp40) cc_final: 0.7702 (tp40) REVERT: C 199 SER cc_start: 0.8587 (t) cc_final: 0.8283 (p) REVERT: C 205 PHE cc_start: 0.7745 (t80) cc_final: 0.7488 (t80) REVERT: C 206 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6141 (mp0) REVERT: C 222 GLN cc_start: 0.7560 (tp40) cc_final: 0.7165 (tm-30) REVERT: C 224 PHE cc_start: 0.6828 (m-10) cc_final: 0.6456 (m-80) REVERT: C 234 ILE cc_start: 0.8645 (mm) cc_final: 0.8236 (tp) REVERT: C 235 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7928 (mtmm) REVERT: C 238 GLU cc_start: 0.7478 (tp30) cc_final: 0.6718 (tm-30) REVERT: C 243 GLU cc_start: 0.8323 (pt0) cc_final: 0.7534 (pp20) REVERT: C 246 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7462 (tm-30) REVERT: C 247 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7970 (ttm110) REVERT: C 250 HIS cc_start: 0.8008 (t-90) cc_final: 0.7244 (t-90) REVERT: C 258 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7059 (mm-30) REVERT: C 262 LYS cc_start: 0.8062 (tmtm) cc_final: 0.7357 (ttpp) REVERT: C 265 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7177 (mm-30) REVERT: C 274 LYS cc_start: 0.8414 (tppt) cc_final: 0.7806 (tppt) REVERT: C 282 SER cc_start: 0.7633 (m) cc_final: 0.7387 (m) REVERT: C 288 LEU cc_start: 0.8861 (tp) cc_final: 0.8449 (tp) REVERT: C 292 LYS cc_start: 0.8513 (mmmm) cc_final: 0.7880 (mmtm) REVERT: C 301 LYS cc_start: 0.8381 (ptpt) cc_final: 0.8147 (ptpp) REVERT: C 306 VAL cc_start: 0.8694 (t) cc_final: 0.8326 (p) REVERT: C 314 CYS cc_start: 0.7524 (m) cc_final: 0.7288 (m) REVERT: C 346 LEU cc_start: 0.8277 (tp) cc_final: 0.8032 (tp) REVERT: C 353 ASP cc_start: 0.7980 (t0) cc_final: 0.7691 (t0) REVERT: C 368 GLN cc_start: 0.7358 (tm-30) cc_final: 0.6665 (tm-30) REVERT: C 369 THR cc_start: 0.8131 (p) cc_final: 0.7714 (t) REVERT: C 373 ASP cc_start: 0.6387 (OUTLIER) cc_final: 0.6031 (t0) REVERT: C 386 GLU cc_start: 0.8330 (mp0) cc_final: 0.6503 (mp0) REVERT: C 394 ASP cc_start: 0.7922 (t0) cc_final: 0.7525 (t0) REVERT: C 395 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8173 (mmmm) REVERT: C 409 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 412 LEU cc_start: 0.8709 (mt) cc_final: 0.8466 (mm) REVERT: C 413 ASP cc_start: 0.8586 (m-30) cc_final: 0.8277 (m-30) REVERT: C 418 LEU cc_start: 0.8789 (tt) cc_final: 0.8516 (tp) REVERT: C 423 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7117 (pt0) REVERT: C 424 GLU cc_start: 0.7275 (mp0) cc_final: 0.6608 (mp0) REVERT: C 431 TYR cc_start: 0.8241 (m-80) cc_final: 0.6701 (m-10) REVERT: C 438 ARG cc_start: 0.7741 (tpm170) cc_final: 0.6906 (tpm170) REVERT: C 441 LEU cc_start: 0.8235 (mt) cc_final: 0.7728 (mt) REVERT: C 457 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8674 (mmtp) REVERT: C 473 MET cc_start: 0.7828 (mmt) cc_final: 0.7005 (mmt) REVERT: C 477 MET cc_start: 0.7525 (tmm) cc_final: 0.7006 (tmm) REVERT: C 534 ILE cc_start: 0.8228 (mt) cc_final: 0.8027 (mt) REVERT: C 554 MET cc_start: 0.6713 (tpp) cc_final: 0.6295 (tpp) REVERT: C 603 MET cc_start: 0.7380 (tmm) cc_final: 0.6887 (tmm) REVERT: C 687 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5831 (pp20) REVERT: C 688 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7639 (mmm-85) REVERT: C 692 ARG cc_start: 0.8438 (tpp-160) cc_final: 0.8154 (mmp80) REVERT: B 19 GLU cc_start: 0.7584 (pp20) cc_final: 0.6838 (pp20) REVERT: B 20 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8187 (tp40) REVERT: B 21 LEU cc_start: 0.8660 (mt) cc_final: 0.8311 (mm) REVERT: B 24 PHE cc_start: 0.8509 (m-10) cc_final: 0.8149 (m-80) REVERT: B 25 TYR cc_start: 0.8666 (t80) cc_final: 0.8460 (t80) REVERT: B 29 LEU cc_start: 0.8228 (mp) cc_final: 0.7931 (mp) REVERT: B 46 LYS cc_start: 0.8675 (mttm) cc_final: 0.8222 (mttm) REVERT: B 57 ARG cc_start: 0.8509 (ptm160) cc_final: 0.8224 (ttm110) REVERT: B 69 GLN cc_start: 0.7848 (tt0) cc_final: 0.7617 (tt0) REVERT: B 72 VAL cc_start: 0.8854 (m) cc_final: 0.8414 (p) REVERT: B 85 ILE cc_start: 0.8657 (mt) cc_final: 0.8350 (tp) REVERT: B 87 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8319 (p) REVERT: B 88 TYR cc_start: 0.8782 (t80) cc_final: 0.7871 (t80) REVERT: B 112 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7443 (mm110) REVERT: B 115 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.6949 (p0) REVERT: B 123 TYR cc_start: 0.7880 (t80) cc_final: 0.7249 (t80) REVERT: B 132 ASN cc_start: 0.8001 (p0) cc_final: 0.7661 (p0) REVERT: B 149 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7620 (tptp) REVERT: B 155 MET cc_start: 0.7775 (tpt) cc_final: 0.7392 (tpp) REVERT: B 170 MET cc_start: 0.7858 (mmm) cc_final: 0.7599 (mmm) REVERT: B 184 ASP cc_start: 0.7994 (t70) cc_final: 0.7611 (t0) REVERT: B 192 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 199 MET cc_start: 0.7811 (mmp) cc_final: 0.7406 (mmp) REVERT: B 209 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7887 (mmt90) REVERT: B 212 TYR cc_start: 0.7903 (m-10) cc_final: 0.7559 (m-80) REVERT: B 215 SER cc_start: 0.8176 (m) cc_final: 0.7849 (p) REVERT: B 242 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7855 (mmtt) REVERT: B 294 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7172 (mmtm) REVERT: B 307 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7910 (mmtm) REVERT: B 363 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8082 (mmtp) REVERT: B 381 TYR cc_start: 0.7455 (m-80) cc_final: 0.6695 (m-80) REVERT: B 383 TYR cc_start: 0.5537 (m-80) cc_final: 0.5155 (m-80) REVERT: B 429 ASP cc_start: 0.8098 (m-30) cc_final: 0.7278 (m-30) REVERT: B 430 CYS cc_start: 0.5498 (m) cc_final: 0.4658 (t) REVERT: B 452 MET cc_start: 0.6313 (mpp) cc_final: 0.5809 (mpp) REVERT: B 469 ASP cc_start: 0.7410 (t70) cc_final: 0.6944 (t70) REVERT: B 470 LYS cc_start: 0.7257 (tttm) cc_final: 0.6951 (tttp) REVERT: B 502 TYR cc_start: 0.6567 (t80) cc_final: 0.6243 (t80) REVERT: B 503 ASP cc_start: 0.8293 (t0) cc_final: 0.7943 (t0) REVERT: B 529 VAL cc_start: 0.6314 (t) cc_final: 0.5351 (m) REVERT: B 583 VAL cc_start: 0.7935 (p) cc_final: 0.7628 (t) REVERT: F 28 LYS cc_start: 0.7870 (mmmm) cc_final: 0.7536 (mmmm) REVERT: F 46 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6991 (ttp-110) REVERT: F 56 GLU cc_start: 0.8000 (mp0) cc_final: 0.7394 (pm20) REVERT: F 62 TYR cc_start: 0.8049 (t80) cc_final: 0.7146 (t80) REVERT: F 63 THR cc_start: 0.7551 (t) cc_final: 0.7199 (p) REVERT: F 64 MET cc_start: 0.7582 (tpt) cc_final: 0.7065 (tpt) REVERT: F 68 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8418 (mttm) REVERT: F 71 GLU cc_start: 0.7670 (tm-30) cc_final: 0.6989 (tm-30) REVERT: F 78 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7966 (ttm-80) REVERT: F 79 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6737 (tp30) REVERT: F 103 GLN cc_start: 0.8556 (tp40) cc_final: 0.8073 (tp40) REVERT: F 113 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7567 (tp40) REVERT: F 116 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8205 (tpp) REVERT: F 118 MET cc_start: 0.7399 (mtm) cc_final: 0.7121 (mtm) REVERT: F 124 MET cc_start: 0.4583 (tmm) cc_final: 0.3859 (tmm) REVERT: F 126 MET cc_start: 0.8124 (tmt) cc_final: 0.7580 (tmm) REVERT: F 140 TYR cc_start: 0.8003 (t80) cc_final: 0.7028 (t80) REVERT: F 145 ILE cc_start: 0.8768 (mt) cc_final: 0.8526 (tt) REVERT: F 154 TYR cc_start: 0.7204 (t80) cc_final: 0.5580 (t80) REVERT: F 158 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: F 163 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7169 (mm110) REVERT: F 167 ASP cc_start: 0.7397 (t0) cc_final: 0.6978 (t0) REVERT: F 168 MET cc_start: 0.7518 (ptp) cc_final: 0.7143 (ptp) REVERT: F 188 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7896 (mm-40) REVERT: F 205 PHE cc_start: 0.8542 (t80) cc_final: 0.8144 (t80) REVERT: F 233 TYR cc_start: 0.7597 (t80) cc_final: 0.7181 (t80) REVERT: F 238 GLU cc_start: 0.8267 (tp30) cc_final: 0.7728 (tp30) REVERT: F 240 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7666 (tpp80) REVERT: F 243 GLU cc_start: 0.7682 (pp20) cc_final: 0.7246 (pp20) REVERT: F 246 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7248 (tp30) REVERT: F 249 MET cc_start: 0.7807 (ppp) cc_final: 0.7382 (ppp) REVERT: F 257 GLU cc_start: 0.7346 (pp20) cc_final: 0.7102 (pp20) REVERT: F 258 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7517 (mp0) REVERT: F 265 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7149 (mm-30) REVERT: F 270 SER cc_start: 0.8552 (m) cc_final: 0.8054 (t) REVERT: F 272 HIS cc_start: 0.6607 (m-70) cc_final: 0.6033 (m170) REVERT: F 273 MET cc_start: 0.7484 (ttp) cc_final: 0.7019 (ttp) REVERT: F 274 LYS cc_start: 0.8399 (tppt) cc_final: 0.7873 (tmmt) REVERT: F 276 ILE cc_start: 0.7626 (tp) cc_final: 0.7280 (tt) REVERT: F 287 MET cc_start: 0.7590 (ptm) cc_final: 0.7046 (ppp) REVERT: F 301 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7926 (ptpp) REVERT: F 303 PHE cc_start: 0.8031 (m-80) cc_final: 0.7492 (m-80) REVERT: F 322 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7688 (mmt180) REVERT: F 323 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7615 (tm-30) REVERT: F 332 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6348 (pm20) REVERT: F 352 PHE cc_start: 0.8026 (m-80) cc_final: 0.7786 (m-10) REVERT: F 353 ASP cc_start: 0.7315 (t0) cc_final: 0.7106 (t0) REVERT: F 368 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7106 (tm-30) REVERT: F 414 LYS cc_start: 0.8965 (mmtm) cc_final: 0.8705 (mmtm) REVERT: F 423 GLN cc_start: 0.7830 (tt0) cc_final: 0.7341 (tt0) REVERT: F 671 ARG cc_start: 0.6014 (tpt90) cc_final: 0.3732 (tpt90) REVERT: F 673 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7678 (pptt) REVERT: F 687 GLU cc_start: 0.4658 (OUTLIER) cc_final: 0.2122 (tt0) REVERT: F 734 PHE cc_start: 0.7252 (p90) cc_final: 0.6798 (p90) REVERT: F 735 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5450 (mp) REVERT: D 42 CYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5931 (m) outliers start: 115 outliers final: 72 residues processed: 790 average time/residue: 0.3710 time to fit residues: 436.6508 Evaluate side-chains 797 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 709 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 THR 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 249 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 397 ARG 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 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 423 GLN 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 596 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 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 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 87 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 GLN 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 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 536 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 39 ASN 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 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 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 735 LEU 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 182 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 152 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 165 HIS ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 729 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 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** F 434 GLN F 489 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.164655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.138264 restraints weight = 48964.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.142721 restraints weight = 26195.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.145584 restraints weight = 15943.866| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22753 Z= 0.199 Angle : 0.755 17.759 30696 Z= 0.386 Chirality : 0.046 0.236 3385 Planarity : 0.005 0.068 3934 Dihedral : 4.782 26.430 3006 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.90 % Favored : 89.99 % Rotamer: Outliers : 4.94 % Allowed : 24.93 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2718 helix: 0.67 (0.15), residues: 1261 sheet: -1.01 (0.31), residues: 269 loop : -2.46 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 233 HIS 0.019 0.002 HIS F 490 PHE 0.050 0.002 PHE A 256 TYR 0.026 0.002 TYR A 164 ARG 0.012 0.001 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 1102) hydrogen bonds : angle 5.07804 ( 3228) metal coordination : bond 0.01544 ( 22) metal coordination : angle 4.32468 ( 12) covalent geometry : bond 0.00411 (22731) covalent geometry : angle 0.75023 (30684) *********************** 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 846 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 724 time to evaluate : 2.574 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: A 9 ILE cc_start: 0.8276 (tp) cc_final: 0.7877 (pt) REVERT: A 13 TYR cc_start: 0.7408 (t80) cc_final: 0.6919 (t80) REVERT: A 19 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7596 (pp20) REVERT: A 20 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8084 (mm110) REVERT: A 22 LYS cc_start: 0.8556 (ttmt) cc_final: 0.7802 (ttmt) REVERT: A 26 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 29 LEU cc_start: 0.8622 (mp) cc_final: 0.8084 (mm) REVERT: A 49 LEU cc_start: 0.8217 (mt) cc_final: 0.7921 (mt) REVERT: A 57 ARG cc_start: 0.8201 (ptm160) cc_final: 0.7724 (ttm-80) REVERT: A 60 PHE cc_start: 0.8439 (m-80) cc_final: 0.8158 (m-10) REVERT: A 66 GLU cc_start: 0.7717 (mp0) cc_final: 0.7217 (mp0) REVERT: A 68 LYS cc_start: 0.8105 (tptp) cc_final: 0.7805 (tptp) REVERT: A 84 ILE cc_start: 0.8654 (tp) cc_final: 0.8283 (tt) REVERT: A 87 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 102 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 106 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 109 CYS cc_start: 0.8205 (t) cc_final: 0.6625 (t) REVERT: A 115 ASP cc_start: 0.8038 (p0) cc_final: 0.7426 (p0) REVERT: A 118 GLN cc_start: 0.8274 (tt0) cc_final: 0.7839 (tt0) REVERT: A 122 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 127 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8345 (mmmm) REVERT: A 131 GLU cc_start: 0.7503 (pm20) cc_final: 0.7162 (pm20) REVERT: A 147 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 149 LYS cc_start: 0.8156 (tttt) cc_final: 0.7854 (ttmt) REVERT: A 157 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7031 (mm-30) REVERT: A 164 TYR cc_start: 0.3653 (p90) cc_final: 0.3356 (p90) REVERT: A 170 MET cc_start: 0.6908 (mmp) cc_final: 0.6385 (mmp) REVERT: A 191 GLU cc_start: 0.7570 (pp20) cc_final: 0.7224 (tm-30) REVERT: A 195 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7805 (ttm-80) REVERT: A 196 GLU cc_start: 0.7698 (pp20) cc_final: 0.7032 (pp20) REVERT: A 199 MET cc_start: 0.8177 (mmm) cc_final: 0.7805 (mmp) REVERT: A 209 ARG cc_start: 0.7594 (mtm180) cc_final: 0.7041 (mtm180) REVERT: A 211 GLN cc_start: 0.7894 (pm20) cc_final: 0.7529 (pm20) REVERT: A 225 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5658 (mt) REVERT: A 291 GLN cc_start: 0.8154 (mp10) cc_final: 0.7771 (mp10) REVERT: A 294 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8165 (mmmm) REVERT: A 297 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7913 (ptpt) REVERT: A 357 GLN cc_start: 0.7619 (mm-40) cc_final: 0.6854 (mm-40) REVERT: A 361 PHE cc_start: 0.7320 (m-80) cc_final: 0.6261 (m-80) REVERT: A 397 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7047 (ptt-90) REVERT: A 430 CYS cc_start: 0.6991 (p) cc_final: 0.6419 (p) REVERT: A 443 PHE cc_start: 0.8396 (t80) cc_final: 0.8153 (t80) REVERT: A 454 MET cc_start: 0.6955 (tpp) cc_final: 0.6553 (tpp) REVERT: A 536 VAL cc_start: 0.7631 (m) cc_final: 0.7409 (p) REVERT: E 23 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7237 (mp0) REVERT: E 35 TRP cc_start: 0.3297 (m-10) cc_final: 0.3044 (m-10) REVERT: E 48 HIS cc_start: 0.5369 (t-90) cc_final: 0.4779 (t-90) REVERT: C 28 LYS cc_start: 0.8176 (mmmm) cc_final: 0.7778 (tptp) REVERT: C 33 ILE cc_start: 0.8964 (mm) cc_final: 0.8701 (mm) REVERT: C 35 ASP cc_start: 0.7424 (t0) cc_final: 0.7147 (m-30) REVERT: C 36 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7993 (tp) REVERT: C 43 GLU cc_start: 0.7354 (tp30) cc_final: 0.6983 (tp30) REVERT: C 45 GLN cc_start: 0.7832 (mt0) cc_final: 0.7558 (tt0) REVERT: C 62 TYR cc_start: 0.8014 (t80) cc_final: 0.7390 (t80) REVERT: C 64 MET cc_start: 0.7694 (tpp) cc_final: 0.7230 (tpp) REVERT: C 68 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8316 (mptt) REVERT: C 71 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 72 LYS cc_start: 0.8504 (tttt) cc_final: 0.8081 (tptm) REVERT: C 83 GLU cc_start: 0.7847 (tp30) cc_final: 0.7448 (tp30) REVERT: C 124 MET cc_start: 0.3337 (tmm) cc_final: 0.2941 (tmm) REVERT: C 125 TYR cc_start: 0.5178 (t80) cc_final: 0.4882 (t80) REVERT: C 140 TYR cc_start: 0.8601 (t80) cc_final: 0.8358 (t80) REVERT: C 153 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7431 (mmm-85) REVERT: C 163 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7842 (mm110) REVERT: C 188 GLN cc_start: 0.8122 (tp40) cc_final: 0.7714 (tp40) REVERT: C 191 MET cc_start: 0.8086 (tpp) cc_final: 0.7818 (mmm) REVERT: C 199 SER cc_start: 0.8599 (t) cc_final: 0.8314 (m) REVERT: C 205 PHE cc_start: 0.7784 (t80) cc_final: 0.7524 (t80) REVERT: C 206 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6277 (mp0) REVERT: C 222 GLN cc_start: 0.7540 (tp40) cc_final: 0.7091 (tm-30) REVERT: C 224 PHE cc_start: 0.6585 (m-10) cc_final: 0.5854 (m-10) REVERT: C 233 TYR cc_start: 0.7915 (t80) cc_final: 0.7571 (t80) REVERT: C 234 ILE cc_start: 0.8585 (mm) cc_final: 0.8022 (tp) REVERT: C 235 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7774 (mtmm) REVERT: C 238 GLU cc_start: 0.7575 (tp30) cc_final: 0.6812 (tm-30) REVERT: C 246 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 247 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7718 (ttm110) REVERT: C 250 HIS cc_start: 0.8012 (t-90) cc_final: 0.7233 (t-90) REVERT: C 258 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7125 (mp0) REVERT: C 262 LYS cc_start: 0.8141 (tmtm) cc_final: 0.7429 (ttmm) REVERT: C 265 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7213 (mm-30) REVERT: C 274 LYS cc_start: 0.8362 (tppt) cc_final: 0.7844 (tppt) REVERT: C 282 SER cc_start: 0.7921 (m) cc_final: 0.7668 (m) REVERT: C 288 LEU cc_start: 0.8977 (tp) cc_final: 0.8763 (tp) REVERT: C 292 LYS cc_start: 0.8457 (mmmm) cc_final: 0.7985 (mmtm) REVERT: C 301 LYS cc_start: 0.8342 (ptpt) cc_final: 0.8023 (ptpp) REVERT: C 306 VAL cc_start: 0.8689 (t) cc_final: 0.8360 (p) REVERT: C 314 CYS cc_start: 0.7540 (m) cc_final: 0.7311 (m) REVERT: C 346 LEU cc_start: 0.8323 (tp) cc_final: 0.8072 (tp) REVERT: C 353 ASP cc_start: 0.8058 (t0) cc_final: 0.7787 (t0) REVERT: C 354 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7823 (ttp-110) REVERT: C 368 GLN cc_start: 0.7495 (tm-30) cc_final: 0.6827 (tm-30) REVERT: C 369 THR cc_start: 0.8237 (p) cc_final: 0.7842 (t) REVERT: C 373 ASP cc_start: 0.6538 (OUTLIER) cc_final: 0.6270 (t0) REVERT: C 386 GLU cc_start: 0.8370 (mp0) cc_final: 0.6653 (mp0) REVERT: C 394 ASP cc_start: 0.7934 (t0) cc_final: 0.7560 (t0) REVERT: C 395 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8188 (mmmm) REVERT: C 409 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7570 (mt-10) REVERT: C 412 LEU cc_start: 0.8740 (mt) cc_final: 0.8471 (mm) REVERT: C 413 ASP cc_start: 0.8579 (m-30) cc_final: 0.8141 (m-30) REVERT: C 416 MET cc_start: 0.7185 (tpp) cc_final: 0.6955 (tpp) REVERT: C 418 LEU cc_start: 0.8861 (tt) cc_final: 0.8595 (tp) REVERT: C 424 GLU cc_start: 0.7353 (mp0) cc_final: 0.6838 (mp0) REVERT: C 431 TYR cc_start: 0.8392 (m-80) cc_final: 0.6982 (m-10) REVERT: C 433 LYS cc_start: 0.7931 (ttpp) cc_final: 0.7505 (ptmm) REVERT: C 438 ARG cc_start: 0.7825 (tpm170) cc_final: 0.7106 (tpm170) REVERT: C 441 LEU cc_start: 0.8305 (mt) cc_final: 0.7804 (mt) REVERT: C 457 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8584 (mmmm) REVERT: C 473 MET cc_start: 0.7932 (mmt) cc_final: 0.7351 (mmt) REVERT: C 484 MET cc_start: 0.3535 (OUTLIER) cc_final: 0.3268 (tpt) REVERT: C 554 MET cc_start: 0.6708 (tpp) cc_final: 0.6387 (tpp) REVERT: C 687 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5946 (pp20) REVERT: C 688 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7538 (mmm-85) REVERT: C 692 ARG cc_start: 0.8409 (tpp-160) cc_final: 0.8131 (mmp80) REVERT: B 19 GLU cc_start: 0.7657 (pp20) cc_final: 0.6997 (pp20) REVERT: B 21 LEU cc_start: 0.8676 (mt) cc_final: 0.8297 (mm) REVERT: B 24 PHE cc_start: 0.8533 (m-10) cc_final: 0.8174 (m-80) REVERT: B 29 LEU cc_start: 0.8313 (mp) cc_final: 0.7998 (mp) REVERT: B 46 LYS cc_start: 0.8645 (mttm) cc_final: 0.8249 (mttm) REVERT: B 57 ARG cc_start: 0.8523 (ptm160) cc_final: 0.8234 (ttm110) REVERT: B 72 VAL cc_start: 0.8794 (m) cc_final: 0.8441 (p) REVERT: B 85 ILE cc_start: 0.8671 (mt) cc_final: 0.8393 (tp) REVERT: B 87 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 112 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7139 (mm-40) REVERT: B 123 TYR cc_start: 0.7903 (t80) cc_final: 0.7255 (t80) REVERT: B 132 ASN cc_start: 0.7948 (p0) cc_final: 0.7664 (p0) REVERT: B 145 CYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7731 (m) REVERT: B 149 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7536 (tptm) REVERT: B 155 MET cc_start: 0.7958 (tpt) cc_final: 0.7516 (tpp) REVERT: B 166 GLN cc_start: 0.5628 (mp10) cc_final: 0.5137 (mp10) REVERT: B 170 MET cc_start: 0.7966 (mmm) cc_final: 0.7600 (mmm) REVERT: B 171 GLN cc_start: 0.8118 (pt0) cc_final: 0.7501 (pm20) REVERT: B 178 ILE cc_start: 0.8060 (tp) cc_final: 0.7792 (mm) REVERT: B 184 ASP cc_start: 0.7996 (t70) cc_final: 0.7574 (t0) REVERT: B 195 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7461 (ttt180) REVERT: B 199 MET cc_start: 0.7818 (mmp) cc_final: 0.7415 (mmp) REVERT: B 209 ARG cc_start: 0.8272 (mmt90) cc_final: 0.7883 (mmt90) REVERT: B 212 TYR cc_start: 0.7899 (m-10) cc_final: 0.7586 (m-80) REVERT: B 215 SER cc_start: 0.8359 (m) cc_final: 0.7951 (p) REVERT: B 242 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7841 (mmtt) REVERT: B 294 LYS cc_start: 0.7412 (mmtm) cc_final: 0.7149 (mmtm) REVERT: B 307 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7884 (mmtm) REVERT: B 363 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8158 (mmmm) REVERT: B 381 TYR cc_start: 0.7458 (m-80) cc_final: 0.6710 (m-80) REVERT: B 383 TYR cc_start: 0.5565 (m-80) cc_final: 0.5171 (m-80) REVERT: B 429 ASP cc_start: 0.8209 (m-30) cc_final: 0.7089 (m-30) REVERT: B 469 ASP cc_start: 0.7403 (t70) cc_final: 0.6991 (t70) REVERT: B 470 LYS cc_start: 0.7259 (tttm) cc_final: 0.6910 (tttp) REVERT: B 502 TYR cc_start: 0.6624 (t80) cc_final: 0.6166 (t80) REVERT: B 503 ASP cc_start: 0.8243 (t0) cc_final: 0.7935 (t0) REVERT: B 583 VAL cc_start: 0.8003 (p) cc_final: 0.7625 (t) REVERT: B 585 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8408 (mtmm) REVERT: F 28 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7571 (mmmm) REVERT: F 46 ARG cc_start: 0.7324 (mtm110) cc_final: 0.6999 (ttp-110) REVERT: F 53 SER cc_start: 0.8109 (t) cc_final: 0.7808 (t) REVERT: F 55 GLU cc_start: 0.7756 (tp30) cc_final: 0.7465 (tp30) REVERT: F 56 GLU cc_start: 0.8076 (mp0) cc_final: 0.7785 (mp0) REVERT: F 62 TYR cc_start: 0.8127 (t80) cc_final: 0.6906 (t80) REVERT: F 63 THR cc_start: 0.7640 (t) cc_final: 0.7282 (p) REVERT: F 64 MET cc_start: 0.7569 (tpt) cc_final: 0.7100 (tpt) REVERT: F 68 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8458 (mttm) REVERT: F 71 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7076 (tm-30) REVERT: F 78 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7942 (ttm-80) REVERT: F 79 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6630 (tp30) REVERT: F 103 GLN cc_start: 0.8588 (tp40) cc_final: 0.8094 (tp40) REVERT: F 113 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7482 (tp40) REVERT: F 116 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8228 (tpp) REVERT: F 117 VAL cc_start: 0.8316 (t) cc_final: 0.7928 (p) REVERT: F 118 MET cc_start: 0.7452 (mtm) cc_final: 0.7110 (mtm) REVERT: F 124 MET cc_start: 0.4427 (tmm) cc_final: 0.3769 (tmm) REVERT: F 126 MET cc_start: 0.8030 (tmt) cc_final: 0.7556 (tmm) REVERT: F 140 TYR cc_start: 0.8054 (t80) cc_final: 0.7158 (t80) REVERT: F 145 ILE cc_start: 0.8799 (mt) cc_final: 0.8503 (tt) REVERT: F 154 TYR cc_start: 0.7298 (t80) cc_final: 0.5785 (t80) REVERT: F 163 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7246 (mm110) REVERT: F 167 ASP cc_start: 0.7436 (t0) cc_final: 0.7077 (t0) REVERT: F 168 MET cc_start: 0.7639 (ptp) cc_final: 0.7361 (ptp) REVERT: F 180 ARG cc_start: 0.7792 (ptp-110) cc_final: 0.7445 (ptp-110) REVERT: F 205 PHE cc_start: 0.8483 (t80) cc_final: 0.8076 (t80) REVERT: F 233 TYR cc_start: 0.7642 (t80) cc_final: 0.7172 (t80) REVERT: F 238 GLU cc_start: 0.8280 (tp30) cc_final: 0.7638 (tp30) REVERT: F 240 ARG cc_start: 0.7944 (mmt180) cc_final: 0.7724 (tpp80) REVERT: F 243 GLU cc_start: 0.7696 (pp20) cc_final: 0.7250 (pp20) REVERT: F 246 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7297 (tp30) REVERT: F 249 MET cc_start: 0.7774 (ppp) cc_final: 0.7314 (ppp) REVERT: F 258 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7863 (mp0) REVERT: F 265 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7145 (mm-30) REVERT: F 270 SER cc_start: 0.8501 (m) cc_final: 0.8069 (t) REVERT: F 272 HIS cc_start: 0.6671 (m-70) cc_final: 0.5757 (m170) REVERT: F 273 MET cc_start: 0.7598 (ttp) cc_final: 0.7105 (ttp) REVERT: F 274 LYS cc_start: 0.8490 (tppt) cc_final: 0.8032 (tmmt) REVERT: F 276 ILE cc_start: 0.7786 (tp) cc_final: 0.7260 (mt) REVERT: F 301 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7927 (ptpp) REVERT: F 303 PHE cc_start: 0.8069 (m-80) cc_final: 0.7497 (m-80) REVERT: F 322 ARG cc_start: 0.8218 (mmt90) cc_final: 0.7901 (mmt-90) REVERT: F 332 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: F 353 ASP cc_start: 0.7379 (t0) cc_final: 0.7156 (t0) REVERT: F 368 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7153 (tm-30) REVERT: F 369 THR cc_start: 0.8078 (p) cc_final: 0.7825 (t) REVERT: F 414 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8739 (mmtm) REVERT: F 423 GLN cc_start: 0.7867 (tt0) cc_final: 0.7577 (pt0) REVERT: F 457 LYS cc_start: 0.8528 (mmmt) cc_final: 0.7974 (mmtm) REVERT: F 671 ARG cc_start: 0.6178 (tpt90) cc_final: 0.3764 (tpt90) REVERT: F 673 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7626 (pptt) REVERT: F 687 GLU cc_start: 0.4767 (OUTLIER) cc_final: 0.2053 (tt0) REVERT: F 717 MET cc_start: 0.2891 (tpp) cc_final: 0.2291 (tpt) REVERT: D 42 CYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6205 (m) outliers start: 122 outliers final: 73 residues processed: 785 average time/residue: 0.3642 time to fit residues: 424.9785 Evaluate side-chains 790 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 703 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 THR 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 263 MET Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 397 ARG 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 25 MET 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 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP 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 594 VAL 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 729 GLN 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 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 87 THR 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 245 VAL Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 357 GLN 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 39 ASN 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 248 VAL Chi-restraints excluded: chain F residue 251 CYS 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 400 VAL Chi-restraints excluded: chain F residue 418 LEU 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 599 MET Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 667 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 199 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 12 optimal weight: 0.0010 chunk 222 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 100 ASN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 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** F 543 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.166127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.139539 restraints weight = 49020.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.144046 restraints weight = 26170.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.146832 restraints weight = 15917.468| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22753 Z= 0.166 Angle : 0.775 15.987 30696 Z= 0.390 Chirality : 0.046 0.278 3385 Planarity : 0.005 0.063 3934 Dihedral : 4.751 24.737 3006 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.42 % Favored : 90.51 % Rotamer: Outliers : 4.05 % Allowed : 26.79 % Favored : 69.16 % 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: 0.63 (0.15), residues: 1261 sheet: -1.00 (0.30), residues: 280 loop : -2.45 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP B 561 HIS 0.020 0.001 HIS F 490 PHE 0.037 0.002 PHE C 419 TYR 0.028 0.002 TYR A 164 ARG 0.011 0.001 ARG F 266 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 1102) hydrogen bonds : angle 5.06574 ( 3228) metal coordination : bond 0.01383 ( 22) metal coordination : angle 3.88637 ( 12) covalent geometry : bond 0.00355 (22731) covalent geometry : angle 0.77154 (30684) *********************** 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 803 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 703 time to evaluate : 2.260 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: A 9 ILE cc_start: 0.8239 (tp) cc_final: 0.7835 (pt) REVERT: A 13 TYR cc_start: 0.7389 (t80) cc_final: 0.6957 (t80) REVERT: A 19 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7576 (pp20) REVERT: A 20 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8110 (mm110) REVERT: A 22 LYS cc_start: 0.8509 (ttmt) cc_final: 0.7788 (ttmt) REVERT: A 26 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7418 (mt-10) REVERT: A 49 LEU cc_start: 0.8200 (mt) cc_final: 0.7913 (mt) REVERT: A 57 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7770 (ttp80) REVERT: A 59 MET cc_start: 0.7467 (ttp) cc_final: 0.7165 (ttp) REVERT: A 60 PHE cc_start: 0.8245 (m-80) cc_final: 0.7916 (m-10) REVERT: A 68 LYS cc_start: 0.8000 (tptp) cc_final: 0.7758 (tptp) REVERT: A 84 ILE cc_start: 0.8617 (tp) cc_final: 0.8251 (tt) REVERT: A 87 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 102 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 106 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 109 CYS cc_start: 0.8185 (t) cc_final: 0.6616 (t) REVERT: A 115 ASP cc_start: 0.8022 (p0) cc_final: 0.7383 (p0) REVERT: A 118 GLN cc_start: 0.8268 (tt0) cc_final: 0.7837 (tt0) REVERT: A 122 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 127 LYS cc_start: 0.8669 (mmmm) cc_final: 0.8349 (mmmm) REVERT: A 147 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 149 LYS cc_start: 0.8155 (tttt) cc_final: 0.7841 (ttmt) REVERT: A 157 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7036 (mm-30) REVERT: A 159 LYS cc_start: 0.7517 (mtmt) cc_final: 0.7257 (mmtm) REVERT: A 164 TYR cc_start: 0.3481 (p90) cc_final: 0.3237 (p90) REVERT: A 170 MET cc_start: 0.6791 (mmp) cc_final: 0.6381 (mmp) REVERT: A 191 GLU cc_start: 0.7583 (pp20) cc_final: 0.7180 (tm-30) REVERT: A 195 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7286 (ttm-80) REVERT: A 196 GLU cc_start: 0.7609 (pp20) cc_final: 0.7102 (pp20) REVERT: A 199 MET cc_start: 0.8169 (mmm) cc_final: 0.7736 (mmp) REVERT: A 209 ARG cc_start: 0.7508 (mtm180) cc_final: 0.7080 (mtm180) REVERT: A 211 GLN cc_start: 0.7854 (pm20) cc_final: 0.7494 (pm20) REVERT: A 267 GLU cc_start: 0.7277 (tp30) cc_final: 0.6982 (tp30) REVERT: A 291 GLN cc_start: 0.8101 (mp10) cc_final: 0.7737 (mp10) REVERT: A 294 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8116 (mmmm) REVERT: A 297 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7876 (ptpt) REVERT: A 357 GLN cc_start: 0.7586 (mm-40) cc_final: 0.6886 (mm-40) REVERT: A 361 PHE cc_start: 0.7288 (m-80) cc_final: 0.6293 (m-80) REVERT: A 397 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7044 (ptt-90) REVERT: A 430 CYS cc_start: 0.7188 (p) cc_final: 0.6612 (p) REVERT: A 443 PHE cc_start: 0.8364 (t80) cc_final: 0.8073 (t80) REVERT: A 454 MET cc_start: 0.6941 (tpp) cc_final: 0.6445 (tpp) REVERT: A 536 VAL cc_start: 0.7665 (m) cc_final: 0.7410 (p) REVERT: E 23 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7308 (mp0) REVERT: E 35 TRP cc_start: 0.3390 (m-10) cc_final: 0.3142 (m-10) REVERT: E 48 HIS cc_start: 0.5364 (t-90) cc_final: 0.4736 (t-90) REVERT: C 28 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7789 (tptp) REVERT: C 33 ILE cc_start: 0.8956 (mm) cc_final: 0.8698 (mm) REVERT: C 35 ASP cc_start: 0.7408 (t0) cc_final: 0.7122 (m-30) REVERT: C 36 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7979 (tp) REVERT: C 43 GLU cc_start: 0.7466 (tp30) cc_final: 0.6614 (tp30) REVERT: C 45 GLN cc_start: 0.7850 (mt0) cc_final: 0.7611 (tt0) REVERT: C 62 TYR cc_start: 0.7926 (t80) cc_final: 0.7294 (t80) REVERT: C 64 MET cc_start: 0.7680 (tpp) cc_final: 0.7191 (tpp) REVERT: C 68 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8325 (mptt) REVERT: C 71 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 72 LYS cc_start: 0.8493 (tttt) cc_final: 0.8071 (tptm) REVERT: C 83 GLU cc_start: 0.7827 (tp30) cc_final: 0.7447 (tp30) REVERT: C 124 MET cc_start: 0.3294 (tmm) cc_final: 0.2933 (tmm) REVERT: C 125 TYR cc_start: 0.5163 (t80) cc_final: 0.4841 (t80) REVERT: C 153 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7240 (mmm-85) REVERT: C 163 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7730 (mm110) REVERT: C 188 GLN cc_start: 0.8101 (tp40) cc_final: 0.7684 (tp40) REVERT: C 191 MET cc_start: 0.8139 (tpp) cc_final: 0.7540 (tmm) REVERT: C 205 PHE cc_start: 0.7469 (t80) cc_final: 0.7169 (t80) REVERT: C 206 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6328 (mm-30) REVERT: C 222 GLN cc_start: 0.7550 (tp40) cc_final: 0.7132 (tm-30) REVERT: C 234 ILE cc_start: 0.8569 (mm) cc_final: 0.8009 (tp) REVERT: C 235 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7796 (ttpp) REVERT: C 238 GLU cc_start: 0.7560 (tp30) cc_final: 0.6777 (tm-30) REVERT: C 243 GLU cc_start: 0.8514 (pt0) cc_final: 0.7390 (pp20) REVERT: C 246 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7503 (tm-30) REVERT: C 247 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7846 (ttm110) REVERT: C 250 HIS cc_start: 0.8026 (t-90) cc_final: 0.7249 (t-90) REVERT: C 258 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7104 (mp0) REVERT: C 262 LYS cc_start: 0.8064 (tmtm) cc_final: 0.7372 (ttmm) REVERT: C 265 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7203 (mm-30) REVERT: C 274 LYS cc_start: 0.8368 (tppt) cc_final: 0.7719 (tppt) REVERT: C 282 SER cc_start: 0.7787 (m) cc_final: 0.7521 (m) REVERT: C 292 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8043 (mmtm) REVERT: C 301 LYS cc_start: 0.8395 (ptpt) cc_final: 0.8084 (ptpp) REVERT: C 306 VAL cc_start: 0.8735 (t) cc_final: 0.8409 (p) REVERT: C 346 LEU cc_start: 0.8315 (tp) cc_final: 0.8076 (tp) REVERT: C 353 ASP cc_start: 0.8030 (t0) cc_final: 0.7710 (t0) REVERT: C 368 GLN cc_start: 0.7405 (tm-30) cc_final: 0.6801 (tm-30) REVERT: C 369 THR cc_start: 0.8203 (p) cc_final: 0.7823 (t) REVERT: C 373 ASP cc_start: 0.6492 (OUTLIER) cc_final: 0.6260 (t0) REVERT: C 386 GLU cc_start: 0.8349 (mp0) cc_final: 0.6609 (mp0) REVERT: C 394 ASP cc_start: 0.7926 (t0) cc_final: 0.7536 (t0) REVERT: C 395 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8192 (mmmm) REVERT: C 409 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 412 LEU cc_start: 0.8751 (mt) cc_final: 0.8490 (mm) REVERT: C 413 ASP cc_start: 0.8582 (m-30) cc_final: 0.8279 (m-30) REVERT: C 416 MET cc_start: 0.7376 (tpp) cc_final: 0.7133 (tpp) REVERT: C 418 LEU cc_start: 0.8855 (tt) cc_final: 0.8563 (tp) REVERT: C 423 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6540 (pt0) REVERT: C 424 GLU cc_start: 0.7427 (mp0) cc_final: 0.6774 (mp0) REVERT: C 431 TYR cc_start: 0.8325 (m-80) cc_final: 0.6852 (m-10) REVERT: C 438 ARG cc_start: 0.7745 (tpm170) cc_final: 0.6866 (tpm170) REVERT: C 439 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7933 (ptp-170) REVERT: C 441 LEU cc_start: 0.8215 (mt) cc_final: 0.7726 (mt) REVERT: C 473 MET cc_start: 0.7589 (mmt) cc_final: 0.6406 (tpp) REVERT: C 484 MET cc_start: 0.3443 (OUTLIER) cc_final: 0.3142 (tpt) REVERT: C 554 MET cc_start: 0.6695 (tpp) cc_final: 0.6364 (tpp) REVERT: C 603 MET cc_start: 0.7528 (tmm) cc_final: 0.6931 (tmm) REVERT: C 692 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.8168 (mmp80) REVERT: B 19 GLU cc_start: 0.7608 (pp20) cc_final: 0.6934 (pp20) REVERT: B 21 LEU cc_start: 0.8666 (mt) cc_final: 0.8298 (mm) REVERT: B 24 PHE cc_start: 0.8535 (m-10) cc_final: 0.8200 (m-80) REVERT: B 25 TYR cc_start: 0.8676 (t80) cc_final: 0.8469 (t80) REVERT: B 29 LEU cc_start: 0.8286 (mp) cc_final: 0.7973 (mt) REVERT: B 46 LYS cc_start: 0.8612 (mttm) cc_final: 0.8179 (mttm) REVERT: B 57 ARG cc_start: 0.8473 (ptm160) cc_final: 0.8166 (ttm110) REVERT: B 61 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6797 (tmm) REVERT: B 69 GLN cc_start: 0.7921 (tt0) cc_final: 0.7660 (tt0) REVERT: B 72 VAL cc_start: 0.8803 (m) cc_final: 0.8423 (p) REVERT: B 85 ILE cc_start: 0.8655 (mt) cc_final: 0.8374 (tp) REVERT: B 112 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7148 (mm-40) REVERT: B 123 TYR cc_start: 0.7845 (t80) cc_final: 0.7220 (t80) REVERT: B 132 ASN cc_start: 0.7888 (p0) cc_final: 0.7583 (p0) REVERT: B 145 CYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7987 (m) REVERT: B 149 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7601 (tppt) REVERT: B 155 MET cc_start: 0.7905 (tpt) cc_final: 0.7423 (tpp) REVERT: B 166 GLN cc_start: 0.5477 (mp10) cc_final: 0.5059 (mp10) REVERT: B 178 ILE cc_start: 0.7950 (tp) cc_final: 0.7591 (mm) REVERT: B 184 ASP cc_start: 0.7965 (t70) cc_final: 0.7532 (t0) REVERT: B 195 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7321 (ttt180) REVERT: B 199 MET cc_start: 0.7788 (mmp) cc_final: 0.7440 (mmp) REVERT: B 209 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7788 (mmt90) REVERT: B 212 TYR cc_start: 0.7687 (m-10) cc_final: 0.7412 (m-80) REVERT: B 215 SER cc_start: 0.8385 (m) cc_final: 0.8009 (p) REVERT: B 242 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7777 (mmtt) REVERT: B 297 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7375 (ptpp) REVERT: B 301 PRO cc_start: 0.7552 (Cg_exo) cc_final: 0.7320 (Cg_endo) REVERT: B 307 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7746 (mmtm) REVERT: B 363 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8073 (mmtp) REVERT: B 381 TYR cc_start: 0.7392 (m-80) cc_final: 0.6795 (m-80) REVERT: B 383 TYR cc_start: 0.5618 (m-80) cc_final: 0.5246 (m-80) REVERT: B 429 ASP cc_start: 0.8290 (m-30) cc_final: 0.7231 (m-30) REVERT: B 454 MET cc_start: 0.7416 (mmm) cc_final: 0.7061 (tmm) REVERT: B 469 ASP cc_start: 0.7425 (t70) cc_final: 0.6995 (t70) REVERT: B 470 LYS cc_start: 0.7413 (tttm) cc_final: 0.7025 (tttp) REVERT: B 503 ASP cc_start: 0.8284 (t0) cc_final: 0.7992 (t0) REVERT: B 583 VAL cc_start: 0.8004 (p) cc_final: 0.7645 (t) REVERT: F 28 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7567 (mmmm) REVERT: F 45 GLN cc_start: 0.8071 (tt0) cc_final: 0.7755 (tp-100) REVERT: F 46 ARG cc_start: 0.7342 (mtm110) cc_final: 0.7084 (ttp-110) REVERT: F 53 SER cc_start: 0.8112 (t) cc_final: 0.7816 (t) REVERT: F 56 GLU cc_start: 0.8087 (mp0) cc_final: 0.7770 (mp0) REVERT: F 62 TYR cc_start: 0.8118 (t80) cc_final: 0.7350 (t80) REVERT: F 63 THR cc_start: 0.7630 (t) cc_final: 0.7288 (p) REVERT: F 64 MET cc_start: 0.7567 (tpt) cc_final: 0.7094 (tpt) REVERT: F 68 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8427 (mttm) REVERT: F 71 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7033 (tm-30) REVERT: F 78 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7974 (ttm-80) REVERT: F 79 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6616 (tp30) REVERT: F 98 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8007 (p0) REVERT: F 103 GLN cc_start: 0.8583 (tp40) cc_final: 0.8090 (tp40) REVERT: F 113 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7489 (tp40) REVERT: F 116 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8253 (tpp) REVERT: F 117 VAL cc_start: 0.8302 (t) cc_final: 0.7957 (p) REVERT: F 118 MET cc_start: 0.7500 (mtm) cc_final: 0.7167 (mtm) REVERT: F 124 MET cc_start: 0.4573 (tmm) cc_final: 0.3899 (tmm) REVERT: F 126 MET cc_start: 0.8030 (tmt) cc_final: 0.7584 (tmm) REVERT: F 140 TYR cc_start: 0.8029 (t80) cc_final: 0.7138 (t80) REVERT: F 145 ILE cc_start: 0.8773 (mt) cc_final: 0.8501 (tt) REVERT: F 154 TYR cc_start: 0.7221 (t80) cc_final: 0.5831 (t80) REVERT: F 163 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7236 (mm110) REVERT: F 167 ASP cc_start: 0.7425 (t0) cc_final: 0.7047 (t0) REVERT: F 168 MET cc_start: 0.7623 (ptp) cc_final: 0.7312 (ptp) REVERT: F 205 PHE cc_start: 0.8446 (t80) cc_final: 0.7691 (t80) REVERT: F 233 TYR cc_start: 0.7713 (t80) cc_final: 0.7116 (t80) REVERT: F 238 GLU cc_start: 0.8276 (tp30) cc_final: 0.7616 (tp30) REVERT: F 240 ARG cc_start: 0.7979 (mmt180) cc_final: 0.7717 (tpp80) REVERT: F 243 GLU cc_start: 0.7704 (pp20) cc_final: 0.7275 (pp20) REVERT: F 246 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7281 (tp30) REVERT: F 249 MET cc_start: 0.7767 (ppp) cc_final: 0.7299 (ppp) REVERT: F 265 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7127 (mm-30) REVERT: F 270 SER cc_start: 0.8484 (m) cc_final: 0.8025 (t) REVERT: F 272 HIS cc_start: 0.6642 (m-70) cc_final: 0.5780 (m170) REVERT: F 273 MET cc_start: 0.7577 (ttp) cc_final: 0.7202 (ttp) REVERT: F 274 LYS cc_start: 0.8465 (tppt) cc_final: 0.8147 (tmmt) REVERT: F 276 ILE cc_start: 0.7787 (tp) cc_final: 0.7260 (mt) REVERT: F 301 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7892 (ptpp) REVERT: F 303 PHE cc_start: 0.8007 (m-80) cc_final: 0.7559 (m-80) REVERT: F 322 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7662 (mmt180) REVERT: F 332 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6415 (pm20) REVERT: F 346 LEU cc_start: 0.7712 (tp) cc_final: 0.7394 (pp) REVERT: F 360 PHE cc_start: 0.7872 (m-80) cc_final: 0.7370 (m-80) REVERT: F 368 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7125 (tm-30) REVERT: F 369 THR cc_start: 0.7994 (p) cc_final: 0.7661 (t) REVERT: F 378 LEU cc_start: 0.5092 (OUTLIER) cc_final: 0.4540 (tp) REVERT: F 414 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8660 (mmtm) REVERT: F 423 GLN cc_start: 0.7832 (tt0) cc_final: 0.7593 (pt0) REVERT: F 671 ARG cc_start: 0.6104 (tpt90) cc_final: 0.5541 (tpt90) REVERT: F 673 LYS cc_start: 0.8045 (ptmm) cc_final: 0.7767 (pptt) REVERT: F 687 GLU cc_start: 0.4445 (OUTLIER) cc_final: 0.1615 (tt0) REVERT: F 717 MET cc_start: 0.2802 (tpp) cc_final: 0.2215 (tpt) REVERT: D 42 CYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6464 (m) outliers start: 100 outliers final: 74 residues processed: 749 average time/residue: 0.3677 time to fit residues: 408.0302 Evaluate side-chains 774 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 685 time to evaluate : 2.569 ------------------------------------------------------------------------------- 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 87 THR 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 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 25 MET 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 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 423 GLN 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 594 VAL Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 723 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 55 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR 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 158 HIS Chi-restraints excluded: chain B residue 193 THR 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 245 VAL 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 550 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 98 ASN 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 165 LEU Chi-restraints excluded: chain F residue 166 LEU 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 306 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 418 LEU Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 517 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 97 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 173 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 88 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 106 optimal weight: 0.0000 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 165 HIS ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 729 GLN B 73 HIS B 103 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.166607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140059 restraints weight = 48964.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.144568 restraints weight = 26157.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147449 restraints weight = 15934.886| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22753 Z= 0.161 Angle : 0.777 14.454 30696 Z= 0.393 Chirality : 0.046 0.293 3385 Planarity : 0.005 0.061 3934 Dihedral : 4.804 26.666 3006 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.20 % Favored : 90.69 % Rotamer: Outliers : 3.93 % Allowed : 27.40 % 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: -1.24 (0.16), residues: 2718 helix: 0.58 (0.14), residues: 1266 sheet: -0.95 (0.32), residues: 266 loop : -2.42 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP B 561 HIS 0.021 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 F 266 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 1102) hydrogen bonds : angle 5.07533 ( 3228) metal coordination : bond 0.01276 ( 22) metal coordination : angle 3.83042 ( 12) covalent geometry : bond 0.00348 (22731) covalent geometry : angle 0.77372 (30684) *********************** 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 800 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 703 time to evaluate : 2.525 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: 0.8226 (tp) cc_final: 0.7863 (pt) REVERT: A 13 TYR cc_start: 0.7443 (t80) cc_final: 0.6988 (t80) REVERT: A 19 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7542 (pp20) REVERT: A 20 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8137 (mm110) REVERT: A 26 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 37 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.7919 (m) REVERT: A 49 LEU cc_start: 0.8185 (mt) cc_final: 0.7928 (mt) REVERT: A 57 ARG cc_start: 0.8123 (ptm160) cc_final: 0.7710 (ttm-80) REVERT: A 59 MET cc_start: 0.7346 (ttp) cc_final: 0.7006 (ttp) REVERT: A 60 PHE cc_start: 0.8322 (m-80) cc_final: 0.8005 (m-10) REVERT: A 68 LYS cc_start: 0.7973 (tptp) cc_final: 0.7640 (tptp) REVERT: A 84 ILE cc_start: 0.8653 (tp) cc_final: 0.8354 (tt) REVERT: A 87 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 102 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7178 (mm-30) REVERT: A 106 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 109 CYS cc_start: 0.8191 (t) cc_final: 0.6600 (t) REVERT: A 115 ASP cc_start: 0.8020 (p0) cc_final: 0.7396 (p0) REVERT: A 118 GLN cc_start: 0.8258 (tt0) cc_final: 0.7842 (tt0) REVERT: A 122 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 127 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8277 (mmtm) REVERT: A 147 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 149 LYS cc_start: 0.8147 (tttt) cc_final: 0.7820 (ttmt) REVERT: A 157 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 159 LYS cc_start: 0.7607 (mtmt) cc_final: 0.7351 (mmtm) REVERT: A 170 MET cc_start: 0.6837 (mmp) cc_final: 0.6333 (mmp) REVERT: A 191 GLU cc_start: 0.7604 (pp20) cc_final: 0.7158 (pp20) REVERT: A 195 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7292 (ttm-80) REVERT: A 196 GLU cc_start: 0.7647 (pp20) cc_final: 0.7104 (pp20) REVERT: A 199 MET cc_start: 0.8123 (mmm) cc_final: 0.7758 (mmp) REVERT: A 209 ARG cc_start: 0.7387 (mtm180) cc_final: 0.6953 (mtm180) REVERT: A 211 GLN cc_start: 0.7844 (pm20) cc_final: 0.7464 (pm20) REVERT: A 249 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7040 (tp) REVERT: A 272 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7351 (tp) REVERT: A 291 GLN cc_start: 0.8126 (mp10) cc_final: 0.7751 (mp10) REVERT: A 294 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8110 (mmmm) REVERT: A 297 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7866 (ptpt) REVERT: A 352 TRP cc_start: 0.7651 (t60) cc_final: 0.7355 (t60) REVERT: A 357 GLN cc_start: 0.7636 (mm-40) cc_final: 0.6769 (mm-40) REVERT: A 360 TRP cc_start: 0.7917 (m100) cc_final: 0.5633 (m100) REVERT: A 361 PHE cc_start: 0.7240 (m-80) cc_final: 0.6252 (m-80) REVERT: A 397 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6996 (ptt-90) REVERT: A 430 CYS cc_start: 0.7148 (p) cc_final: 0.6576 (p) REVERT: A 443 PHE cc_start: 0.8333 (t80) cc_final: 0.7990 (t80) REVERT: A 454 MET cc_start: 0.6844 (tpp) cc_final: 0.6387 (tpp) REVERT: A 536 VAL cc_start: 0.7683 (m) cc_final: 0.7419 (p) REVERT: E 23 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7242 (mp0) REVERT: E 48 HIS cc_start: 0.5374 (t-90) cc_final: 0.4833 (t-90) REVERT: C 28 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7767 (tptp) REVERT: C 33 ILE cc_start: 0.8949 (mm) cc_final: 0.8671 (mm) REVERT: C 35 ASP cc_start: 0.7375 (t0) cc_final: 0.7138 (m-30) REVERT: C 36 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7980 (tp) REVERT: C 43 GLU cc_start: 0.7488 (tp30) cc_final: 0.6637 (tp30) REVERT: C 49 ASN cc_start: 0.8131 (p0) cc_final: 0.7898 (p0) REVERT: C 62 TYR cc_start: 0.7919 (t80) cc_final: 0.7276 (t80) REVERT: C 64 MET cc_start: 0.7728 (tpp) cc_final: 0.7232 (tpp) REVERT: C 68 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8444 (mptt) REVERT: C 71 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 72 LYS cc_start: 0.8483 (tttt) cc_final: 0.7786 (tptp) REVERT: C 83 GLU cc_start: 0.7829 (tp30) cc_final: 0.7459 (tp30) REVERT: C 124 MET cc_start: 0.3240 (tmm) cc_final: 0.2988 (tmm) REVERT: C 125 TYR cc_start: 0.5181 (t80) cc_final: 0.4842 (t80) REVERT: C 153 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7279 (mmm-85) REVERT: C 163 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7755 (mm110) REVERT: C 188 GLN cc_start: 0.8181 (tp40) cc_final: 0.7788 (tp40) REVERT: C 191 MET cc_start: 0.8104 (tpp) cc_final: 0.7703 (tpp) REVERT: C 205 PHE cc_start: 0.7416 (t80) cc_final: 0.7133 (t80) REVERT: C 206 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6313 (mp0) REVERT: C 222 GLN cc_start: 0.7567 (tp40) cc_final: 0.7118 (tm-30) REVERT: C 234 ILE cc_start: 0.8501 (mm) cc_final: 0.7903 (tp) REVERT: C 235 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7696 (ttpp) REVERT: C 238 GLU cc_start: 0.7533 (tp30) cc_final: 0.6771 (tm-30) REVERT: C 246 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7492 (tm-30) REVERT: C 247 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7588 (ttm170) REVERT: C 250 HIS cc_start: 0.8016 (t-90) cc_final: 0.7260 (t-90) REVERT: C 258 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7074 (mp0) REVERT: C 262 LYS cc_start: 0.8059 (tmtm) cc_final: 0.7381 (ttmm) REVERT: C 265 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7197 (mm-30) REVERT: C 274 LYS cc_start: 0.8394 (tppt) cc_final: 0.7723 (tppt) REVERT: C 282 SER cc_start: 0.7902 (m) cc_final: 0.7635 (m) REVERT: C 292 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8046 (mmtt) REVERT: C 301 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8116 (ptpp) REVERT: C 306 VAL cc_start: 0.8733 (t) cc_final: 0.8443 (p) REVERT: C 346 LEU cc_start: 0.8314 (tp) cc_final: 0.8066 (tp) REVERT: C 353 ASP cc_start: 0.8018 (t0) cc_final: 0.7752 (t0) REVERT: C 354 ARG cc_start: 0.7994 (ptp-170) cc_final: 0.7212 (ptt-90) REVERT: C 368 GLN cc_start: 0.7413 (tm-30) cc_final: 0.6844 (tm-30) REVERT: C 369 THR cc_start: 0.8243 (p) cc_final: 0.7879 (t) REVERT: C 373 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6302 (t0) REVERT: C 386 GLU cc_start: 0.8324 (mp0) cc_final: 0.6602 (mp0) REVERT: C 394 ASP cc_start: 0.7911 (t0) cc_final: 0.7529 (t0) REVERT: C 395 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8197 (mmmm) REVERT: C 409 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7577 (mt-10) REVERT: C 412 LEU cc_start: 0.8721 (mt) cc_final: 0.8468 (mm) REVERT: C 413 ASP cc_start: 0.8557 (m-30) cc_final: 0.8233 (m-30) REVERT: C 416 MET cc_start: 0.7354 (tpp) cc_final: 0.7139 (tpp) REVERT: C 418 LEU cc_start: 0.8787 (tt) cc_final: 0.8501 (tp) REVERT: C 423 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6549 (pt0) REVERT: C 424 GLU cc_start: 0.7454 (mp0) cc_final: 0.6791 (mp0) REVERT: C 431 TYR cc_start: 0.8320 (m-80) cc_final: 0.6864 (m-10) REVERT: C 438 ARG cc_start: 0.7757 (tpm170) cc_final: 0.6770 (tpm170) REVERT: C 439 ARG cc_start: 0.8044 (ptp90) cc_final: 0.7824 (ptp-170) REVERT: C 441 LEU cc_start: 0.8167 (mt) cc_final: 0.7674 (mt) REVERT: C 473 MET cc_start: 0.7517 (mmt) cc_final: 0.6128 (mmt) REVERT: C 484 MET cc_start: 0.3480 (OUTLIER) cc_final: 0.3212 (tpt) REVERT: C 554 MET cc_start: 0.6657 (tpp) cc_final: 0.6337 (tpp) REVERT: C 603 MET cc_start: 0.7513 (tmm) cc_final: 0.6924 (tmm) REVERT: C 688 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7727 (mmm-85) REVERT: C 692 ARG cc_start: 0.8432 (tpp-160) cc_final: 0.8182 (mmp80) REVERT: B 19 GLU cc_start: 0.7598 (pp20) cc_final: 0.7083 (pp20) REVERT: B 24 PHE cc_start: 0.8539 (m-10) cc_final: 0.8227 (m-80) REVERT: B 25 TYR cc_start: 0.8655 (t80) cc_final: 0.8423 (t80) REVERT: B 29 LEU cc_start: 0.8297 (mp) cc_final: 0.7978 (mt) REVERT: B 37 VAL cc_start: 0.8648 (t) cc_final: 0.8316 (m) REVERT: B 46 LYS cc_start: 0.8572 (mttm) cc_final: 0.8163 (mttm) REVERT: B 57 ARG cc_start: 0.8487 (ptm160) cc_final: 0.8098 (ttm110) REVERT: B 72 VAL cc_start: 0.8755 (m) cc_final: 0.8414 (p) REVERT: B 73 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7966 (m-70) REVERT: B 85 ILE cc_start: 0.8656 (mt) cc_final: 0.8369 (tp) REVERT: B 88 TYR cc_start: 0.8770 (t80) cc_final: 0.8502 (t80) REVERT: B 112 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7181 (mm-40) REVERT: B 123 TYR cc_start: 0.7811 (t80) cc_final: 0.7206 (t80) REVERT: B 132 ASN cc_start: 0.7754 (p0) cc_final: 0.7510 (p0) REVERT: B 149 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7583 (ttmt) REVERT: B 155 MET cc_start: 0.7835 (tpt) cc_final: 0.7397 (tpp) REVERT: B 166 GLN cc_start: 0.5554 (mp10) cc_final: 0.5195 (mp10) REVERT: B 170 MET cc_start: 0.7717 (mmm) cc_final: 0.7489 (mmm) REVERT: B 178 ILE cc_start: 0.7898 (tp) cc_final: 0.7579 (mm) REVERT: B 184 ASP cc_start: 0.7961 (t70) cc_final: 0.7316 (t0) REVERT: B 191 GLU cc_start: 0.7637 (pm20) cc_final: 0.7104 (pp20) REVERT: B 199 MET cc_start: 0.7810 (mmp) cc_final: 0.7466 (mmm) REVERT: B 209 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7739 (mmt90) REVERT: B 212 TYR cc_start: 0.7661 (m-10) cc_final: 0.7399 (m-80) REVERT: B 215 SER cc_start: 0.8357 (m) cc_final: 0.7925 (p) REVERT: B 242 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7881 (mmtt) REVERT: B 296 TYR cc_start: 0.6650 (m-80) cc_final: 0.6449 (m-80) REVERT: B 307 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7670 (mmtm) REVERT: B 363 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8105 (mmtp) REVERT: B 381 TYR cc_start: 0.7448 (m-80) cc_final: 0.6756 (m-80) REVERT: B 383 TYR cc_start: 0.5592 (m-80) cc_final: 0.5202 (m-80) REVERT: B 429 ASP cc_start: 0.8293 (m-30) cc_final: 0.7224 (m-30) REVERT: B 454 MET cc_start: 0.7116 (mmm) cc_final: 0.6798 (tmm) REVERT: B 469 ASP cc_start: 0.7539 (t70) cc_final: 0.7049 (t70) REVERT: B 470 LYS cc_start: 0.7308 (tttm) cc_final: 0.6916 (tttp) REVERT: B 502 TYR cc_start: 0.6378 (t80) cc_final: 0.5286 (m-80) REVERT: B 514 ASN cc_start: 0.5750 (p0) cc_final: 0.5519 (p0) REVERT: B 583 VAL cc_start: 0.7972 (p) cc_final: 0.7595 (t) REVERT: F 28 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7562 (mmmm) REVERT: F 45 GLN cc_start: 0.8071 (tt0) cc_final: 0.7783 (tp-100) REVERT: F 46 ARG cc_start: 0.7343 (mtm110) cc_final: 0.7089 (ttp-110) REVERT: F 53 SER cc_start: 0.8187 (t) cc_final: 0.7810 (t) REVERT: F 56 GLU cc_start: 0.8098 (mp0) cc_final: 0.7748 (mp0) REVERT: F 62 TYR cc_start: 0.8107 (t80) cc_final: 0.7428 (t80) REVERT: F 63 THR cc_start: 0.7656 (t) cc_final: 0.7197 (p) REVERT: F 64 MET cc_start: 0.7581 (tpt) cc_final: 0.7066 (tpt) REVERT: F 68 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8443 (mttm) REVERT: F 71 GLU cc_start: 0.7689 (tm-30) cc_final: 0.6978 (tm-30) REVERT: F 78 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7952 (ttm-80) REVERT: F 79 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6577 (tp30) REVERT: F 103 GLN cc_start: 0.8587 (tp40) cc_final: 0.8091 (tp40) REVERT: F 113 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7476 (tp40) REVERT: F 116 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8220 (tpp) REVERT: F 117 VAL cc_start: 0.8220 (t) cc_final: 0.7860 (p) REVERT: F 118 MET cc_start: 0.7478 (mtm) cc_final: 0.7195 (mtm) REVERT: F 124 MET cc_start: 0.4603 (tmm) cc_final: 0.3895 (tmm) REVERT: F 126 MET cc_start: 0.8012 (tmt) cc_final: 0.7567 (tmm) REVERT: F 140 TYR cc_start: 0.8017 (t80) cc_final: 0.7148 (t80) REVERT: F 145 ILE cc_start: 0.8785 (mt) cc_final: 0.8535 (tt) REVERT: F 154 TYR cc_start: 0.7204 (t80) cc_final: 0.5859 (t80) REVERT: F 163 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7213 (mm110) REVERT: F 167 ASP cc_start: 0.7405 (t0) cc_final: 0.7023 (t0) REVERT: F 168 MET cc_start: 0.7639 (ptp) cc_final: 0.7305 (ptp) REVERT: F 205 PHE cc_start: 0.8475 (t80) cc_final: 0.7552 (t80) REVERT: F 233 TYR cc_start: 0.7649 (t80) cc_final: 0.7119 (t80) REVERT: F 238 GLU cc_start: 0.8271 (tp30) cc_final: 0.7644 (tp30) REVERT: F 240 ARG cc_start: 0.8015 (mmt180) cc_final: 0.7789 (tpp80) REVERT: F 243 GLU cc_start: 0.7738 (pp20) cc_final: 0.7517 (pp20) REVERT: F 246 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7179 (tp30) REVERT: F 249 MET cc_start: 0.7668 (ppp) cc_final: 0.7232 (ppp) REVERT: F 265 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7106 (mm-30) REVERT: F 270 SER cc_start: 0.8470 (m) cc_final: 0.8007 (t) REVERT: F 272 HIS cc_start: 0.6656 (m-70) cc_final: 0.5835 (m170) REVERT: F 273 MET cc_start: 0.7597 (ttp) cc_final: 0.7169 (ttp) REVERT: F 274 LYS cc_start: 0.8459 (tppt) cc_final: 0.8172 (tmmt) REVERT: F 276 ILE cc_start: 0.7790 (tp) cc_final: 0.7262 (mt) REVERT: F 301 LYS cc_start: 0.8189 (ptpt) cc_final: 0.7953 (ptpp) REVERT: F 303 PHE cc_start: 0.7983 (m-80) cc_final: 0.7522 (m-80) REVERT: F 311 LYS cc_start: 0.7711 (tmmt) cc_final: 0.7252 (ttmm) REVERT: F 317 MET cc_start: 0.7942 (ttp) cc_final: 0.7682 (ptt) REVERT: F 322 ARG cc_start: 0.8196 (mmt90) cc_final: 0.7722 (mmt180) REVERT: F 332 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: F 346 LEU cc_start: 0.7696 (tp) cc_final: 0.7389 (pp) REVERT: F 352 PHE cc_start: 0.7741 (m-10) cc_final: 0.7494 (m-10) REVERT: F 360 PHE cc_start: 0.7717 (m-80) cc_final: 0.7364 (m-80) REVERT: F 365 LEU cc_start: 0.7753 (tp) cc_final: 0.7297 (tp) REVERT: F 368 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7145 (tm-30) REVERT: F 369 THR cc_start: 0.8017 (p) cc_final: 0.7448 (p) REVERT: F 378 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4586 (mt) REVERT: F 414 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8610 (mmtm) REVERT: F 671 ARG cc_start: 0.6066 (tpt90) cc_final: 0.5641 (tpt-90) REVERT: F 673 LYS cc_start: 0.8051 (ptmm) cc_final: 0.7802 (pptt) REVERT: F 687 GLU cc_start: 0.4396 (OUTLIER) cc_final: 0.1572 (tt0) REVERT: F 717 MET cc_start: 0.2868 (tpp) cc_final: 0.2305 (tpt) REVERT: F 725 GLU cc_start: 0.8147 (tt0) cc_final: 0.7911 (mt-10) REVERT: D 42 CYS cc_start: 0.6505 (OUTLIER) cc_final: 0.6264 (m) REVERT: D 68 CYS cc_start: 0.5397 (OUTLIER) cc_final: 0.4798 (t) outliers start: 97 outliers final: 65 residues processed: 751 average time/residue: 0.3791 time to fit residues: 422.3103 Evaluate side-chains 789 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 707 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS 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 272 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 25 MET 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 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 423 GLN 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 627 LEU Chi-restraints excluded: chain C residue 701 HIS 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 53 SER Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 HIS 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 245 VAL Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 556 LEU 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 131 VAL Chi-restraints excluded: chain F residue 166 LEU 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 306 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 418 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 18 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 254 optimal weight: 0.0370 chunk 265 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 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 = 0.4304 r_free = 0.4304 target = 0.166469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.139817 restraints weight = 48993.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.144332 restraints weight = 26286.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.147272 restraints weight = 16046.276| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22753 Z= 0.170 Angle : 0.803 13.898 30696 Z= 0.405 Chirality : 0.046 0.277 3385 Planarity : 0.005 0.061 3934 Dihedral : 4.867 27.336 3006 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.23 % Favored : 90.65 % Rotamer: Outliers : 3.97 % Allowed : 27.11 % Favored : 68.92 % 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: -1.26 (0.16), residues: 2718 helix: 0.54 (0.14), residues: 1264 sheet: -0.89 (0.32), residues: 264 loop : -2.42 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP C 513 HIS 0.024 0.001 HIS F 490 PHE 0.032 0.002 PHE C 419 TYR 0.026 0.002 TYR F 125 ARG 0.014 0.001 ARG C 266 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 1102) hydrogen bonds : angle 5.09081 ( 3228) metal coordination : bond 0.01316 ( 22) metal coordination : angle 3.82182 ( 12) covalent geometry : bond 0.00367 (22731) covalent geometry : angle 0.79915 (30684) ********************** 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 803 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 705 time to evaluate : 2.329 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: 0.8219 (tp) cc_final: 0.7886 (pt) REVERT: A 13 TYR cc_start: 0.7464 (t80) cc_final: 0.6973 (t80) REVERT: A 19 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7539 (pp20) REVERT: A 20 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8105 (mm110) REVERT: A 26 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 29 LEU cc_start: 0.8565 (mp) cc_final: 0.8238 (mm) REVERT: A 49 LEU cc_start: 0.8201 (mt) cc_final: 0.7953 (mt) REVERT: A 57 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7700 (ttm-80) REVERT: A 59 MET cc_start: 0.7426 (ttp) cc_final: 0.7108 (ttp) REVERT: A 60 PHE cc_start: 0.8264 (m-80) cc_final: 0.7964 (m-10) REVERT: A 68 LYS cc_start: 0.7954 (tptp) cc_final: 0.7670 (tptp) REVERT: A 73 HIS cc_start: 0.7459 (m-70) cc_final: 0.7045 (m-70) REVERT: A 84 ILE cc_start: 0.8646 (tp) cc_final: 0.8355 (tt) REVERT: A 87 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8223 (p) REVERT: A 88 TYR cc_start: 0.8519 (t80) cc_final: 0.8059 (t80) REVERT: A 102 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7170 (mm-30) REVERT: A 106 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 109 CYS cc_start: 0.8195 (t) cc_final: 0.6582 (t) REVERT: A 115 ASP cc_start: 0.8021 (p0) cc_final: 0.7674 (p0) REVERT: A 118 GLN cc_start: 0.8259 (tt0) cc_final: 0.7969 (tt0) REVERT: A 122 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 127 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8380 (mmtm) REVERT: A 147 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 149 LYS cc_start: 0.8171 (tttt) cc_final: 0.7845 (ttmt) REVERT: A 157 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6923 (mm-30) REVERT: A 159 LYS cc_start: 0.7639 (mtmt) cc_final: 0.7381 (mmtm) REVERT: A 170 MET cc_start: 0.6809 (mmp) cc_final: 0.6399 (mmp) REVERT: A 195 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7704 (ttm170) REVERT: A 196 GLU cc_start: 0.7634 (pp20) cc_final: 0.7301 (pp20) REVERT: A 199 MET cc_start: 0.8108 (mmm) cc_final: 0.7761 (mmp) REVERT: A 209 ARG cc_start: 0.7385 (mtm180) cc_final: 0.6968 (mtm180) REVERT: A 211 GLN cc_start: 0.7815 (pm20) cc_final: 0.7433 (pm20) REVERT: A 249 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7056 (tp) REVERT: A 291 GLN cc_start: 0.8121 (mp10) cc_final: 0.7756 (mp10) REVERT: A 294 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8134 (mmmm) REVERT: A 297 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7826 (ptpt) REVERT: A 352 TRP cc_start: 0.7697 (t60) cc_final: 0.7437 (t60) REVERT: A 357 GLN cc_start: 0.7602 (mm-40) cc_final: 0.6738 (mm-40) REVERT: A 360 TRP cc_start: 0.7982 (m100) cc_final: 0.5686 (m100) REVERT: A 361 PHE cc_start: 0.7235 (m-80) cc_final: 0.6260 (m-80) REVERT: A 430 CYS cc_start: 0.7160 (p) cc_final: 0.6604 (p) REVERT: A 443 PHE cc_start: 0.8312 (t80) cc_final: 0.7971 (t80) REVERT: A 454 MET cc_start: 0.6839 (tpp) cc_final: 0.6426 (tpp) REVERT: A 502 TYR cc_start: 0.5953 (t80) cc_final: 0.4908 (t80) REVERT: A 536 VAL cc_start: 0.7676 (m) cc_final: 0.7413 (p) REVERT: A 580 ARG cc_start: 0.4799 (mpp-170) cc_final: 0.4034 (mpp-170) REVERT: E 23 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7213 (mp0) REVERT: E 35 TRP cc_start: 0.3537 (m-10) cc_final: 0.3126 (m-10) REVERT: E 48 HIS cc_start: 0.5441 (t-90) cc_final: 0.4923 (t-90) REVERT: C 28 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7793 (tptp) REVERT: C 33 ILE cc_start: 0.9024 (mm) cc_final: 0.8737 (mm) REVERT: C 35 ASP cc_start: 0.7360 (t0) cc_final: 0.7117 (m-30) REVERT: C 36 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8009 (tp) REVERT: C 49 ASN cc_start: 0.8103 (p0) cc_final: 0.7875 (p0) REVERT: C 62 TYR cc_start: 0.7898 (t80) cc_final: 0.7272 (t80) REVERT: C 64 MET cc_start: 0.7717 (tpp) cc_final: 0.7365 (tpp) REVERT: C 68 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8464 (mptt) REVERT: C 71 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 72 LYS cc_start: 0.8495 (tttt) cc_final: 0.7935 (tptp) REVERT: C 83 GLU cc_start: 0.7819 (tp30) cc_final: 0.7412 (tp30) REVERT: C 124 MET cc_start: 0.3236 (tmm) cc_final: 0.3009 (tmm) REVERT: C 125 TYR cc_start: 0.5187 (t80) cc_final: 0.4815 (t80) REVERT: C 153 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7523 (mmm-85) REVERT: C 163 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7774 (mm110) REVERT: C 188 GLN cc_start: 0.8179 (tp40) cc_final: 0.7773 (tp40) REVERT: C 191 MET cc_start: 0.8139 (tpp) cc_final: 0.7568 (tpp) REVERT: C 205 PHE cc_start: 0.7405 (t80) cc_final: 0.7102 (t80) REVERT: C 206 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6455 (mm-30) REVERT: C 222 GLN cc_start: 0.7604 (tp40) cc_final: 0.7145 (tm-30) REVERT: C 234 ILE cc_start: 0.8492 (mm) cc_final: 0.7879 (tp) REVERT: C 238 GLU cc_start: 0.7509 (tp30) cc_final: 0.6568 (tm-30) REVERT: C 246 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7488 (tm-30) REVERT: C 247 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7641 (ttm170) REVERT: C 250 HIS cc_start: 0.8002 (t-90) cc_final: 0.7217 (t-90) REVERT: C 258 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7063 (mp0) REVERT: C 262 LYS cc_start: 0.8077 (tmtm) cc_final: 0.7406 (ttmm) REVERT: C 274 LYS cc_start: 0.8434 (tppt) cc_final: 0.7717 (tppt) REVERT: C 282 SER cc_start: 0.7791 (m) cc_final: 0.7580 (m) REVERT: C 292 LYS cc_start: 0.8455 (mmmm) cc_final: 0.8082 (mmtt) REVERT: C 301 LYS cc_start: 0.8398 (ptpt) cc_final: 0.8056 (ptpp) REVERT: C 306 VAL cc_start: 0.8745 (t) cc_final: 0.8492 (p) REVERT: C 314 CYS cc_start: 0.7583 (m) cc_final: 0.7357 (m) REVERT: C 346 LEU cc_start: 0.8336 (tp) cc_final: 0.8083 (tp) REVERT: C 353 ASP cc_start: 0.7970 (t0) cc_final: 0.7695 (t0) REVERT: C 354 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7509 (ptp-170) REVERT: C 368 GLN cc_start: 0.7403 (tm-30) cc_final: 0.6781 (tm-30) REVERT: C 369 THR cc_start: 0.8225 (p) cc_final: 0.7856 (t) REVERT: C 373 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6299 (t0) REVERT: C 386 GLU cc_start: 0.8319 (mp0) cc_final: 0.6573 (mp0) REVERT: C 394 ASP cc_start: 0.7888 (t0) cc_final: 0.7515 (t0) REVERT: C 395 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8192 (mmmm) REVERT: C 409 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 412 LEU cc_start: 0.8718 (mt) cc_final: 0.8453 (mm) REVERT: C 413 ASP cc_start: 0.8546 (m-30) cc_final: 0.8213 (m-30) REVERT: C 418 LEU cc_start: 0.8826 (tt) cc_final: 0.8543 (tp) REVERT: C 423 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: C 424 GLU cc_start: 0.7471 (mp0) cc_final: 0.6803 (mp0) REVERT: C 431 TYR cc_start: 0.8357 (m-80) cc_final: 0.6885 (m-10) REVERT: C 438 ARG cc_start: 0.7735 (tpm170) cc_final: 0.6780 (tpm170) REVERT: C 441 LEU cc_start: 0.8172 (mt) cc_final: 0.7698 (mt) REVERT: C 473 MET cc_start: 0.7385 (mmt) cc_final: 0.7183 (mmt) REVERT: C 484 MET cc_start: 0.3490 (OUTLIER) cc_final: 0.3222 (tpt) REVERT: C 554 MET cc_start: 0.6690 (tpp) cc_final: 0.6361 (tpp) REVERT: C 603 MET cc_start: 0.7535 (tmm) cc_final: 0.7077 (tmm) REVERT: C 692 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.8080 (mmp80) REVERT: B 19 GLU cc_start: 0.7596 (pp20) cc_final: 0.7090 (pp20) REVERT: B 24 PHE cc_start: 0.8537 (m-10) cc_final: 0.8190 (m-80) REVERT: B 29 LEU cc_start: 0.8289 (mp) cc_final: 0.7951 (mp) REVERT: B 37 VAL cc_start: 0.8582 (t) cc_final: 0.8259 (m) REVERT: B 46 LYS cc_start: 0.8595 (mttm) cc_final: 0.8173 (mttm) REVERT: B 57 ARG cc_start: 0.8473 (ptm160) cc_final: 0.8196 (ttm110) REVERT: B 85 ILE cc_start: 0.8670 (mt) cc_final: 0.8353 (tp) REVERT: B 88 TYR cc_start: 0.8781 (t80) cc_final: 0.7796 (t80) REVERT: B 112 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7633 (mm-40) REVERT: B 115 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.6576 (p0) REVERT: B 123 TYR cc_start: 0.7810 (t80) cc_final: 0.7206 (t80) REVERT: B 149 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7619 (ttmt) REVERT: B 155 MET cc_start: 0.7892 (tpt) cc_final: 0.7454 (tpp) REVERT: B 166 GLN cc_start: 0.5659 (mp10) cc_final: 0.5272 (mp10) REVERT: B 170 MET cc_start: 0.7688 (mmm) cc_final: 0.7468 (mmm) REVERT: B 178 ILE cc_start: 0.7862 (tp) cc_final: 0.7518 (mm) REVERT: B 184 ASP cc_start: 0.7941 (t70) cc_final: 0.7543 (t0) REVERT: B 189 GLU cc_start: 0.7313 (pm20) cc_final: 0.6919 (pm20) REVERT: B 191 GLU cc_start: 0.7645 (pm20) cc_final: 0.7060 (pp20) REVERT: B 199 MET cc_start: 0.7801 (mmp) cc_final: 0.7413 (mmp) REVERT: B 209 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7702 (mmt90) REVERT: B 212 TYR cc_start: 0.7650 (m-10) cc_final: 0.7399 (m-80) REVERT: B 215 SER cc_start: 0.8304 (m) cc_final: 0.7978 (p) REVERT: B 242 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7877 (mmtt) REVERT: B 294 LYS cc_start: 0.6954 (mmtm) cc_final: 0.6686 (mmtm) REVERT: B 307 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7668 (mmtm) REVERT: B 361 PHE cc_start: 0.7964 (t80) cc_final: 0.7754 (t80) REVERT: B 363 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8051 (mmtp) REVERT: B 381 TYR cc_start: 0.7443 (m-80) cc_final: 0.6817 (m-80) REVERT: B 383 TYR cc_start: 0.5610 (m-80) cc_final: 0.5223 (m-80) REVERT: B 429 ASP cc_start: 0.8345 (m-30) cc_final: 0.7642 (m-30) REVERT: B 452 MET cc_start: 0.7549 (mmt) cc_final: 0.6869 (mmm) REVERT: B 454 MET cc_start: 0.7273 (mmm) cc_final: 0.6984 (tmm) REVERT: B 469 ASP cc_start: 0.7539 (t70) cc_final: 0.7079 (t70) REVERT: B 470 LYS cc_start: 0.7290 (tttm) cc_final: 0.6959 (tttp) REVERT: B 502 TYR cc_start: 0.6238 (t80) cc_final: 0.4904 (m-80) REVERT: B 503 ASP cc_start: 0.8133 (t0) cc_final: 0.7775 (t0) REVERT: B 583 VAL cc_start: 0.8000 (p) cc_final: 0.7634 (t) REVERT: F 28 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7567 (mmmm) REVERT: F 45 GLN cc_start: 0.8041 (tt0) cc_final: 0.7788 (tp-100) REVERT: F 46 ARG cc_start: 0.7506 (mtm110) cc_final: 0.7229 (ttp-110) REVERT: F 53 SER cc_start: 0.8223 (t) cc_final: 0.7841 (t) REVERT: F 56 GLU cc_start: 0.8097 (mp0) cc_final: 0.7733 (mp0) REVERT: F 62 TYR cc_start: 0.8052 (t80) cc_final: 0.7414 (t80) REVERT: F 63 THR cc_start: 0.7568 (t) cc_final: 0.7230 (p) REVERT: F 64 MET cc_start: 0.7574 (tpt) cc_final: 0.7049 (tpt) REVERT: F 68 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8473 (mttm) REVERT: F 71 GLU cc_start: 0.7633 (tm-30) cc_final: 0.6910 (tm-30) REVERT: F 78 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7970 (ttm-80) REVERT: F 79 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6568 (tp30) REVERT: F 103 GLN cc_start: 0.8591 (tp40) cc_final: 0.8094 (tp40) REVERT: F 113 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7457 (tp40) REVERT: F 116 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8231 (tpp) REVERT: F 117 VAL cc_start: 0.8223 (t) cc_final: 0.7877 (p) REVERT: F 118 MET cc_start: 0.7442 (mtm) cc_final: 0.7174 (mtm) REVERT: F 124 MET cc_start: 0.4617 (tmm) cc_final: 0.3903 (tmm) REVERT: F 126 MET cc_start: 0.7982 (tmt) cc_final: 0.7547 (tmm) REVERT: F 140 TYR cc_start: 0.8018 (t80) cc_final: 0.7176 (t80) REVERT: F 145 ILE cc_start: 0.8771 (mt) cc_final: 0.8488 (tt) REVERT: F 154 TYR cc_start: 0.7188 (t80) cc_final: 0.5851 (t80) REVERT: F 158 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7398 (ttm-80) REVERT: F 163 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7176 (mm-40) REVERT: F 167 ASP cc_start: 0.7482 (t0) cc_final: 0.7103 (t0) REVERT: F 168 MET cc_start: 0.7665 (ptp) cc_final: 0.7327 (ptp) REVERT: F 205 PHE cc_start: 0.8484 (t80) cc_final: 0.7560 (t80) REVERT: F 233 TYR cc_start: 0.7745 (t80) cc_final: 0.7157 (t80) REVERT: F 238 GLU cc_start: 0.8270 (tp30) cc_final: 0.7624 (tp30) REVERT: F 240 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7805 (tpp80) REVERT: F 246 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7178 (tp30) REVERT: F 249 MET cc_start: 0.7645 (ppp) cc_final: 0.7213 (ppp) REVERT: F 265 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7109 (mm-30) REVERT: F 270 SER cc_start: 0.8457 (m) cc_final: 0.7980 (t) REVERT: F 272 HIS cc_start: 0.6641 (m-70) cc_final: 0.5796 (m170) REVERT: F 273 MET cc_start: 0.7571 (ttp) cc_final: 0.7156 (ttp) REVERT: F 274 LYS cc_start: 0.8457 (tppt) cc_final: 0.8202 (tmmt) REVERT: F 276 ILE cc_start: 0.7817 (tp) cc_final: 0.7263 (mt) REVERT: F 301 LYS cc_start: 0.8187 (ptpt) cc_final: 0.7963 (ptpp) REVERT: F 303 PHE cc_start: 0.7972 (m-80) cc_final: 0.7528 (m-80) REVERT: F 311 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7257 (ttmm) REVERT: F 322 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7721 (mmt180) REVERT: F 346 LEU cc_start: 0.7691 (tp) cc_final: 0.7403 (pp) REVERT: F 360 PHE cc_start: 0.7626 (m-10) cc_final: 0.7281 (m-80) REVERT: F 365 LEU cc_start: 0.7855 (tp) cc_final: 0.7618 (tp) REVERT: F 368 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7091 (tm-30) REVERT: F 369 THR cc_start: 0.8027 (p) cc_final: 0.7718 (t) REVERT: F 378 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.4958 (mt) REVERT: F 414 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8591 (mmtm) REVERT: F 461 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6990 (mp0) REVERT: F 671 ARG cc_start: 0.6092 (tpt90) cc_final: 0.5649 (tpt-90) REVERT: F 673 LYS cc_start: 0.8051 (ptmm) cc_final: 0.7805 (pptt) REVERT: F 687 GLU cc_start: 0.4500 (OUTLIER) cc_final: 0.1589 (tt0) REVERT: F 717 MET cc_start: 0.2548 (tpp) cc_final: 0.1956 (tpt) REVERT: D 68 CYS cc_start: 0.5382 (OUTLIER) cc_final: 0.4778 (t) outliers start: 98 outliers final: 65 residues processed: 751 average time/residue: 0.3602 time to fit residues: 401.7405 Evaluate side-chains 763 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 686 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 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 310 THR 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 25 MET 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 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 420 ARG Chi-restraints excluded: chain C residue 423 GLN 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 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 723 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 53 SER Chi-restraints excluded: chain B residue 87 THR 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 158 HIS Chi-restraints excluded: chain B residue 193 THR 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 245 VAL Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 556 LEU 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 131 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 517 SER 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 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 253 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 215 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 255 optimal weight: 0.0030 chunk 251 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 165 HIS ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN C 45 GLN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN B 103 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.168429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142299 restraints weight = 49016.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.146715 restraints weight = 26494.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.149559 restraints weight = 16237.776| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22753 Z= 0.150 Angle : 0.803 13.424 30696 Z= 0.403 Chirality : 0.046 0.340 3385 Planarity : 0.005 0.061 3934 Dihedral : 4.827 29.261 3006 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.12 % Favored : 90.80 % Rotamer: Outliers : 3.60 % Allowed : 27.64 % Favored : 68.76 % 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: 0.59 (0.15), residues: 1263 sheet: -0.92 (0.32), residues: 267 loop : -2.42 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP C 513 HIS 0.023 0.001 HIS F 490 PHE 0.032 0.002 PHE B 537 TYR 0.031 0.002 TYR B 55 ARG 0.013 0.001 ARG C 266 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1102) hydrogen bonds : angle 5.02465 ( 3228) metal coordination : bond 0.01249 ( 22) metal coordination : angle 3.66580 ( 12) covalent geometry : bond 0.00331 (22731) covalent geometry : angle 0.79982 (30684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9813.26 seconds wall clock time: 171 minutes 40.93 seconds (10300.93 seconds total)