Starting phenix.real_space_refine on Sun Aug 9 01:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tom_41456/08_2026/8tom_41456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tom_41456/08_2026/8tom_41456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tom_41456/08_2026/8tom_41456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tom_41456/08_2026/8tom_41456.map" model { file = "/net/cci-nas-00/data/ceres_data/8tom_41456/08_2026/8tom_41456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tom_41456/08_2026/8tom_41456.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.075 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 80 5.49 5 Mg 1 5.21 5 S 135 5.16 5 C 19683 2.51 5 N 5592 2.21 5 O 6260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31753 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1773 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 221} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1684 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 10563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10563 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 10402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10402 Classifications: {'peptide': 1338} Link IDs: {'PTRANS': 55, 'TRANS': 1282} Chain breaks: 2 Chain: "K" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "L" Number of atoms: 4413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4413 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 534} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "O" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 821 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "P" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 819 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14469 SG CYS J 70 99.621 122.467 122.446 1.00113.73 S ATOM 14483 SG CYS J 72 98.911 124.307 123.384 1.00122.82 S ATOM 14591 SG CYS J 85 101.141 123.863 125.226 1.00122.34 S ATOM 14615 SG CYS J 88 99.091 120.308 124.853 1.00113.10 S ATOM 20303 SG CYS J 814 128.635 76.439 81.957 1.00108.42 S ATOM 20868 SG CYS J 888 125.632 76.132 84.118 1.00100.14 S ATOM 20919 SG CYS J 895 127.257 77.302 81.814 1.00113.52 S ATOM 20940 SG CYS J 898 127.140 76.491 80.826 1.00112.23 S Time building chain proxies: 6.51, per 1000 atoms: 0.21 Number of scatterers: 31753 At special positions: 0 Unit cell: (151.8, 194.7, 194.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 135 16.00 P 80 15.00 Mg 1 11.99 O 6260 8.00 N 5592 7.00 C 19683 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: 2.66 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7112 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 45 sheets defined 42.7% alpha, 11.5% beta 40 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.697A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY G 40 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 3.544A pdb=" N ILE G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU G 83 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.568A pdb=" N ASP G 114 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 161 removed outlier: 3.693A pdb=" N HIS G 160 " --> pdb=" O THR G 157 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER G 161 " --> pdb=" O ARG G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.253A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.122A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.501A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.570A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 57 removed outlier: 3.586A pdb=" N PHE I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.233A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.529A pdb=" N LEU I 246 " --> pdb=" O VAL I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 379 through 390 removed outlier: 3.524A pdb=" N LEU I 388 " --> pdb=" O LEU I 384 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 removed outlier: 3.506A pdb=" N SER I 408 " --> pdb=" O LYS I 404 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU I 409 " --> pdb=" O PHE I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 438 removed outlier: 4.112A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.805A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 525 Processing helix chain 'I' and resid 610 through 614 removed outlier: 3.900A pdb=" N TYR I 614 " --> pdb=" O GLU I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.530A pdb=" N SER I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.712A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 944 through 981 removed outlier: 3.908A pdb=" N LEU I 964 " --> pdb=" O LEU I 960 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER I 973 " --> pdb=" O ALA I 969 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.577A pdb=" N THR I1037 " --> pdb=" O ARG I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.504A pdb=" N ASP I1084 " --> pdb=" O PRO I1081 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1081 through 1085' Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.703A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.715A pdb=" N HIS I1116 " --> pdb=" O ILE I1112 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET I1131 " --> pdb=" O LYS I1127 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I1132 " --> pdb=" O ILE I1128 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.844A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1171 through 1176 removed outlier: 3.595A pdb=" N ASN I1175 " --> pdb=" O ARG I1171 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1272 through 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.812A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1299 through 1309 removed outlier: 3.532A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.896A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS I1328 " --> pdb=" O ASN I1324 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU I1329 " --> pdb=" O VAL I1325 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 removed outlier: 4.062A pdb=" N LEU J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.518A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 231 removed outlier: 3.835A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS J 216 " --> pdb=" O THR J 212 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.856A pdb=" N GLY J 258 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG J 259 " --> pdb=" O ASP J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 255 through 259' Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.438A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.501A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 removed outlier: 3.732A pdb=" N ILE J 331 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 332 " --> pdb=" O ALA J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 343 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.656A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU J 376 " --> pdb=" O MET J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.135A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.573A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 593 Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.971A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.517A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.039A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.507A pdb=" N TYR J 772 " --> pdb=" O ASN J 768 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE J 773 " --> pdb=" O VAL J 769 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE J 774 " --> pdb=" O LEU J 770 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.710A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 874 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.012A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1259 removed outlier: 4.559A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.820A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1361 through 1375 removed outlier: 4.720A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 4.006A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET K 30 " --> pdb=" O ARG K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 25 through 30 removed outlier: 3.614A pdb=" N HIS L 30 " --> pdb=" O GLU L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 52 removed outlier: 3.901A pdb=" N ILE L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 removed outlier: 3.770A pdb=" N GLU L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 108 removed outlier: 3.562A pdb=" N VAL L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 125 removed outlier: 3.958A pdb=" N ASP L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 136 removed outlier: 3.661A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 152 Processing helix chain 'L' and resid 157 through 161 Processing helix chain 'L' and resid 214 through 233 Processing helix chain 'L' and resid 244 through 257 removed outlier: 4.009A pdb=" N GLU L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU L 250 " --> pdb=" O GLN L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 289 Processing helix chain 'L' and resid 298 through 305 Processing helix chain 'L' and resid 305 through 310 removed outlier: 4.256A pdb=" N ASN L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 323 removed outlier: 3.643A pdb=" N MET L 322 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN L 323 " --> pdb=" O ILE L 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 319 through 323' Processing helix chain 'L' and resid 326 through 330 removed outlier: 3.534A pdb=" N LYS L 329 " --> pdb=" O TRP L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 352 removed outlier: 3.731A pdb=" N VAL L 337 " --> pdb=" O VAL L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 392 removed outlier: 3.926A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN L 383 " --> pdb=" O MET L 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 426 through 446 removed outlier: 4.658A pdb=" N THR L 432 " --> pdb=" O SER L 428 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 490 through 502 removed outlier: 4.616A pdb=" N LYS L 502 " --> pdb=" O LEU L 498 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.840A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 Processing helix chain 'L' and resid 552 through 564 Processing helix chain 'L' and resid 572 through 580 removed outlier: 3.698A pdb=" N PHE L 580 " --> pdb=" O VAL L 576 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.502A pdb=" N ILE L 587 " --> pdb=" O THR L 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 605 through 612 Processing helix chain 'M' and resid 256 through 261 removed outlier: 3.550A pdb=" N ASP M 259 " --> pdb=" O PRO M 256 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU M 261 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 278 through 283 removed outlier: 3.918A pdb=" N GLN M 283 " --> pdb=" O GLY M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 310 Processing sheet with id=AA1, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.823A pdb=" N GLU G 17 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 204 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 58 removed outlier: 6.752A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 102 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.509A pdb=" N VAL G 110 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 151 through 153 Processing sheet with id=AA5, first strand: chain 'H' and resid 23 through 24 removed outlier: 6.469A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 53 through 61 removed outlier: 6.641A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 109 through 111 removed outlier: 6.699A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 187 through 188 Processing sheet with id=AA9, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.999A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.823A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY I 125 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL I 98 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR I 123 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU I 100 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU I 121 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.189A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'I' and resid 195 through 196 Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.549A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.549A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AB9, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.394A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY I 722 " --> pdb=" O VAL I 777 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC2, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC3, first strand: chain 'I' and resid 798 through 804 removed outlier: 9.082A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 846 through 847 removed outlier: 5.745A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU I1047 " --> pdb=" O THR I 935 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR I 935 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE I1049 " --> pdb=" O VAL I 933 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL I 933 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.912A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AC7, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AC8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.318A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.575A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1268 through 1269 removed outlier: 3.507A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.507A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 103 through 112 removed outlier: 6.660A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.841A pdb=" N TYR J 144 " --> pdb=" O LEU J 160 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 261 through 262 Processing sheet with id=AD6, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AD7, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AD8, first strand: chain 'J' and resid 809 through 811 removed outlier: 5.969A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU J 811 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.165A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 Processing sheet with id=AE3, first strand: chain 'J' and resid 957 through 961 removed outlier: 6.998A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 965 through 966 removed outlier: 3.606A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AE6, first strand: chain 'J' and resid 1047 through 1051 Processing sheet with id=AE7, first strand: chain 'J' and resid 1106 through 1107 Processing sheet with id=AE8, first strand: chain 'J' and resid 1175 through 1178 Processing sheet with id=AE9, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.313A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 8.99 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10537 1.34 - 1.46: 6451 1.46 - 1.58: 14983 1.58 - 1.70: 170 1.70 - 1.83: 250 Bond restraints: 32391 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.734 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 32386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 43221 2.11 - 4.21: 832 4.21 - 6.32: 42 6.32 - 8.42: 14 8.42 - 10.53: 1 Bond angle restraints: 44110 Sorted by residual: angle pdb=" O4' DG P 47 " pdb=" C1' DG P 47 " pdb=" N9 DG P 47 " ideal model delta sigma weight residual 108.00 111.14 -3.14 7.00e-01 2.04e+00 2.02e+01 angle pdb=" N3 DT O 36 " pdb=" C4 DT O 36 " pdb=" O4 DT O 36 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT O 35 " pdb=" C4 DT O 35 " pdb=" O4 DT O 35 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT P 49 " pdb=" C4 DT P 49 " pdb=" O4 DT P 49 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT O 33 " pdb=" C4 DT O 33 " pdb=" O4 DT O 33 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 44105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 19103 30.79 - 61.59: 858 61.59 - 92.38: 25 92.38 - 123.18: 3 123.18 - 153.97: 2 Dihedral angle restraints: 19991 sinusoidal: 8966 harmonic: 11025 Sorted by residual: dihedral pdb=" CA LEU J 120 " pdb=" C LEU J 120 " pdb=" N PRO J 121 " pdb=" CA PRO J 121 " ideal model delta harmonic sigma weight residual 180.00 123.03 56.97 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 128.41 51.59 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA LYS J 585 " pdb=" C LYS J 585 " pdb=" N GLY J 586 " pdb=" CA GLY J 586 " ideal model delta harmonic sigma weight residual -180.00 -137.55 -42.45 0 5.00e+00 4.00e-02 7.21e+01 ... (remaining 19988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4693 0.089 - 0.179: 355 0.179 - 0.268: 9 0.268 - 0.358: 6 0.358 - 0.447: 6 Chirality restraints: 5069 Sorted by residual: chirality pdb=" CA SER J 948 " pdb=" N SER J 948 " pdb=" C SER J 948 " pdb=" CB SER J 948 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.98 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.97 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 5066 not shown) Planarity restraints: 5462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 120 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO J 121 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO J 121 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 121 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 178 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO G 179 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 179 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 179 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO I 698 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " 0.023 5.00e-02 4.00e+02 ... (remaining 5459 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 336 2.58 - 3.16: 27810 3.16 - 3.74: 47036 3.74 - 4.32: 65622 4.32 - 4.90: 109304 Nonbonded interactions: 250108 Sorted by model distance: nonbonded pdb=" O PRO L 601 " pdb=" OG SER L 602 " model vdw 2.005 3.040 nonbonded pdb=" OG SER J1058 " pdb=" OE1 GLN J1108 " model vdw 2.013 3.040 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.017 3.040 nonbonded pdb=" O LYS J 964 " pdb=" OG1 THR J 976 " model vdw 2.057 3.040 nonbonded pdb=" O VAL G 5 " pdb=" OG1 THR G 6 " model vdw 2.073 3.040 ... (remaining 250103 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 'G' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 158 or resid 171 through 233 or (resid 234 and (name N or n \ ame CA or name C or name O or name CB )))) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.470 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4717 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 : 0.007 0.293 32399 Z= 0.375 Angle : 0.972 76.915 44122 Z= 0.457 Chirality : 0.048 0.447 5069 Planarity : 0.004 0.069 5462 Dihedral : 15.482 153.970 12879 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.79 % Favored : 92.00 % Rotamer: Outliers : 4.60 % Allowed : 8.68 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3801 helix: 0.47 (0.14), residues: 1456 sheet: -2.25 (0.24), residues: 423 loop : -2.24 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 278 TYR 0.011 0.001 TYR I1281 PHE 0.007 0.001 PHE J1319 TRP 0.007 0.001 TRP J 409 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.37 (32391) covalent geometry : angle 0.69319 / 0.44 (44110) hydrogen bonds : bond 0.17043 / 11.38 ( 1311) hydrogen bonds : angle 6.73976 / 4.66 ( 3615) metal coordination : bond 0.06463 / 4.30 ( 8) metal coordination : angle 41.27937 / 24.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 721 time to evaluate : 1.104 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: G 15 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.5879 (m-30) REVERT: G 214 GLU cc_start: 0.6594 (pt0) cc_final: 0.6285 (tt0) REVERT: H 147 GLN cc_start: 0.5281 (mt0) cc_final: 0.4638 (mt0) REVERT: I 43 PRO cc_start: 0.8790 (Cg_exo) cc_final: 0.8277 (Cg_endo) REVERT: I 47 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5860 (p90) REVERT: I 90 VAL cc_start: 0.3334 (OUTLIER) cc_final: 0.3119 (m) REVERT: I 197 ARG cc_start: 0.2146 (OUTLIER) cc_final: 0.1695 (tpp80) REVERT: I 239 MET cc_start: 0.7349 (ttt) cc_final: 0.7137 (mtp) REVERT: I 343 HIS cc_start: 0.6434 (OUTLIER) cc_final: 0.6102 (t-170) REVERT: I 349 GLU cc_start: 0.6620 (mm-30) cc_final: 0.5980 (mp0) REVERT: I 423 ASP cc_start: 0.7326 (m-30) cc_final: 0.7053 (m-30) REVERT: I 699 LEU cc_start: 0.4827 (OUTLIER) cc_final: 0.4621 (tp) REVERT: I 750 ILE cc_start: 0.5954 (OUTLIER) cc_final: 0.5498 (tt) REVERT: I 778 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5656 (mp0) REVERT: I 899 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6223 (mt-10) REVERT: I 1143 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6649 (pp20) REVERT: I 1162 SER cc_start: 0.7516 (m) cc_final: 0.7297 (p) REVERT: I 1172 LEU cc_start: 0.5418 (OUTLIER) cc_final: 0.5090 (tp) REVERT: I 1210 ILE cc_start: 0.5047 (mm) cc_final: 0.4804 (mm) REVERT: I 1253 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.5161 (tp) REVERT: I 1262 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6018 (mtmm) REVERT: J 93 THR cc_start: 0.6517 (OUTLIER) cc_final: 0.6189 (p) REVERT: J 198 CYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6368 (p) REVERT: J 204 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: J 506 VAL cc_start: 0.4806 (OUTLIER) cc_final: 0.4252 (p) REVERT: J 1173 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7579 (ptt-90) REVERT: J 1192 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8785 (mtpp) REVERT: J 1230 THR cc_start: 0.5184 (OUTLIER) cc_final: 0.4826 (t) REVERT: J 1258 ARG cc_start: 0.5789 (ttt90) cc_final: 0.5511 (ttt90) REVERT: J 1370 MET cc_start: 0.5784 (tpp) cc_final: 0.5565 (tpp) REVERT: L 144 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7301 (pp) REVERT: L 273 MET cc_start: 0.8933 (tpp) cc_final: 0.8625 (tmm) REVERT: L 407 GLU cc_start: 0.5472 (mm-30) cc_final: 0.4869 (mm-30) REVERT: L 474 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7276 (mtt) REVERT: L 590 ILE cc_start: 0.5680 (mt) cc_final: 0.5032 (mm) REVERT: M 258 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8095 (p0) outliers start: 150 outliers final: 45 residues processed: 841 average time/residue: 0.2082 time to fit residues: 276.3259 Evaluate side-chains 524 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 460 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 272 ARG Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1262 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 258 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 1.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN I 276 GLN I 649 GLN I 932 GLN I1070 HIS J 80 HIS J 113 HIS J 266 ASN J 545 HIS J 593 ASN J 861 ASN J1108 GLN J1195 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS M 283 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.219349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154416 restraints weight = 38326.924| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.42 r_work: 0.3537 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32399 Z= 0.200 Angle : 0.816 25.325 44122 Z= 0.406 Chirality : 0.049 0.596 5069 Planarity : 0.006 0.074 5462 Dihedral : 15.888 150.149 5477 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.92 % Favored : 92.95 % Rotamer: Outliers : 4.29 % Allowed : 14.36 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 3801 helix: 0.42 (0.13), residues: 1519 sheet: -1.81 (0.24), residues: 434 loop : -2.13 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 279 TYR 0.029 0.002 TYR J1099 PHE 0.041 0.002 PHE J1100 TRP 0.011 0.001 TRP J 115 HIS 0.009 0.002 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (32391) covalent geometry : angle 0.78466 / 0.40 (44110) hydrogen bonds : bond 0.05181 / 3.59 ( 1311) hydrogen bonds : angle 4.92990 / 3.43 ( 3615) metal coordination : bond 0.01799 / 1.34 ( 8) metal coordination : angle 13.54581 / 8.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 528 time to evaluate : 1.100 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: G 4 SER cc_start: 0.6823 (p) cc_final: 0.6501 (t) REVERT: G 15 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6226 (m-30) REVERT: H 95 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7255 (pttm) REVERT: H 103 ASN cc_start: 0.5862 (OUTLIER) cc_final: 0.5661 (p0) REVERT: I 39 ILE cc_start: 0.5221 (OUTLIER) cc_final: 0.4722 (mp) REVERT: I 47 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5700 (p90) REVERT: I 74 ARG cc_start: 0.5446 (ptt180) cc_final: 0.5219 (ptt-90) REVERT: I 239 MET cc_start: 0.7317 (ttt) cc_final: 0.6939 (mtt) REVERT: I 337 PHE cc_start: 0.7738 (t80) cc_final: 0.7342 (t80) REVERT: I 343 HIS cc_start: 0.6394 (OUTLIER) cc_final: 0.5744 (t70) REVERT: I 349 GLU cc_start: 0.6310 (mm-30) cc_final: 0.5922 (mp0) REVERT: I 763 THR cc_start: 0.6184 (p) cc_final: 0.5886 (p) REVERT: I 778 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6687 (mp0) REVERT: I 899 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6314 (mt-10) REVERT: I 1210 ILE cc_start: 0.6722 (mm) cc_final: 0.6324 (mm) REVERT: J 29 MET cc_start: 0.5012 (mmm) cc_final: 0.4614 (mmm) REVERT: J 93 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6840 (p) REVERT: J 219 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7878 (tptp) REVERT: J 506 VAL cc_start: 0.5934 (OUTLIER) cc_final: 0.5420 (p) REVERT: J 1173 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7676 (ptt-90) REVERT: J 1195 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6900 (pp30) REVERT: J 1223 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5782 (mm) REVERT: J 1275 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5055 (mm) REVERT: J 1286 LYS cc_start: 0.6039 (mtmt) cc_final: 0.5778 (ttpp) REVERT: J 1293 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5850 (mm-30) REVERT: J 1340 LYS cc_start: 0.6462 (mmmt) cc_final: 0.5843 (mtpt) REVERT: K 7 GLN cc_start: 0.5835 (tp-100) cc_final: 0.5399 (tt0) REVERT: K 8 ASP cc_start: 0.7089 (t0) cc_final: 0.6878 (t0) REVERT: L 27 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7980 (m) REVERT: L 474 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6996 (mtt) outliers start: 140 outliers final: 69 residues processed: 638 average time/residue: 0.1862 time to fit residues: 193.7603 Evaluate side-chains 488 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 406 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1195 GLN Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 274 ARG Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 565 ILE Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 607 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 366 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 342 optimal weight: 50.0000 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 276 GLN I 343 HIS I 725 GLN I 811 ASN I 932 GLN I1116 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 HIS J 364 HIS J 469 HIS J 489 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 HIS J1367 GLN L 317 ASN L 409 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.223161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.156249 restraints weight = 38920.345| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.21 r_work: 0.3585 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.170 32399 Z= 0.282 Angle : 0.967 19.672 44122 Z= 0.494 Chirality : 0.053 0.351 5069 Planarity : 0.008 0.170 5462 Dihedral : 15.475 148.954 5406 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.23 % Favored : 92.58 % Rotamer: Outliers : 6.41 % Allowed : 15.83 % Favored : 77.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.13), residues: 3801 helix: -0.02 (0.13), residues: 1506 sheet: -1.93 (0.23), residues: 429 loop : -2.17 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.001 ARG I 245 TYR 0.079 0.003 TYR I 584 PHE 0.045 0.003 PHE I1025 TRP 0.012 0.002 TRP J 115 HIS 0.091 0.003 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.28 (32391) covalent geometry : angle 0.96164 / 0.49 (44110) hydrogen bonds : bond 0.05927 / 4.12 ( 1311) hydrogen bonds : angle 5.06085 / 3.52 ( 3615) metal coordination : bond 0.01791 / 1.35 ( 8) metal coordination : angle 6.27410 / 3.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 507 time to evaluate : 1.021 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: G 51 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8243 (mmp) REVERT: G 76 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: H 58 GLU cc_start: 0.6996 (pt0) cc_final: 0.6752 (pt0) REVERT: H 95 LYS cc_start: 0.7623 (pttm) cc_final: 0.7367 (pttm) REVERT: I 29 SER cc_start: 0.8005 (m) cc_final: 0.7592 (p) REVERT: I 39 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6173 (mp) REVERT: I 47 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5971 (p90) REVERT: I 70 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.5264 (t80) REVERT: I 74 ARG cc_start: 0.6256 (ptt180) cc_final: 0.5946 (ptt-90) REVERT: I 126 GLU cc_start: 0.7376 (mp0) cc_final: 0.7166 (mp0) REVERT: I 189 ASP cc_start: 0.4447 (OUTLIER) cc_final: 0.4182 (p0) REVERT: I 239 MET cc_start: 0.7417 (ttt) cc_final: 0.6938 (mtt) REVERT: I 315 MET cc_start: 0.6557 (tpt) cc_final: 0.6240 (tpp) REVERT: I 337 PHE cc_start: 0.7774 (t80) cc_final: 0.7527 (t80) REVERT: I 343 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.5389 (t-170) REVERT: I 349 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6295 (mp0) REVERT: I 369 MET cc_start: 0.7164 (tmm) cc_final: 0.6455 (ttm) REVERT: I 684 ASN cc_start: 0.8273 (t0) cc_final: 0.7643 (m-40) REVERT: I 750 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8074 (mt) REVERT: I 781 ASP cc_start: 0.7892 (m-30) cc_final: 0.7617 (m-30) REVERT: I 785 ASP cc_start: 0.8431 (p0) cc_final: 0.8210 (p0) REVERT: I 818 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8818 (p) REVERT: I 899 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6970 (mt-10) REVERT: I 925 SER cc_start: 0.8247 (t) cc_final: 0.8019 (m) REVERT: I 1090 ASN cc_start: 0.8149 (t0) cc_final: 0.7853 (t0) REVERT: I 1174 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8173 (tm-30) REVERT: I 1303 LYS cc_start: 0.7468 (mmtt) cc_final: 0.7110 (mttt) REVERT: J 37 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: J 107 LEU cc_start: 0.8045 (mt) cc_final: 0.7632 (mp) REVERT: J 164 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6897 (tt0) REVERT: J 185 ILE cc_start: 0.8083 (mm) cc_final: 0.7874 (mp) REVERT: J 485 MET cc_start: 0.8911 (mmt) cc_final: 0.8627 (mmt) REVERT: J 725 MET cc_start: 0.8496 (ttm) cc_final: 0.8057 (ttm) REVERT: J 1195 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7824 (pp30) REVERT: J 1219 ASP cc_start: 0.6816 (m-30) cc_final: 0.6512 (m-30) REVERT: J 1286 LYS cc_start: 0.6742 (mtmt) cc_final: 0.6504 (ttpp) REVERT: J 1340 LYS cc_start: 0.7482 (mmmt) cc_final: 0.7039 (mtpt) REVERT: J 1370 MET cc_start: 0.6819 (tpp) cc_final: 0.6593 (ttm) REVERT: K 15 ASN cc_start: 0.7009 (m110) cc_final: 0.6780 (m110) REVERT: K 18 ASP cc_start: 0.7381 (t70) cc_final: 0.7071 (m-30) REVERT: K 63 ILE cc_start: 0.6294 (mt) cc_final: 0.6076 (mt) REVERT: L 24 TYR cc_start: 0.6885 (t80) cc_final: 0.6463 (m-80) REVERT: L 27 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7926 (m) REVERT: L 474 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7159 (mtt) REVERT: L 489 MET cc_start: 0.5100 (mtt) cc_final: 0.4826 (mtt) REVERT: L 502 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7499 (mtmt) REVERT: M 316 MET cc_start: 0.8590 (ppp) cc_final: 0.7376 (pmm) outliers start: 209 outliers final: 78 residues processed: 657 average time/residue: 0.1699 time to fit residues: 184.7081 Evaluate side-chains 466 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 374 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 272 ARG Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1217 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1195 GLN Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 268 TYR Chi-restraints excluded: chain L residue 343 LYS Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 135 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 338 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 36 GLN I 173 ASN I 450 ASN I 686 GLN I 725 GLN I1070 HIS I1220 GLN I1236 ASN J 488 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 HIS ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 HIS ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.218024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149989 restraints weight = 37837.649| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.56 r_work: 0.3437 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 32399 Z= 0.222 Angle : 0.794 13.832 44122 Z= 0.401 Chirality : 0.048 0.323 5069 Planarity : 0.006 0.103 5462 Dihedral : 15.204 147.518 5384 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.39 % Favored : 93.45 % Rotamer: Outliers : 5.37 % Allowed : 17.58 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3801 helix: 0.25 (0.13), residues: 1500 sheet: -1.56 (0.25), residues: 420 loop : -2.05 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG L 373 TYR 0.021 0.002 TYR I 123 PHE 0.027 0.002 PHE L 316 TRP 0.012 0.002 TRP I 183 HIS 0.009 0.002 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (32391) covalent geometry : angle 0.78690 / 0.40 (44110) hydrogen bonds : bond 0.04998 / 3.48 ( 1311) hydrogen bonds : angle 4.72217 / 3.28 ( 3615) metal coordination : bond 0.01478 / 1.31 ( 8) metal coordination : angle 6.44375 / 3.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 424 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 MET cc_start: 0.8937 (mmp) cc_final: 0.8610 (mmp) REVERT: G 91 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7702 (ttt90) REVERT: H 58 GLU cc_start: 0.7294 (pt0) cc_final: 0.7075 (pt0) REVERT: H 95 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7653 (pttm) REVERT: I 29 SER cc_start: 0.8184 (m) cc_final: 0.7689 (p) REVERT: I 36 GLN cc_start: 0.7283 (mt0) cc_final: 0.6951 (mt0) REVERT: I 39 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6827 (mp) REVERT: I 47 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.6029 (p90) REVERT: I 74 ARG cc_start: 0.6860 (ptt180) cc_final: 0.6521 (ptt-90) REVERT: I 126 GLU cc_start: 0.7277 (mp0) cc_final: 0.6776 (pt0) REVERT: I 173 ASN cc_start: 0.6951 (OUTLIER) cc_final: 0.6478 (p0) REVERT: I 187 GLU cc_start: 0.7517 (pt0) cc_final: 0.7002 (pt0) REVERT: I 239 MET cc_start: 0.7306 (ttt) cc_final: 0.6956 (mtp) REVERT: I 337 PHE cc_start: 0.7892 (t80) cc_final: 0.7685 (t80) REVERT: I 343 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.5411 (t-170) REVERT: I 349 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6551 (mp0) REVERT: I 369 MET cc_start: 0.7349 (tmm) cc_final: 0.6262 (ttm) REVERT: I 561 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8211 (pt) REVERT: I 639 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8068 (ptpp) REVERT: I 684 ASN cc_start: 0.8364 (t0) cc_final: 0.8021 (m-40) REVERT: I 765 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8180 (mt) REVERT: I 778 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7459 (mt-10) REVERT: I 781 ASP cc_start: 0.8009 (m-30) cc_final: 0.7691 (m-30) REVERT: I 1090 ASN cc_start: 0.8347 (t0) cc_final: 0.8110 (t0) REVERT: I 1174 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8002 (tp30) REVERT: I 1226 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8632 (m) REVERT: I 1303 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7581 (mtmt) REVERT: I 1325 VAL cc_start: 0.8771 (t) cc_final: 0.8511 (m) REVERT: J 37 GLU cc_start: 0.7479 (mp0) cc_final: 0.7128 (tt0) REVERT: J 219 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8173 (tmmt) REVERT: J 372 MET cc_start: 0.9254 (ttp) cc_final: 0.8948 (ttt) REVERT: J 485 MET cc_start: 0.9086 (mmt) cc_final: 0.8703 (mmt) REVERT: J 566 LYS cc_start: 0.7793 (tttt) cc_final: 0.7327 (ttpp) REVERT: J 572 THR cc_start: 0.8351 (t) cc_final: 0.7312 (m) REVERT: J 776 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8082 (p) REVERT: J 795 TYR cc_start: 0.8578 (t80) cc_final: 0.8189 (t80) REVERT: J 1189 MET cc_start: 0.8504 (tmm) cc_final: 0.8195 (mmp) REVERT: J 1219 ASP cc_start: 0.7085 (m-30) cc_final: 0.6671 (m-30) REVERT: J 1223 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7350 (mm) REVERT: J 1239 ASP cc_start: 0.7665 (t0) cc_final: 0.7382 (m-30) REVERT: J 1268 ASN cc_start: 0.7918 (t0) cc_final: 0.7632 (t0) REVERT: J 1282 TYR cc_start: 0.8289 (t80) cc_final: 0.7901 (t80) REVERT: J 1340 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7457 (mtmt) REVERT: K 18 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: L 24 TYR cc_start: 0.6721 (t80) cc_final: 0.6229 (m-80) REVERT: L 27 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8001 (m) REVERT: L 365 MET cc_start: 0.8436 (mtt) cc_final: 0.8233 (mtm) REVERT: L 396 ASN cc_start: 0.8688 (m110) cc_final: 0.8446 (m110) REVERT: L 474 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7320 (mtt) REVERT: L 487 MET cc_start: 0.6245 (tpp) cc_final: 0.5700 (ttt) REVERT: L 567 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5338 (ttt) REVERT: M 316 MET cc_start: 0.8035 (ppp) cc_final: 0.6801 (pmm) outliers start: 175 outliers final: 106 residues processed: 560 average time/residue: 0.1891 time to fit residues: 173.5135 Evaluate side-chains 476 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 356 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 735 LYS Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 14 optimal weight: 0.5980 chunk 339 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 351 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 chunk 310 optimal weight: 0.7980 chunk 371 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN J 80 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN J 910 ASN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN L 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.218179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150517 restraints weight = 37796.679| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.24 r_work: 0.3441 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.8051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32399 Z= 0.142 Angle : 0.665 13.311 44122 Z= 0.335 Chirality : 0.044 0.264 5069 Planarity : 0.005 0.122 5462 Dihedral : 15.061 148.539 5382 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.55 % Rotamer: Outliers : 4.48 % Allowed : 18.90 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3801 helix: 0.64 (0.14), residues: 1506 sheet: -1.36 (0.25), residues: 427 loop : -1.88 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1290 TYR 0.030 0.001 TYR L 425 PHE 0.021 0.001 PHE L 302 TRP 0.009 0.001 TRP I 807 HIS 0.006 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32391) covalent geometry : angle 0.66149 / 0.33 (44110) hydrogen bonds : bond 0.04353 / 3.04 ( 1311) hydrogen bonds : angle 4.46505 / 3.11 ( 3615) metal coordination : bond 0.00951 / 0.79 ( 8) metal coordination : angle 4.13802 / 2.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 379 time to evaluate : 1.075 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: G 14 VAL cc_start: 0.7876 (t) cc_final: 0.7486 (t) REVERT: G 15 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: G 51 MET cc_start: 0.8940 (mmp) cc_final: 0.8665 (mmp) REVERT: G 215 GLU cc_start: 0.7362 (tp30) cc_final: 0.6857 (tt0) REVERT: H 58 GLU cc_start: 0.7359 (pt0) cc_final: 0.7023 (pt0) REVERT: H 80 GLU cc_start: 0.7705 (tp30) cc_final: 0.7404 (tm-30) REVERT: H 95 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7450 (pttm) REVERT: H 194 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7507 (tp40) REVERT: I 29 SER cc_start: 0.8159 (m) cc_final: 0.7657 (p) REVERT: I 39 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6970 (mp) REVERT: I 47 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.6003 (p90) REVERT: I 70 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.5195 (t80) REVERT: I 74 ARG cc_start: 0.7017 (ptt180) cc_final: 0.6714 (ptt-90) REVERT: I 84 GLU cc_start: 0.7460 (tt0) cc_final: 0.7154 (tt0) REVERT: I 126 GLU cc_start: 0.7043 (mp0) cc_final: 0.6725 (pt0) REVERT: I 130 MET cc_start: 0.8806 (ttm) cc_final: 0.8409 (ttm) REVERT: I 187 GLU cc_start: 0.7482 (pt0) cc_final: 0.7066 (pt0) REVERT: I 239 MET cc_start: 0.7363 (ttt) cc_final: 0.6976 (mtp) REVERT: I 315 MET cc_start: 0.7067 (tpt) cc_final: 0.6533 (tpp) REVERT: I 337 PHE cc_start: 0.7848 (t80) cc_final: 0.7179 (t80) REVERT: I 343 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.6325 (p90) REVERT: I 349 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7199 (tm-30) REVERT: I 369 MET cc_start: 0.7169 (tmm) cc_final: 0.5995 (ttm) REVERT: I 684 ASN cc_start: 0.8338 (t0) cc_final: 0.8009 (m-40) REVERT: I 768 MET cc_start: 0.8201 (mtt) cc_final: 0.7758 (mtm) REVERT: I 778 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7537 (mt-10) REVERT: I 781 ASP cc_start: 0.8059 (m-30) cc_final: 0.7698 (m-30) REVERT: I 899 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7146 (mt-10) REVERT: I 1168 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7174 (mp0) REVERT: I 1174 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8040 (tt0) REVERT: I 1303 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7755 (mtmt) REVERT: J 37 GLU cc_start: 0.7602 (mp0) cc_final: 0.7286 (tt0) REVERT: J 81 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7672 (ptm160) REVERT: J 248 ASP cc_start: 0.8173 (m-30) cc_final: 0.7891 (m-30) REVERT: J 372 MET cc_start: 0.9286 (ttp) cc_final: 0.9039 (ttt) REVERT: J 485 MET cc_start: 0.9079 (mmt) cc_final: 0.8768 (mmt) REVERT: J 795 TYR cc_start: 0.8506 (t80) cc_final: 0.8252 (t80) REVERT: J 1219 ASP cc_start: 0.7210 (m-30) cc_final: 0.6931 (m-30) REVERT: J 1239 ASP cc_start: 0.7742 (t0) cc_final: 0.7346 (m-30) REVERT: J 1282 TYR cc_start: 0.8147 (t80) cc_final: 0.7790 (t80) REVERT: J 1340 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7585 (mtmt) REVERT: J 1370 MET cc_start: 0.7317 (ttm) cc_final: 0.7031 (ttm) REVERT: K 18 ASP cc_start: 0.7759 (t70) cc_final: 0.7531 (m-30) REVERT: K 30 MET cc_start: 0.8591 (mtm) cc_final: 0.8368 (mtp) REVERT: L 24 TYR cc_start: 0.6663 (t80) cc_final: 0.6295 (m-80) REVERT: L 27 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (m) REVERT: L 297 MET cc_start: 0.0133 (tmm) cc_final: -0.0466 (tmm) REVERT: L 396 ASN cc_start: 0.8828 (m110) cc_final: 0.8548 (m110) REVERT: L 470 MET cc_start: 0.7527 (mtt) cc_final: 0.7263 (mtt) REVERT: L 474 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7428 (mtt) REVERT: L 567 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5618 (ttt) REVERT: L 612 ASP cc_start: 0.3645 (OUTLIER) cc_final: 0.3164 (m-30) REVERT: M 316 MET cc_start: 0.8099 (ppp) cc_final: 0.6940 (pmm) outliers start: 146 outliers final: 92 residues processed: 489 average time/residue: 0.1767 time to fit residues: 142.2544 Evaluate side-chains 462 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 359 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 735 LYS Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 343 LYS Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 612 ASP Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 172 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 342 optimal weight: 40.0000 chunk 246 optimal weight: 0.7980 chunk 363 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 327 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 128 HIS G 132 HIS ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1098 GLN J1249 ASN L 19 GLN L 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.216621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148350 restraints weight = 37628.138| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.27 r_work: 0.3430 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.8709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 32399 Z= 0.163 Angle : 0.681 15.137 44122 Z= 0.340 Chirality : 0.044 0.321 5069 Planarity : 0.005 0.107 5462 Dihedral : 14.975 148.766 5380 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.05 % Favored : 93.84 % Rotamer: Outliers : 4.82 % Allowed : 18.96 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3801 helix: 0.80 (0.14), residues: 1518 sheet: -1.20 (0.25), residues: 426 loop : -1.86 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 422 TYR 0.041 0.002 TYR L 425 PHE 0.018 0.002 PHE L 302 TRP 0.007 0.001 TRP I 807 HIS 0.007 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (32391) covalent geometry : angle 0.67769 / 0.34 (44110) hydrogen bonds : bond 0.04336 / 3.06 ( 1311) hydrogen bonds : angle 4.33717 / 3.02 ( 3615) metal coordination : bond 0.01009 / 0.83 ( 8) metal coordination : angle 4.38745 / 2.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 375 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 MET cc_start: 0.9029 (mmp) cc_final: 0.8821 (mmp) REVERT: G 142 MET cc_start: 0.9226 (mtm) cc_final: 0.8969 (mtt) REVERT: G 215 GLU cc_start: 0.7367 (tp30) cc_final: 0.7036 (tt0) REVERT: H 58 GLU cc_start: 0.7340 (pt0) cc_final: 0.7124 (pt0) REVERT: H 80 GLU cc_start: 0.7555 (tp30) cc_final: 0.7351 (tm-30) REVERT: H 95 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7473 (pttm) REVERT: I 29 SER cc_start: 0.8246 (m) cc_final: 0.7778 (p) REVERT: I 47 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.5986 (p90) REVERT: I 70 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.5146 (t80) REVERT: I 74 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6580 (ptt-90) REVERT: I 84 GLU cc_start: 0.7649 (tt0) cc_final: 0.7323 (tt0) REVERT: I 126 GLU cc_start: 0.7096 (mp0) cc_final: 0.6880 (pt0) REVERT: I 239 MET cc_start: 0.7341 (ttt) cc_final: 0.6962 (mtp) REVERT: I 337 PHE cc_start: 0.7950 (t80) cc_final: 0.7356 (t80) REVERT: I 343 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6441 (p90) REVERT: I 349 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7248 (tm-30) REVERT: I 369 MET cc_start: 0.6955 (tmm) cc_final: 0.5907 (ttm) REVERT: I 684 ASN cc_start: 0.8380 (t0) cc_final: 0.8115 (m-40) REVERT: I 742 TYR cc_start: 0.7242 (m-10) cc_final: 0.7001 (m-10) REVERT: I 768 MET cc_start: 0.8195 (mtt) cc_final: 0.7772 (mtm) REVERT: I 781 ASP cc_start: 0.7959 (m-30) cc_final: 0.7605 (m-30) REVERT: I 853 ASP cc_start: 0.8145 (t70) cc_final: 0.7764 (p0) REVERT: I 1174 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8146 (tt0) REVERT: I 1297 ASP cc_start: 0.8372 (t0) cc_final: 0.8086 (t0) REVERT: J 66 LYS cc_start: 0.7920 (ptpp) cc_final: 0.7530 (ptpp) REVERT: J 81 ARG cc_start: 0.8032 (ptm-80) cc_final: 0.7697 (ptm160) REVERT: J 130 MET cc_start: 0.8416 (mtm) cc_final: 0.8112 (mtp) REVERT: J 148 GLU cc_start: 0.7031 (tt0) cc_final: 0.6643 (tm-30) REVERT: J 204 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: J 248 ASP cc_start: 0.8296 (m-30) cc_final: 0.8039 (m-30) REVERT: J 390 LEU cc_start: 0.8366 (mp) cc_final: 0.8089 (mp) REVERT: J 458 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8207 (t0) REVERT: J 560 ASN cc_start: 0.6711 (p0) cc_final: 0.6499 (p0) REVERT: J 1219 ASP cc_start: 0.7504 (m-30) cc_final: 0.7242 (m-30) REVERT: J 1282 TYR cc_start: 0.8336 (t80) cc_final: 0.8114 (t80) REVERT: L 19 GLN cc_start: 0.7723 (tt0) cc_final: 0.7371 (pt0) REVERT: L 145 LEU cc_start: 0.8292 (mt) cc_final: 0.8077 (pp) REVERT: L 161 LEU cc_start: 0.6334 (tt) cc_final: 0.6075 (mt) REVERT: L 353 LEU cc_start: 0.5964 (tp) cc_final: 0.5729 (tt) REVERT: L 474 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7307 (mtt) REVERT: L 567 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6344 (ttt) REVERT: L 612 ASP cc_start: 0.4175 (OUTLIER) cc_final: 0.3744 (m-30) REVERT: M 316 MET cc_start: 0.8016 (ppp) cc_final: 0.6819 (pmm) outliers start: 157 outliers final: 115 residues processed: 491 average time/residue: 0.1801 time to fit residues: 147.6678 Evaluate side-chains 468 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 343 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 74 ARG Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 735 LYS Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain L residue 612 ASP Chi-restraints excluded: chain M residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 167 optimal weight: 0.6980 chunk 315 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 342 optimal weight: 50.0000 chunk 280 optimal weight: 30.0000 chunk 370 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 279 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1070 HIS J 300 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN ** L 409 ASN ** 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 = 0.4497 r_free = 0.4497 target = 0.212265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129013 restraints weight = 37500.384| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.88 r_work: 0.3339 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.9470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 32399 Z= 0.235 Angle : 0.745 18.921 44122 Z= 0.375 Chirality : 0.046 0.266 5069 Planarity : 0.006 0.128 5462 Dihedral : 14.996 149.964 5377 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.66 % Favored : 93.16 % Rotamer: Outliers : 5.09 % Allowed : 19.54 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3801 helix: 0.73 (0.14), residues: 1511 sheet: -1.06 (0.26), residues: 407 loop : -1.93 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 423 TYR 0.023 0.002 TYR J 795 PHE 0.019 0.002 PHE I1025 TRP 0.011 0.001 TRP I 807 HIS 0.009 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (32391) covalent geometry : angle 0.74009 / 0.38 (44110) hydrogen bonds : bond 0.04964 / 3.45 ( 1311) hydrogen bonds : angle 4.46988 / 3.11 ( 3615) metal coordination : bond 0.01447 / 1.19 ( 8) metal coordination : angle 5.06293 / 2.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 357 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: G 76 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: H 38 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.7399 (m) REVERT: H 58 GLU cc_start: 0.7493 (pt0) cc_final: 0.7289 (pt0) REVERT: H 95 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7387 (pttm) REVERT: I 39 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7386 (mp) REVERT: I 47 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6218 (p90) REVERT: I 70 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5353 (t80) REVERT: I 74 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6953 (ptt-90) REVERT: I 84 GLU cc_start: 0.7865 (tt0) cc_final: 0.7518 (tt0) REVERT: I 239 MET cc_start: 0.7329 (ttt) cc_final: 0.6680 (mtm) REVERT: I 315 MET cc_start: 0.7303 (tpt) cc_final: 0.6791 (tpp) REVERT: I 337 PHE cc_start: 0.7958 (t80) cc_final: 0.7247 (t80) REVERT: I 343 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6364 (p90) REVERT: I 349 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7335 (tm-30) REVERT: I 445 ILE cc_start: 0.8497 (pt) cc_final: 0.8005 (mm) REVERT: I 463 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: I 514 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8312 (t80) REVERT: I 684 ASN cc_start: 0.8350 (t0) cc_final: 0.7609 (m-40) REVERT: I 687 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7765 (ttp80) REVERT: I 732 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8817 (mt) REVERT: I 735 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7337 (tmmt) REVERT: I 742 TYR cc_start: 0.7527 (m-10) cc_final: 0.7250 (m-10) REVERT: I 768 MET cc_start: 0.8233 (mtt) cc_final: 0.7797 (mtm) REVERT: I 853 ASP cc_start: 0.8327 (t70) cc_final: 0.8012 (p0) REVERT: I 1090 ASN cc_start: 0.8718 (t0) cc_final: 0.8368 (t0) REVERT: I 1108 ASN cc_start: 0.8393 (p0) cc_final: 0.8174 (p0) REVERT: I 1158 LYS cc_start: 0.8289 (mmtm) cc_final: 0.8033 (mmtp) REVERT: I 1174 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8325 (tt0) REVERT: I 1250 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8731 (m) REVERT: I 1297 ASP cc_start: 0.8604 (t0) cc_final: 0.8270 (t0) REVERT: J 66 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7507 (ptpp) REVERT: J 76 LYS cc_start: 0.7453 (mtmm) cc_final: 0.7181 (mtmm) REVERT: J 100 GLU cc_start: 0.7963 (pt0) cc_final: 0.7588 (mt-10) REVERT: J 148 GLU cc_start: 0.7067 (tt0) cc_final: 0.6675 (tm-30) REVERT: J 204 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: J 248 ASP cc_start: 0.8426 (m-30) cc_final: 0.8136 (m-30) REVERT: J 300 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7083 (mm-40) REVERT: J 304 ASP cc_start: 0.7714 (m-30) cc_final: 0.7401 (m-30) REVERT: J 329 ASP cc_start: 0.8858 (m-30) cc_final: 0.8626 (m-30) REVERT: J 390 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8376 (mp) REVERT: J 485 MET cc_start: 0.9075 (mmt) cc_final: 0.8564 (mmt) REVERT: J 560 ASN cc_start: 0.7071 (p0) cc_final: 0.6804 (p0) REVERT: J 698 MET cc_start: 0.8509 (tpt) cc_final: 0.8154 (tpp) REVERT: J 870 ASP cc_start: 0.7493 (m-30) cc_final: 0.7288 (m-30) REVERT: J 1219 ASP cc_start: 0.7792 (m-30) cc_final: 0.7394 (m-30) REVERT: K 70 GLN cc_start: 0.6132 (tt0) cc_final: 0.5757 (tm-30) REVERT: L 19 GLN cc_start: 0.7841 (tt0) cc_final: 0.7420 (pt0) REVERT: L 27 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8171 (m) REVERT: L 365 MET cc_start: 0.8301 (mtt) cc_final: 0.7984 (ptp) REVERT: L 396 ASN cc_start: 0.8762 (m110) cc_final: 0.8429 (m110) REVERT: L 474 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7746 (mtt) REVERT: L 567 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6971 (ttt) REVERT: M 316 MET cc_start: 0.7906 (ppp) cc_final: 0.6694 (pmm) outliers start: 166 outliers final: 115 residues processed: 482 average time/residue: 0.1819 time to fit residues: 144.1758 Evaluate side-chains 459 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 323 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 74 ARG Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 732 ILE Chi-restraints excluded: chain I residue 735 LYS Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 343 LYS Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 75 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 222 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 370 optimal weight: 1.9990 chunk 367 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 355 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN J1249 ASN ** L 409 ASN ** 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 = 0.4514 r_free = 0.4514 target = 0.214078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133212 restraints weight = 37496.860| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.31 r_work: 0.3367 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.9672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32399 Z= 0.147 Angle : 0.659 14.388 44122 Z= 0.330 Chirality : 0.044 0.413 5069 Planarity : 0.005 0.126 5462 Dihedral : 14.917 149.726 5376 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.89 % Favored : 93.98 % Rotamer: Outliers : 4.20 % Allowed : 21.29 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3801 helix: 0.94 (0.14), residues: 1512 sheet: -0.99 (0.26), residues: 409 loop : -1.82 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 779 TYR 0.025 0.001 TYR L 421 PHE 0.014 0.001 PHE J1325 TRP 0.008 0.001 TRP L 315 HIS 0.005 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (32391) covalent geometry : angle 0.65437 / 0.33 (44110) hydrogen bonds : bond 0.04269 / 2.95 ( 1311) hydrogen bonds : angle 4.35283 / 3.02 ( 3615) metal coordination : bond 0.01073 / 0.86 ( 8) metal coordination : angle 4.57290 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 347 time to evaluate : 1.174 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: G 76 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: H 95 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7423 (pttm) REVERT: H 127 GLN cc_start: 0.7419 (mp10) cc_final: 0.7180 (mt0) REVERT: I 47 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.6055 (p90) REVERT: I 70 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5315 (t80) REVERT: I 74 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7063 (ptt-90) REVERT: I 84 GLU cc_start: 0.7686 (tt0) cc_final: 0.7337 (tt0) REVERT: I 239 MET cc_start: 0.7335 (ttt) cc_final: 0.6661 (mtm) REVERT: I 315 MET cc_start: 0.7294 (tpt) cc_final: 0.6599 (tpp) REVERT: I 337 PHE cc_start: 0.7952 (t80) cc_final: 0.7326 (t80) REVERT: I 343 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6349 (p90) REVERT: I 349 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7305 (tm-30) REVERT: I 445 ILE cc_start: 0.8415 (pt) cc_final: 0.7899 (mm) REVERT: I 463 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: I 684 ASN cc_start: 0.8194 (t0) cc_final: 0.7625 (m-40) REVERT: I 687 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7615 (ttp80) REVERT: I 742 TYR cc_start: 0.7587 (m-10) cc_final: 0.7343 (m-10) REVERT: I 768 MET cc_start: 0.8204 (mtt) cc_final: 0.7763 (mtm) REVERT: I 853 ASP cc_start: 0.8363 (t70) cc_final: 0.8053 (p0) REVERT: I 1090 ASN cc_start: 0.8518 (t0) cc_final: 0.8209 (t0) REVERT: I 1158 LYS cc_start: 0.8247 (mmtm) cc_final: 0.7973 (mmtp) REVERT: I 1174 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8057 (mm-30) REVERT: I 1250 SER cc_start: 0.8942 (m) cc_final: 0.8721 (m) REVERT: I 1297 ASP cc_start: 0.8454 (t0) cc_final: 0.8176 (t0) REVERT: J 66 LYS cc_start: 0.7733 (ptpp) cc_final: 0.7373 (ptpp) REVERT: J 76 LYS cc_start: 0.7463 (mtmm) cc_final: 0.7116 (mtmm) REVERT: J 100 GLU cc_start: 0.7910 (pt0) cc_final: 0.7669 (mt-10) REVERT: J 148 GLU cc_start: 0.7059 (tt0) cc_final: 0.6777 (tm-30) REVERT: J 155 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6930 (mm-30) REVERT: J 204 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: J 248 ASP cc_start: 0.8389 (m-30) cc_final: 0.8076 (m-30) REVERT: J 304 ASP cc_start: 0.7719 (m-30) cc_final: 0.7379 (m-30) REVERT: J 329 ASP cc_start: 0.8797 (m-30) cc_final: 0.8525 (m-30) REVERT: J 390 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8369 (mp) REVERT: J 400 MET cc_start: 0.8668 (mtp) cc_final: 0.8343 (mtp) REVERT: J 485 MET cc_start: 0.9031 (mmt) cc_final: 0.8501 (mmt) REVERT: J 560 ASN cc_start: 0.7155 (p0) cc_final: 0.6835 (p0) REVERT: J 677 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6848 (tp30) REVERT: J 698 MET cc_start: 0.8424 (tpt) cc_final: 0.8097 (tpp) REVERT: J 1189 MET cc_start: 0.8077 (tpt) cc_final: 0.7692 (tpt) REVERT: J 1219 ASP cc_start: 0.7744 (m-30) cc_final: 0.7406 (m-30) REVERT: K 15 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7554 (t0) REVERT: L 19 GLN cc_start: 0.7740 (tt0) cc_final: 0.7383 (pt0) REVERT: L 27 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8247 (m) REVERT: L 161 LEU cc_start: 0.5968 (tt) cc_final: 0.5707 (mt) REVERT: L 297 MET cc_start: -0.0504 (tmm) cc_final: -0.1040 (tmm) REVERT: L 474 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7692 (mtt) REVERT: L 567 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7091 (ttt) REVERT: M 316 MET cc_start: 0.7901 (ppp) cc_final: 0.6673 (pmm) outliers start: 137 outliers final: 105 residues processed: 448 average time/residue: 0.1833 time to fit residues: 136.5940 Evaluate side-chains 452 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 333 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 74 ARG Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 735 LYS Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 343 LYS Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 196 optimal weight: 7.9990 chunk 201 optimal weight: 0.0470 chunk 221 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 370 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 387 optimal weight: 50.0000 chunk 346 optimal weight: 20.0000 chunk 373 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 752 ASN I 799 ASN J 300 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1244 GLN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.213211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130693 restraints weight = 37278.978| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.00 r_work: 0.3324 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.9912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32399 Z= 0.164 Angle : 0.676 16.002 44122 Z= 0.337 Chirality : 0.044 0.305 5069 Planarity : 0.005 0.131 5462 Dihedral : 14.891 149.991 5376 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 4.45 % Allowed : 21.07 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3801 helix: 1.02 (0.14), residues: 1512 sheet: -1.06 (0.25), residues: 429 loop : -1.78 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 470 TYR 0.019 0.001 TYR J 46 PHE 0.022 0.001 PHE I 906 TRP 0.007 0.001 TRP I 807 HIS 0.007 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (32391) covalent geometry : angle 0.67184 / 0.34 (44110) hydrogen bonds : bond 0.04315 / 2.99 ( 1311) hydrogen bonds : angle 4.32043 / 3.01 ( 3615) metal coordination : bond 0.01083 / 0.87 ( 8) metal coordination : angle 4.33596 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 342 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 VAL cc_start: 0.8252 (t) cc_final: 0.8015 (t) REVERT: G 15 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.6341 (m-30) REVERT: G 76 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: H 50 SER cc_start: 0.8916 (m) cc_final: 0.8678 (m) REVERT: H 95 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7364 (pttm) REVERT: H 127 GLN cc_start: 0.7565 (mp10) cc_final: 0.7308 (mt0) REVERT: I 47 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.6120 (p90) REVERT: I 70 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5309 (t80) REVERT: I 74 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7154 (ptt-90) REVERT: I 239 MET cc_start: 0.7353 (ttt) cc_final: 0.6665 (mtm) REVERT: I 315 MET cc_start: 0.7314 (tpt) cc_final: 0.6602 (tpp) REVERT: I 337 PHE cc_start: 0.7966 (t80) cc_final: 0.7269 (t80) REVERT: I 343 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6351 (p90) REVERT: I 349 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7314 (tm-30) REVERT: I 369 MET cc_start: 0.6815 (tmm) cc_final: 0.5856 (ttp) REVERT: I 445 ILE cc_start: 0.8404 (pt) cc_final: 0.7881 (mm) REVERT: I 463 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: I 472 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.5390 (tt0) REVERT: I 514 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8331 (t80) REVERT: I 684 ASN cc_start: 0.8239 (t0) cc_final: 0.7747 (m-40) REVERT: I 687 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7654 (ttp80) REVERT: I 742 TYR cc_start: 0.7668 (m-10) cc_final: 0.7428 (m-10) REVERT: I 768 MET cc_start: 0.8291 (mtt) cc_final: 0.7878 (mtm) REVERT: I 853 ASP cc_start: 0.8437 (t70) cc_final: 0.8181 (p0) REVERT: I 1090 ASN cc_start: 0.8598 (t0) cc_final: 0.8150 (m-40) REVERT: I 1158 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7999 (mmtp) REVERT: I 1174 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8157 (mm-30) REVERT: I 1250 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8745 (m) REVERT: I 1297 ASP cc_start: 0.8517 (t0) cc_final: 0.8257 (t0) REVERT: J 66 LYS cc_start: 0.7740 (ptpp) cc_final: 0.7415 (ptpp) REVERT: J 76 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7277 (mtmt) REVERT: J 100 GLU cc_start: 0.7993 (pt0) cc_final: 0.7792 (mt-10) REVERT: J 148 GLU cc_start: 0.7117 (tt0) cc_final: 0.6825 (tm-30) REVERT: J 204 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6952 (tm-30) REVERT: J 248 ASP cc_start: 0.8384 (m-30) cc_final: 0.8112 (m-30) REVERT: J 283 LEU cc_start: 0.7853 (mt) cc_final: 0.7631 (mp) REVERT: J 300 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7346 (mm-40) REVERT: J 304 ASP cc_start: 0.7750 (m-30) cc_final: 0.7479 (m-30) REVERT: J 329 ASP cc_start: 0.8818 (m-30) cc_final: 0.8562 (m-30) REVERT: J 550 VAL cc_start: 0.9021 (m) cc_final: 0.8755 (t) REVERT: J 560 ASN cc_start: 0.7295 (p0) cc_final: 0.6950 (p0) REVERT: J 638 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8643 (t) REVERT: J 677 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6964 (tp30) REVERT: J 698 MET cc_start: 0.8500 (tpt) cc_final: 0.8165 (tpp) REVERT: J 818 GLU cc_start: 0.8104 (mp0) cc_final: 0.7868 (mt-10) REVERT: J 1219 ASP cc_start: 0.7817 (m-30) cc_final: 0.7429 (m-30) REVERT: K 15 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7610 (t0) REVERT: L 19 GLN cc_start: 0.7750 (tt0) cc_final: 0.7405 (pt0) REVERT: L 27 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (m) REVERT: L 161 LEU cc_start: 0.5989 (tt) cc_final: 0.5696 (mt) REVERT: L 365 MET cc_start: 0.8403 (mtt) cc_final: 0.8085 (ptp) REVERT: L 474 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7804 (mtt) REVERT: M 316 MET cc_start: 0.7977 (ppp) cc_final: 0.6754 (pmm) outliers start: 145 outliers final: 109 residues processed: 452 average time/residue: 0.1856 time to fit residues: 139.3009 Evaluate side-chains 456 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 329 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 74 ARG Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 379 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 185 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.213382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132069 restraints weight = 37284.845| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.91 r_work: 0.3348 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.9921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.247 32399 Z= 0.212 Angle : 0.824 59.178 44122 Z= 0.454 Chirality : 0.044 0.508 5069 Planarity : 0.005 0.134 5462 Dihedral : 14.894 149.999 5376 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 4.26 % Allowed : 21.26 % Favored : 74.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3801 helix: 1.02 (0.14), residues: 1512 sheet: -1.08 (0.25), residues: 429 loop : -1.77 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.019 0.001 TYR J 46 PHE 0.019 0.001 PHE I 906 TRP 0.007 0.001 TRP L 315 HIS 0.007 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (32391) covalent geometry : angle 0.82103 / 0.45 (44110) hydrogen bonds : bond 0.04300 / 2.98 ( 1311) hydrogen bonds : angle 4.32914 / 3.01 ( 3615) metal coordination : bond 0.01033 / 0.84 ( 8) metal coordination : angle 4.32856 / 2.27 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 327 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 VAL cc_start: 0.8220 (t) cc_final: 0.7983 (t) REVERT: G 15 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: G 76 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: H 50 SER cc_start: 0.8926 (m) cc_final: 0.8680 (m) REVERT: H 95 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7343 (pttm) REVERT: H 127 GLN cc_start: 0.7527 (mp10) cc_final: 0.7288 (mt0) REVERT: I 47 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.6070 (p90) REVERT: I 50 GLU cc_start: 0.7542 (pm20) cc_final: 0.7253 (pm20) REVERT: I 70 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.5295 (t80) REVERT: I 74 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7135 (ptt-90) REVERT: I 239 MET cc_start: 0.7365 (ttt) cc_final: 0.6672 (mtm) REVERT: I 315 MET cc_start: 0.7321 (tpt) cc_final: 0.6616 (tpp) REVERT: I 337 PHE cc_start: 0.7929 (t80) cc_final: 0.7205 (t80) REVERT: I 343 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.6246 (p90) REVERT: I 349 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7256 (tm-30) REVERT: I 369 MET cc_start: 0.6798 (tmm) cc_final: 0.5835 (ttp) REVERT: I 445 ILE cc_start: 0.8381 (pt) cc_final: 0.7845 (mm) REVERT: I 463 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: I 472 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.5318 (tt0) REVERT: I 514 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8303 (t80) REVERT: I 684 ASN cc_start: 0.8178 (t0) cc_final: 0.7642 (m-40) REVERT: I 687 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7622 (ttp80) REVERT: I 742 TYR cc_start: 0.7670 (m-10) cc_final: 0.7434 (m-10) REVERT: I 768 MET cc_start: 0.8278 (mtt) cc_final: 0.7846 (mtm) REVERT: I 783 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8311 (pp) REVERT: I 853 ASP cc_start: 0.8431 (t70) cc_final: 0.8124 (p0) REVERT: I 1090 ASN cc_start: 0.8500 (t0) cc_final: 0.8098 (m-40) REVERT: I 1158 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7955 (mmtp) REVERT: I 1174 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8077 (mm-30) REVERT: I 1250 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8721 (m) REVERT: I 1297 ASP cc_start: 0.8487 (t0) cc_final: 0.8201 (t0) REVERT: J 66 LYS cc_start: 0.7672 (ptpp) cc_final: 0.7334 (ptpp) REVERT: J 76 LYS cc_start: 0.7534 (mtmm) cc_final: 0.7228 (mtmt) REVERT: J 100 GLU cc_start: 0.7921 (pt0) cc_final: 0.7694 (mt-10) REVERT: J 148 GLU cc_start: 0.7125 (tt0) cc_final: 0.6767 (tm-30) REVERT: J 204 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: J 248 ASP cc_start: 0.8418 (m-30) cc_final: 0.8097 (m-30) REVERT: J 283 LEU cc_start: 0.7728 (mt) cc_final: 0.7502 (mp) REVERT: J 304 ASP cc_start: 0.7655 (m-30) cc_final: 0.7363 (m-30) REVERT: J 329 ASP cc_start: 0.8776 (m-30) cc_final: 0.8509 (m-30) REVERT: J 550 VAL cc_start: 0.8996 (m) cc_final: 0.8762 (t) REVERT: J 560 ASN cc_start: 0.7287 (p0) cc_final: 0.6944 (p0) REVERT: J 638 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8702 (t) REVERT: J 677 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6938 (tp30) REVERT: J 698 MET cc_start: 0.8411 (tpt) cc_final: 0.8073 (tpp) REVERT: J 776 THR cc_start: 0.8826 (m) cc_final: 0.8509 (p) REVERT: J 818 GLU cc_start: 0.8098 (mp0) cc_final: 0.7855 (mt-10) REVERT: J 1115 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5908 (pt) REVERT: J 1219 ASP cc_start: 0.7746 (m-30) cc_final: 0.7339 (m-30) REVERT: K 15 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7542 (t0) REVERT: L 19 GLN cc_start: 0.7786 (tt0) cc_final: 0.7431 (pt0) REVERT: L 27 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8250 (m) REVERT: L 161 LEU cc_start: 0.6016 (tt) cc_final: 0.5714 (mt) REVERT: L 365 MET cc_start: 0.8431 (mtt) cc_final: 0.8111 (ptp) REVERT: L 474 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7825 (mtt) REVERT: M 316 MET cc_start: 0.8050 (ppp) cc_final: 0.6843 (pmm) outliers start: 139 outliers final: 117 residues processed: 434 average time/residue: 0.1779 time to fit residues: 128.4525 Evaluate side-chains 462 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 326 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 74 ARG Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 165 PHE Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 343 LYS Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 101 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 226 optimal weight: 0.0470 chunk 142 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 381 optimal weight: 40.0000 chunk 222 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.213510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132300 restraints weight = 37272.420| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.25 r_work: 0.3332 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.9920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.286 32399 Z= 0.224 Angle : 0.811 44.798 44122 Z= 0.474 Chirality : 0.045 0.668 5069 Planarity : 0.006 0.136 5462 Dihedral : 14.894 149.999 5376 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 4.20 % Allowed : 21.32 % Favored : 74.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3801 helix: 1.02 (0.14), residues: 1512 sheet: -1.08 (0.25), residues: 429 loop : -1.77 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.019 0.001 TYR J 46 PHE 0.019 0.001 PHE I 906 TRP 0.007 0.001 TRP L 315 HIS 0.007 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (32391) covalent geometry : angle 0.80824 / 0.47 (44110) hydrogen bonds : bond 0.04300 / 2.98 ( 1311) hydrogen bonds : angle 4.32914 / 3.01 ( 3615) metal coordination : bond 0.01033 / 0.84 ( 8) metal coordination : angle 4.32855 / 2.27 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9459.63 seconds wall clock time: 162 minutes 2.63 seconds (9722.63 seconds total)