Starting phenix.real_space_refine on Sun Aug 9 05:40:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ftd_29423/08_2026/8ftd_29423.cif" } resolution = 2.76 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= 0.004 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 87 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 117 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 20054 2.51 5 N 5751 2.21 5 O 6471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 32529 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1789 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1681 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10575 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10386 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3812 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 455} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1252 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain breaks: 1 Chain: "Q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1142 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "Z" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 603 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14494 SG CYS J 70 101.969 62.929 73.551 1.00133.93 S ATOM 14508 SG CYS J 72 99.763 60.771 71.305 1.00132.75 S ATOM 14616 SG CYS J 85 103.108 61.951 70.042 1.00132.39 S ATOM 14640 SG CYS J 88 100.313 64.497 70.569 1.00131.77 S ATOM 20328 SG CYS J 814 124.449 117.562 108.315 1.00128.67 S ATOM 20893 SG CYS J 888 121.123 116.038 107.248 1.00127.41 S ATOM 20944 SG CYS J 895 122.722 114.917 110.519 1.00119.54 S ATOM 20965 SG CYS J 898 121.292 118.386 110.225 1.00121.44 S Time building chain proxies: 6.12, per 1000 atoms: 0.19 Number of scatterers: 32529 At special positions: 0 Unit cell: (154.212, 189.144, 193.404, 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 133 16.00 P 117 15.00 Mg 1 11.99 O 6471 8.00 N 5751 7.00 C 20054 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 47 sheets defined 43.4% alpha, 14.3% beta 33 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.533A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.860A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 230 removed outlier: 3.589A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.580A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.861A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 229 Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.828A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.847A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.918A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 246 removed outlier: 3.600A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 292 removed outlier: 3.871A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.111A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.614A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.616A pdb=" N LYS I 527 " --> pdb=" O GLU I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.853A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.677A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.209A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.967A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 862 Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 982 Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.872A pdb=" N LEU I 998 " --> pdb=" O ARG I 994 " (cutoff:3.500A) Processing helix chain 'I' and resid 1008 through 1038 removed outlier: 3.538A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU I1014 " --> pdb=" O GLN I1010 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU I1016 " --> pdb=" O GLU I1012 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN I1017 " --> pdb=" O GLN I1013 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1101 No H-bonds generated for 'chain 'I' and resid 1099 through 1101' Processing helix chain 'I' and resid 1102 through 1107 removed outlier: 3.508A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1135 Processing helix chain 'I' and resid 1138 through 1151 Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.813A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.706A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.758A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 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 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 4.001A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.742A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.062A 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 802 removed outlier: 3.789A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.839A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.528A pdb=" N SER J 887 " --> pdb=" O SER J 884 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.735A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.617A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1074 removed outlier: 4.148A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1147 Processing helix chain 'J' and resid 1216 through 1245 removed outlier: 7.889A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.451A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.669A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (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 1373 removed outlier: 4.383A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'L' and resid 96 through 107 removed outlier: 3.952A pdb=" N MET L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 136 Processing helix chain 'L' and resid 137 through 153 removed outlier: 4.280A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 233 Processing helix chain 'L' and resid 244 through 258 Processing helix chain 'L' and resid 262 through 292 removed outlier: 3.624A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 330 through 352 removed outlier: 3.981A pdb=" N GLU L 335 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU L 336 " --> pdb=" O ASP L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 392 removed outlier: 5.115A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 400 through 417 Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.923A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.919A 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 removed outlier: 3.905A pdb=" N ALA L 484 " --> pdb=" O PRO L 480 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 500 Processing helix chain 'L' and resid 518 through 523 removed outlier: 4.031A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 551 removed outlier: 3.780A pdb=" N LEU L 551 " --> pdb=" O VAL L 547 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 600 Processing helix chain 'L' and resid 604 through 610 Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.948A pdb=" N GLU R 261 " --> pdb=" O ASP R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 274 Processing helix chain 'R' and resid 277 through 282 Processing helix chain 'R' and resid 285 through 292 removed outlier: 3.541A pdb=" N THR R 292 " --> pdb=" O GLU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 310 removed outlier: 3.650A pdb=" N LEU R 300 " --> pdb=" O GLY R 296 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 76 removed outlier: 3.655A pdb=" N ALA Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 15 removed outlier: 3.856A pdb=" N GLU G 29 " --> pdb=" O ARG G 12 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU G 31 " --> pdb=" O ASP G 199 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.899A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN G 147 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.566A pdb=" N GLY G 151 " --> pdb=" O TYR G 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 109 through 111 removed outlier: 3.658A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.620A pdb=" N ALA H 184 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 52 through 61 removed outlier: 3.797A pdb=" N GLY H 149 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 111 removed outlier: 3.657A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.600A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.673A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.372A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.633A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 230 Processing sheet with id=AB8, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.658A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR I 262 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 4.979A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.724A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.729A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 5.948A pdb=" N ILE I 816 " --> pdb=" O ILE I1076 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS I1078 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL I 818 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.682A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.646A pdb=" N GLN J 448 " --> pdb=" O GLY J 367 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA J 446 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.916A pdb=" N GLU I1340 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.535A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.801A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 254 through 255 removed outlier: 6.779A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 821 Processing sheet with id=AE3, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.757A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.822A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'J' and resid 1024 through 1026 removed outlier: 3.847A pdb=" N MET J1025 " --> pdb=" O ILE J1124 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1034 through 1035 Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.788A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 3.825A pdb=" N VAL J1176 " --> pdb=" O SER J1164 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG J1173 " --> pdb=" O ILE J1190 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE J1190 " --> pdb=" O ARG J1173 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.161A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 46 through 49 removed outlier: 4.392A pdb=" N VAL Z 47 " --> pdb=" O LEU Z 54 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU Z 54 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET Z 49 " --> pdb=" O SER Z 52 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER Z 52 " --> pdb=" O MET Z 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 1322 hydrogen bonds defined for protein. 3753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5469 1.32 - 1.44: 8425 1.44 - 1.56: 18907 1.56 - 1.69: 230 1.69 - 1.81: 234 Bond restraints: 33265 Sorted by residual: bond pdb=" CA GLU G 229 " pdb=" C GLU G 229 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.35e-02 5.49e+03 1.90e+01 bond pdb=" CA THR H 38 " pdb=" C THR H 38 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.40e+01 bond pdb=" CA GLN G 227 " pdb=" C GLN G 227 " ideal model delta sigma weight residual 1.522 1.472 0.050 1.41e-02 5.03e+03 1.24e+01 bond pdb=" C THR H 38 " pdb=" O THR H 38 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" CA LEU H 9 " pdb=" C LEU H 9 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.23e-02 6.61e+03 1.11e+01 ... (remaining 33260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 44483 1.98 - 3.96: 851 3.96 - 5.94: 80 5.94 - 7.92: 14 7.92 - 9.89: 9 Bond angle restraints: 45437 Sorted by residual: angle pdb=" C LEU G 228 " pdb=" N GLU G 229 " pdb=" CA GLU G 229 " ideal model delta sigma weight residual 120.38 110.49 9.89 1.37e+00 5.33e-01 5.22e+01 angle pdb=" N ASP I1004 " pdb=" CA ASP I1004 " pdb=" C ASP I1004 " ideal model delta sigma weight residual 113.37 103.50 9.87 1.38e+00 5.25e-01 5.12e+01 angle pdb=" N GLU I 50 " pdb=" CA GLU I 50 " pdb=" C GLU I 50 " ideal model delta sigma weight residual 111.28 103.79 7.49 1.09e+00 8.42e-01 4.72e+01 angle pdb=" N ASP I 234 " pdb=" CA ASP I 234 " pdb=" C ASP I 234 " ideal model delta sigma weight residual 110.24 100.60 9.64 1.41e+00 5.03e-01 4.67e+01 angle pdb=" N VAL G 232 " pdb=" CA VAL G 232 " pdb=" C VAL G 232 " ideal model delta sigma weight residual 110.09 100.49 9.60 1.50e+00 4.44e-01 4.10e+01 ... (remaining 45432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.86: 18663 26.86 - 53.72: 1475 53.72 - 80.57: 195 80.57 - 107.43: 16 107.43 - 134.29: 4 Dihedral angle restraints: 20353 sinusoidal: 9340 harmonic: 11013 Sorted by residual: dihedral pdb=" CA GLN H 93 " pdb=" C GLN H 93 " pdb=" N GLY H 94 " pdb=" CA GLY H 94 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLN G 93 " pdb=" C GLN G 93 " pdb=" N GLY G 94 " pdb=" CA GLY G 94 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C22 1N7 I1401 " pdb=" C23 1N7 I1401 " pdb=" C24 1N7 I1401 " pdb=" N1 1N7 I1401 " ideal model delta sinusoidal sigma weight residual 227.30 93.01 134.29 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 20350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3998 0.045 - 0.090: 885 0.090 - 0.134: 299 0.134 - 0.179: 10 0.179 - 0.224: 4 Chirality restraints: 5196 Sorted by residual: chirality pdb=" CG LEU I1000 " pdb=" CB LEU I1000 " pdb=" CD1 LEU I1000 " pdb=" CD2 LEU I1000 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PRO H 30 " pdb=" N PRO H 30 " pdb=" C PRO H 30 " pdb=" CB PRO H 30 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA VAL G 232 " pdb=" N VAL G 232 " pdb=" C VAL G 232 " pdb=" CB VAL G 232 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.72e-01 ... (remaining 5193 not shown) Planarity restraints: 5512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 29 " -0.104 5.00e-02 4.00e+02 1.55e-01 3.82e+01 pdb=" N PRO H 30 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO H 30 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO H 30 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR G 27 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C THR G 27 " 0.060 2.00e-02 2.50e+03 pdb=" O THR G 27 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU G 28 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 176 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C CYS H 176 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS H 176 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR H 177 " 0.016 2.00e-02 2.50e+03 ... (remaining 5509 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 751 2.68 - 3.24: 29470 3.24 - 3.79: 49929 3.79 - 4.35: 64135 4.35 - 4.90: 106613 Nonbonded interactions: 250898 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.126 2.170 nonbonded pdb=" N GLN G 194 " pdb=" OE1 GLN G 194 " model vdw 2.143 3.120 nonbonded pdb=" O ARG G 45 " pdb=" OG SER G 49 " model vdw 2.204 3.040 nonbonded pdb=" OG SER J1271 " pdb=" O VAL J1298 " model vdw 2.218 3.040 nonbonded pdb=" NH1 ARG I1223 " pdb=" OG SER J 721 " model vdw 2.231 3.120 ... (remaining 250893 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 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 158 or resid 171 through 233 or (resid 234 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 234)) } 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.420 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 0.004 0.059 33273 Z= 0.291 Angle : 0.613 9.894 45449 Z= 0.418 Chirality : 0.042 0.224 5196 Planarity : 0.004 0.155 5512 Dihedral : 17.818 134.288 13249 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 2.88 % Allowed : 9.77 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.05 (0.14), residues: 3797 helix: 1.38 (0.14), residues: 1518 sheet: 0.13 (0.27), residues: 405 loop : -1.15 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 233 TYR 0.017 0.001 TYR G 177 PHE 0.011 0.001 PHE G 8 TRP 0.008 0.001 TRP J 686 HIS 0.007 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.29 (33265) covalent geometry : angle 0.61309 / 0.42 (45437) hydrogen bonds : bond 0.15156 / 10.35 ( 1395) hydrogen bonds : angle 5.52262 / 3.83 ( 3919) metal coordination : bond 0.00238 / 0.15 ( 8) metal coordination : angle 1.20901 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 569 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.7148 (mtmm) cc_final: 0.6861 (ttpp) REVERT: G 120 ASP cc_start: 0.7522 (m-30) cc_final: 0.7204 (m-30) REVERT: G 226 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6662 (mm-30) REVERT: H 15 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.5479 (p0) REVERT: H 120 ASP cc_start: 0.6478 (m-30) cc_final: 0.5600 (p0) REVERT: H 197 ASP cc_start: 0.6711 (t0) cc_final: 0.6424 (p0) REVERT: H 218 ARG cc_start: 0.5479 (mtp-110) cc_final: 0.5192 (mtt90) REVERT: I 119 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7296 (tm-30) REVERT: I 414 ILE cc_start: 0.8419 (pt) cc_final: 0.7698 (mm) REVERT: I 441 GLU cc_start: 0.7199 (tp30) cc_final: 0.6940 (mp0) REVERT: I 583 GLU cc_start: 0.7382 (tt0) cc_final: 0.6949 (tt0) REVERT: I 658 GLN cc_start: 0.6223 (mt0) cc_final: 0.5973 (pt0) REVERT: I 687 ARG cc_start: 0.7265 (ptt90) cc_final: 0.6999 (mtm-85) REVERT: I 742 TYR cc_start: 0.6696 (m-10) cc_final: 0.6327 (m-10) REVERT: I 778 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6757 (mm-30) REVERT: I 919 ARG cc_start: 0.8049 (ptp-110) cc_final: 0.7725 (mtp85) REVERT: I 958 LYS cc_start: 0.6593 (tttt) cc_final: 0.6374 (tttm) REVERT: I 998 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6623 (pt) REVERT: I 1006 GLU cc_start: 0.3190 (OUTLIER) cc_final: 0.2637 (pm20) REVERT: I 1020 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6141 (tp30) REVERT: I 1080 ASN cc_start: 0.7426 (m110) cc_final: 0.7175 (m-40) REVERT: I 1119 MET cc_start: 0.5978 (tpt) cc_final: 0.5225 (ttt) REVERT: I 1137 GLU cc_start: 0.6347 (mp0) cc_final: 0.6032 (mp0) REVERT: I 1211 ARG cc_start: 0.7265 (ttm170) cc_final: 0.6461 (mmt180) REVERT: I 1321 GLU cc_start: 0.6250 (tp30) cc_final: 0.5786 (tp30) REVERT: J 81 ARG cc_start: 0.7862 (tmm-80) cc_final: 0.7232 (ptm160) REVERT: J 192 MET cc_start: 0.7124 (ttm) cc_final: 0.6919 (ptm) REVERT: J 314 ARG cc_start: 0.7856 (ptp-170) cc_final: 0.7004 (ptm-80) REVERT: J 322 ARG cc_start: 0.7037 (mtp85) cc_final: 0.5702 (mtp-110) REVERT: J 329 ASP cc_start: 0.6664 (m-30) cc_final: 0.5978 (m-30) REVERT: J 464 ASP cc_start: 0.8480 (m-30) cc_final: 0.8217 (m-30) REVERT: J 562 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6381 (tp30) REVERT: J 603 LYS cc_start: 0.6959 (mtmt) cc_final: 0.6741 (mmpt) REVERT: J 802 ASP cc_start: 0.7079 (t0) cc_final: 0.6454 (m-30) REVERT: J 874 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6980 (tt0) REVERT: J 1152 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6521 (pm20) REVERT: J 1278 GLU cc_start: 0.6453 (tt0) cc_final: 0.5932 (tp30) REVERT: K 11 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6325 (mt-10) REVERT: K 43 ASN cc_start: 0.6996 (t0) cc_final: 0.6704 (t0) REVERT: K 55 GLU cc_start: 0.6525 (tt0) cc_final: 0.6245 (mt-10) REVERT: L 133 SER cc_start: 0.4121 (m) cc_final: 0.3759 (p) REVERT: L 244 THR cc_start: 0.3005 (OUTLIER) cc_final: 0.2784 (t) REVERT: L 259 PHE cc_start: 0.6654 (m-10) cc_final: 0.6374 (m-80) REVERT: L 278 ASP cc_start: 0.7262 (m-30) cc_final: 0.7062 (t70) REVERT: L 297 MET cc_start: 0.0897 (ppp) cc_final: 0.0634 (mtt) REVERT: L 322 MET cc_start: 0.2538 (ptt) cc_final: 0.1989 (ttp) REVERT: L 482 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7102 (mt-10) REVERT: L 485 GLU cc_start: 0.7247 (mp0) cc_final: 0.6986 (tt0) REVERT: L 561 MET cc_start: 0.5859 (mmt) cc_final: 0.5396 (ttm) REVERT: R 316 MET cc_start: 0.1620 (ppp) cc_final: 0.0888 (pmm) REVERT: Z 38 MET cc_start: 0.3921 (mmp) cc_final: 0.3569 (mmt) REVERT: Z 49 MET cc_start: 0.4216 (mmm) cc_final: 0.3520 (tmt) outliers start: 94 outliers final: 13 residues processed: 639 average time/residue: 0.7122 time to fit residues: 533.3966 Evaluate side-chains 356 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 338 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 30 PRO Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1006 GLU Chi-restraints excluded: chain I residue 1020 GLU Chi-restraints excluded: chain I residue 1105 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain Z residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS H 41 ASN I 60 GLN I 83 GLN I 238 GLN I 339 ASN I 517 GLN I 628 HIS I 955 GLN I 965 GLN ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN J 335 GLN J 430 HIS J 504 GLN J 817 HIS J 875 ASN J1218 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN R 283 GLN Z 11 GLN Z 66 GLN Z 70 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.176462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107391 restraints weight = 42136.853| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.12 r_work: 0.3146 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 33273 Z= 0.245 Angle : 0.740 12.437 45449 Z= 0.386 Chirality : 0.048 0.280 5196 Planarity : 0.006 0.142 5512 Dihedral : 16.471 135.608 5726 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.81 % Rotamer: Outliers : 3.95 % Allowed : 14.64 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.10 (0.13), residues: 3797 helix: 1.55 (0.13), residues: 1517 sheet: 0.16 (0.26), residues: 394 loop : -1.24 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I1246 TYR 0.022 0.002 TYR I 555 PHE 0.018 0.002 PHE I1144 TRP 0.022 0.002 TRP J1193 HIS 0.019 0.002 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (33265) covalent geometry : angle 0.73707 / 0.39 (45437) hydrogen bonds : bond 0.06204 / 4.18 ( 1395) hydrogen bonds : angle 4.27951 / 2.98 ( 3919) metal coordination : bond 0.01045 / 0.53 ( 8) metal coordination : angle 3.87341 / 2.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 362 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.8530 (tt0) cc_final: 0.8328 (tt0) REVERT: G 33 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7322 (tpp-160) REVERT: G 91 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6570 (ttm170) REVERT: G 95 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7828 (mtmm) REVERT: G 117 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6017 (p-80) REVERT: G 214 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: H 6 THR cc_start: 0.7403 (m) cc_final: 0.7127 (p) REVERT: H 120 ASP cc_start: 0.6538 (m-30) cc_final: 0.5661 (p0) REVERT: H 122 GLU cc_start: 0.7559 (tt0) cc_final: 0.7319 (tm-30) REVERT: H 143 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7317 (mtp180) REVERT: H 197 ASP cc_start: 0.7771 (t0) cc_final: 0.7457 (p0) REVERT: I 119 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7609 (tm-30) REVERT: I 191 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6943 (mtmt) REVERT: I 386 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: I 583 GLU cc_start: 0.8325 (tt0) cc_final: 0.8096 (tt0) REVERT: I 658 GLN cc_start: 0.7956 (mt0) cc_final: 0.7753 (pt0) REVERT: I 681 MET cc_start: 0.8979 (mtp) cc_final: 0.8666 (mtt) REVERT: I 687 ARG cc_start: 0.8586 (ptt90) cc_final: 0.8355 (mtm-85) REVERT: I 694 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7428 (mtm180) REVERT: I 742 TYR cc_start: 0.7235 (m-10) cc_final: 0.6819 (m-10) REVERT: I 854 ILE cc_start: 0.8303 (mm) cc_final: 0.8088 (mp) REVERT: I 955 GLN cc_start: 0.7535 (tp40) cc_final: 0.7313 (mm110) REVERT: I 958 LYS cc_start: 0.7843 (tttt) cc_final: 0.7534 (ttmm) REVERT: I 1119 MET cc_start: 0.8492 (tpt) cc_final: 0.8276 (tpt) REVERT: I 1211 ARG cc_start: 0.8670 (ttm170) cc_final: 0.7948 (mmt180) REVERT: I 1321 GLU cc_start: 0.7751 (tp30) cc_final: 0.7471 (tp30) REVERT: J 77 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6245 (mmm-85) REVERT: J 81 ARG cc_start: 0.8402 (tmm-80) cc_final: 0.7806 (ptm160) REVERT: J 87 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8246 (ttmm) REVERT: J 183 GLU cc_start: 0.8066 (tt0) cc_final: 0.7613 (mp0) REVERT: J 227 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8089 (t80) REVERT: J 314 ARG cc_start: 0.8487 (ptp-170) cc_final: 0.7556 (ptm-80) REVERT: J 322 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7019 (mtp-110) REVERT: J 340 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8006 (tp-100) REVERT: J 562 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6614 (tp30) REVERT: J 603 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7785 (mmpt) REVERT: J 664 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.6279 (mm) REVERT: J 802 ASP cc_start: 0.8327 (t0) cc_final: 0.7868 (m-30) REVERT: J 863 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8160 (tt) REVERT: J 1152 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6906 (pm20) REVERT: J 1169 THR cc_start: 0.5286 (OUTLIER) cc_final: 0.4668 (p) REVERT: J 1327 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: K 11 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7087 (mt-10) REVERT: K 43 ASN cc_start: 0.7955 (t0) cc_final: 0.7389 (t0) REVERT: K 55 GLU cc_start: 0.7747 (tt0) cc_final: 0.7465 (mt-10) REVERT: K 56 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: L 259 PHE cc_start: 0.6707 (m-10) cc_final: 0.6431 (m-80) REVERT: L 260 ARG cc_start: 0.5907 (tpp-160) cc_final: 0.5105 (ttm110) REVERT: L 265 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7084 (mm-40) REVERT: L 284 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4206 (pt0) REVERT: L 322 MET cc_start: 0.2295 (ptt) cc_final: 0.1405 (ttp) REVERT: L 482 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7561 (mt-10) REVERT: L 485 GLU cc_start: 0.7690 (mp0) cc_final: 0.7384 (tt0) REVERT: L 524 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7962 (pp20) REVERT: L 525 ASP cc_start: 0.8402 (t0) cc_final: 0.8157 (t0) REVERT: L 561 MET cc_start: 0.6736 (mmt) cc_final: 0.6119 (ttm) REVERT: L 608 ARG cc_start: 0.7050 (tpp80) cc_final: 0.6503 (mtt90) REVERT: R 316 MET cc_start: 0.1519 (ppp) cc_final: 0.0648 (pmm) REVERT: Z 38 MET cc_start: 0.4101 (mmp) cc_final: 0.3629 (mmt) REVERT: Z 49 MET cc_start: 0.4555 (mmm) cc_final: 0.3898 (tmt) outliers start: 129 outliers final: 49 residues processed: 453 average time/residue: 0.7652 time to fit residues: 404.3812 Evaluate side-chains 367 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1005 GLU Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 15 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 352 optimal weight: 0.0020 chunk 227 optimal weight: 0.6980 chunk 387 optimal weight: 0.7980 chunk 314 optimal weight: 5.9990 chunk 279 optimal weight: 0.0050 chunk 324 optimal weight: 5.9990 overall best weight: 0.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS H 132 HIS H 186 ASN I 83 GLN I 314 ASN I 339 ASN I 494 ASN ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1038 GLN J 430 HIS J 817 HIS L 362 ASN L 472 GLN R 283 GLN Z 11 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109883 restraints weight = 41726.856| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.17 r_work: 0.3196 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 33273 Z= 0.116 Angle : 0.547 11.958 45449 Z= 0.290 Chirality : 0.041 0.217 5196 Planarity : 0.004 0.135 5512 Dihedral : 16.223 131.741 5702 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 3.00 % Allowed : 16.72 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.53 (0.14), residues: 3797 helix: 1.98 (0.13), residues: 1518 sheet: 0.39 (0.26), residues: 395 loop : -1.07 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 67 TYR 0.020 0.001 TYR J 46 PHE 0.015 0.001 PHE I 337 TRP 0.021 0.001 TRP J1193 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (33265) covalent geometry : angle 0.54596 / 0.29 (45437) hydrogen bonds : bond 0.04335 / 2.95 ( 1395) hydrogen bonds : angle 3.96632 / 2.76 ( 3919) metal coordination : bond 0.00444 / 0.23 ( 8) metal coordination : angle 2.43998 / 1.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 310 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: G 91 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6668 (ttm170) REVERT: H 30 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7882 (Cg_endo) REVERT: H 120 ASP cc_start: 0.6472 (m-30) cc_final: 0.5694 (p0) REVERT: H 143 ARG cc_start: 0.7570 (mtp180) cc_final: 0.7327 (mtp180) REVERT: H 219 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6942 (mtm-85) REVERT: I 119 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7534 (tm-30) REVERT: I 583 GLU cc_start: 0.8243 (tt0) cc_final: 0.7958 (tt0) REVERT: I 641 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: I 681 MET cc_start: 0.8912 (mtp) cc_final: 0.8607 (mtt) REVERT: I 742 TYR cc_start: 0.7283 (m-80) cc_final: 0.6823 (m-10) REVERT: I 778 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7972 (mm-30) REVERT: I 799 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8097 (m110) REVERT: I 854 ILE cc_start: 0.8169 (mm) cc_final: 0.7955 (mp) REVERT: I 955 GLN cc_start: 0.7477 (tp40) cc_final: 0.7212 (mm110) REVERT: I 958 LYS cc_start: 0.7728 (tttt) cc_final: 0.7431 (ttmm) REVERT: I 1211 ARG cc_start: 0.8596 (ttm170) cc_final: 0.7852 (mmt180) REVERT: I 1321 GLU cc_start: 0.7506 (tp30) cc_final: 0.7200 (tp30) REVERT: J 60 ARG cc_start: 0.8174 (ttt90) cc_final: 0.7838 (ttp80) REVERT: J 81 ARG cc_start: 0.8334 (tmm-80) cc_final: 0.7785 (ptm160) REVERT: J 183 GLU cc_start: 0.7953 (tt0) cc_final: 0.7505 (mp0) REVERT: J 227 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7827 (t80) REVERT: J 314 ARG cc_start: 0.8435 (ptp-170) cc_final: 0.7484 (ptm-80) REVERT: J 322 ARG cc_start: 0.8028 (mtp85) cc_final: 0.6891 (mtp-110) REVERT: J 340 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7943 (tp-100) REVERT: J 562 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6565 (tp30) REVERT: J 603 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7677 (mmpt) REVERT: J 644 MET cc_start: 0.8792 (mpp) cc_final: 0.8300 (mtt) REVERT: J 731 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6671 (mmp-170) REVERT: J 802 ASP cc_start: 0.8262 (t0) cc_final: 0.7814 (m-30) REVERT: J 1040 MET cc_start: 0.2476 (ptp) cc_final: 0.1282 (mpt) REVERT: J 1152 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6829 (pm20) REVERT: J 1327 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: K 11 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6937 (mt-10) REVERT: K 43 ASN cc_start: 0.7860 (t0) cc_final: 0.7364 (t0) REVERT: K 55 GLU cc_start: 0.7597 (tt0) cc_final: 0.7376 (mt-10) REVERT: K 56 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: L 259 PHE cc_start: 0.6682 (m-10) cc_final: 0.6450 (m-80) REVERT: L 260 ARG cc_start: 0.5794 (tpp-160) cc_final: 0.5052 (ttm110) REVERT: L 265 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7056 (mm-40) REVERT: L 277 MET cc_start: 0.5492 (tpp) cc_final: 0.5126 (tpp) REVERT: L 284 GLU cc_start: 0.4362 (OUTLIER) cc_final: 0.3926 (pt0) REVERT: L 322 MET cc_start: 0.2126 (ptt) cc_final: 0.1541 (ttp) REVERT: L 344 LEU cc_start: 0.3311 (pp) cc_final: 0.2775 (tt) REVERT: L 482 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7551 (mt-10) REVERT: L 485 GLU cc_start: 0.7642 (mp0) cc_final: 0.7317 (tt0) REVERT: L 561 MET cc_start: 0.6503 (mmt) cc_final: 0.5836 (ttm) REVERT: L 608 ARG cc_start: 0.7059 (tpp80) cc_final: 0.6390 (mtt90) REVERT: R 316 MET cc_start: 0.1445 (ppp) cc_final: 0.0571 (pmm) REVERT: Z 20 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6023 (tp30) REVERT: Z 38 MET cc_start: 0.4053 (mmp) cc_final: 0.2108 (ptt) REVERT: Z 44 VAL cc_start: 0.5154 (OUTLIER) cc_final: 0.4868 (t) REVERT: Z 49 MET cc_start: 0.4388 (mmm) cc_final: 0.3810 (tmt) outliers start: 98 outliers final: 42 residues processed: 380 average time/residue: 0.7413 time to fit residues: 329.3554 Evaluate side-chains 336 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 44 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 66 optimal weight: 7.9990 chunk 370 optimal weight: 50.0000 chunk 290 optimal weight: 20.0000 chunk 125 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 344 optimal weight: 2.9990 chunk 378 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 387 optimal weight: 30.0000 chunk 250 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 83 GLN I 628 HIS I 965 GLN ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 817 HIS J 875 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 GLN Z 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103360 restraints weight = 41109.466| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.92 r_work: 0.3104 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 33273 Z= 0.196 Angle : 0.643 12.948 45449 Z= 0.338 Chirality : 0.045 0.224 5196 Planarity : 0.005 0.138 5512 Dihedral : 16.412 131.607 5697 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 3.92 % Allowed : 17.15 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.22 (0.14), residues: 3797 helix: 1.72 (0.13), residues: 1533 sheet: 0.21 (0.25), residues: 407 loop : -1.27 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I1246 TYR 0.025 0.002 TYR I 47 PHE 0.017 0.002 PHE J 719 TRP 0.024 0.001 TRP J1193 HIS 0.011 0.002 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (33265) covalent geometry : angle 0.63977 / 0.34 (45437) hydrogen bonds : bond 0.05906 / 3.98 ( 1395) hydrogen bonds : angle 4.05085 / 2.82 ( 3919) metal coordination : bond 0.00950 / 0.51 ( 8) metal coordination : angle 4.09341 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 299 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7734 (tpp-160) REVERT: G 117 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6070 (p-80) REVERT: G 226 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: H 12 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6036 (ptp-170) REVERT: H 30 PRO cc_start: 0.8359 (Cg_exo) cc_final: 0.8072 (Cg_endo) REVERT: H 76 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: H 120 ASP cc_start: 0.6424 (m-30) cc_final: 0.5610 (p0) REVERT: H 143 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7362 (mtp180) REVERT: H 219 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7156 (mtm-85) REVERT: I 119 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7523 (mm-30) REVERT: I 191 LYS cc_start: 0.7410 (mmmt) cc_final: 0.7195 (mtpp) REVERT: I 289 VAL cc_start: 0.5571 (OUTLIER) cc_final: 0.5369 (m) REVERT: I 334 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: I 545 PHE cc_start: 0.7307 (t80) cc_final: 0.6642 (m-80) REVERT: I 583 GLU cc_start: 0.8314 (tt0) cc_final: 0.8099 (tt0) REVERT: I 681 MET cc_start: 0.8978 (mtp) cc_final: 0.8675 (mtt) REVERT: I 738 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: I 742 TYR cc_start: 0.7413 (m-80) cc_final: 0.6964 (m-10) REVERT: I 799 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.7957 (p0) REVERT: I 854 ILE cc_start: 0.8247 (mm) cc_final: 0.8018 (mp) REVERT: I 908 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: I 955 GLN cc_start: 0.7536 (tp40) cc_final: 0.7253 (mm110) REVERT: I 958 LYS cc_start: 0.7816 (tttt) cc_final: 0.7513 (ttmm) REVERT: I 1008 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6001 (tp40) REVERT: I 1211 ARG cc_start: 0.8683 (ttm170) cc_final: 0.7929 (mmt180) REVERT: I 1321 GLU cc_start: 0.7593 (tp30) cc_final: 0.7327 (tp30) REVERT: I 1327 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8029 (mp) REVERT: J 60 ARG cc_start: 0.8168 (ttt90) cc_final: 0.7784 (ttp80) REVERT: J 81 ARG cc_start: 0.8337 (tmm-80) cc_final: 0.7813 (ptm160) REVERT: J 183 GLU cc_start: 0.8111 (tt0) cc_final: 0.7480 (mp0) REVERT: J 227 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7863 (t80) REVERT: J 314 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.7451 (ptm-80) REVERT: J 322 ARG cc_start: 0.8190 (mtp85) cc_final: 0.6983 (mtp-110) REVERT: J 340 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8018 (tp-100) REVERT: J 562 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6700 (tp30) REVERT: J 603 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7805 (mmpt) REVERT: J 664 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6162 (mm) REVERT: J 802 ASP cc_start: 0.8210 (t0) cc_final: 0.7810 (m-30) REVERT: J 1040 MET cc_start: 0.2327 (ptp) cc_final: 0.1217 (mpt) REVERT: J 1152 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6828 (pm20) REVERT: J 1169 THR cc_start: 0.5161 (OUTLIER) cc_final: 0.4576 (p) REVERT: J 1177 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6408 (mp) REVERT: J 1327 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: K 11 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7118 (mt-10) REVERT: K 55 GLU cc_start: 0.7689 (tt0) cc_final: 0.7447 (mt-10) REVERT: K 56 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: L 259 PHE cc_start: 0.6773 (m-10) cc_final: 0.6497 (m-80) REVERT: L 265 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7147 (mm-40) REVERT: L 277 MET cc_start: 0.5660 (tpp) cc_final: 0.5240 (tpp) REVERT: L 281 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6418 (ptt180) REVERT: L 322 MET cc_start: 0.2198 (ptt) cc_final: 0.1564 (ttp) REVERT: L 344 LEU cc_start: 0.3340 (pp) cc_final: 0.2762 (tt) REVERT: L 482 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7639 (mt-10) REVERT: L 485 GLU cc_start: 0.7791 (mp0) cc_final: 0.7381 (tt0) REVERT: L 524 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7949 (pp20) REVERT: L 561 MET cc_start: 0.6526 (mmt) cc_final: 0.5845 (ttm) REVERT: R 260 LEU cc_start: 0.4743 (mm) cc_final: 0.4225 (tp) REVERT: Z 44 VAL cc_start: 0.5426 (OUTLIER) cc_final: 0.5154 (t) REVERT: Z 49 MET cc_start: 0.4500 (mmm) cc_final: 0.4080 (tmt) outliers start: 128 outliers final: 59 residues processed: 389 average time/residue: 0.7304 time to fit residues: 331.8727 Evaluate side-chains 353 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 272 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 738 GLU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1008 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 281 ARG Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 156 optimal weight: 4.9990 chunk 381 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 247 optimal weight: 0.1980 chunk 240 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN H 186 ASN I 83 GLN I 339 ASN ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1038 GLN J 430 HIS J 495 ASN J 817 HIS J1195 GLN K 43 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.174028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103160 restraints weight = 41134.694| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.91 r_work: 0.3070 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33273 Z= 0.181 Angle : 0.605 12.704 45449 Z= 0.320 Chirality : 0.044 0.220 5196 Planarity : 0.005 0.136 5512 Dihedral : 16.428 129.116 5696 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.94 % Rotamer: Outliers : 3.80 % Allowed : 17.70 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % 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: 0.15 (0.14), residues: 3797 helix: 1.67 (0.13), residues: 1534 sheet: 0.17 (0.25), residues: 408 loop : -1.32 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 158 TYR 0.024 0.002 TYR I 47 PHE 0.017 0.002 PHE I 337 TRP 0.024 0.001 TRP J1193 HIS 0.007 0.001 HIS I 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (33265) covalent geometry : angle 0.60241 / 0.32 (45437) hydrogen bonds : bond 0.05530 / 3.76 ( 1395) hydrogen bonds : angle 4.03069 / 2.80 ( 3919) metal coordination : bond 0.00772 / 0.40 ( 8) metal coordination : angle 3.79258 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 287 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7227 (tpp-160) REVERT: G 117 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6119 (p-80) REVERT: G 188 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: G 226 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: H 12 ARG cc_start: 0.6617 (mtm-85) cc_final: 0.6252 (ptp-170) REVERT: H 30 PRO cc_start: 0.8331 (Cg_exo) cc_final: 0.8042 (Cg_endo) REVERT: H 76 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: H 120 ASP cc_start: 0.6375 (m-30) cc_final: 0.5528 (p0) REVERT: H 143 ARG cc_start: 0.7535 (mtp180) cc_final: 0.7200 (mtp180) REVERT: H 219 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7275 (mtp85) REVERT: I 119 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7397 (mm-30) REVERT: I 334 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7338 (pt0) REVERT: I 583 GLU cc_start: 0.8308 (tt0) cc_final: 0.8066 (tt0) REVERT: I 681 MET cc_start: 0.8949 (mtp) cc_final: 0.8661 (mtt) REVERT: I 742 TYR cc_start: 0.7458 (m-80) cc_final: 0.7096 (m-10) REVERT: I 799 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.7951 (p0) REVERT: I 854 ILE cc_start: 0.8240 (mm) cc_final: 0.8003 (mp) REVERT: I 867 GLU cc_start: 0.8305 (pp20) cc_final: 0.7996 (pm20) REVERT: I 955 GLN cc_start: 0.7537 (tp40) cc_final: 0.7167 (mm110) REVERT: I 958 LYS cc_start: 0.7778 (tttt) cc_final: 0.7465 (ttmm) REVERT: I 1008 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6056 (tp40) REVERT: I 1143 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: I 1211 ARG cc_start: 0.8664 (ttm170) cc_final: 0.7926 (mmt180) REVERT: I 1321 GLU cc_start: 0.7517 (tp30) cc_final: 0.7223 (tp30) REVERT: I 1327 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8015 (mp) REVERT: J 60 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7799 (ttp80) REVERT: J 81 ARG cc_start: 0.8326 (tmm-80) cc_final: 0.7348 (ttt-90) REVERT: J 183 GLU cc_start: 0.8085 (tt0) cc_final: 0.7337 (mp0) REVERT: J 227 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7759 (t80) REVERT: J 314 ARG cc_start: 0.8471 (ptp-170) cc_final: 0.7410 (ptm-80) REVERT: J 322 ARG cc_start: 0.8170 (mtp85) cc_final: 0.6929 (mtp-110) REVERT: J 340 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7949 (tp-100) REVERT: J 562 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6658 (tp30) REVERT: J 603 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7747 (mmpt) REVERT: J 664 ILE cc_start: 0.6466 (OUTLIER) cc_final: 0.6124 (mm) REVERT: J 802 ASP cc_start: 0.8217 (t0) cc_final: 0.7803 (m-30) REVERT: J 1152 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6832 (pm20) REVERT: J 1169 THR cc_start: 0.5046 (OUTLIER) cc_final: 0.4463 (p) REVERT: J 1177 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6437 (mp) REVERT: K 11 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7138 (mt-10) REVERT: K 55 GLU cc_start: 0.7645 (tt0) cc_final: 0.7414 (mt-10) REVERT: K 56 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: L 259 PHE cc_start: 0.6794 (m-10) cc_final: 0.6490 (m-80) REVERT: L 265 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7137 (mm-40) REVERT: L 277 MET cc_start: 0.5774 (tpp) cc_final: 0.5354 (tpp) REVERT: L 281 ARG cc_start: 0.6537 (ptm160) cc_final: 0.6265 (ptt180) REVERT: L 322 MET cc_start: 0.2135 (ptt) cc_final: 0.1653 (ttp) REVERT: L 344 LEU cc_start: 0.3276 (pp) cc_final: 0.2714 (tt) REVERT: L 482 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7727 (mt-10) REVERT: L 524 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: L 561 MET cc_start: 0.6565 (mmt) cc_final: 0.5939 (ttm) REVERT: L 582 VAL cc_start: 0.5003 (t) cc_final: 0.4643 (m) REVERT: L 608 ARG cc_start: 0.7081 (tpp80) cc_final: 0.6366 (mtt90) REVERT: R 316 MET cc_start: 0.2227 (pp-130) cc_final: 0.0906 (pmm) REVERT: Z 20 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5810 (tp30) REVERT: Z 38 MET cc_start: 0.4233 (mmp) cc_final: 0.2370 (ptt) REVERT: Z 44 VAL cc_start: 0.5406 (OUTLIER) cc_final: 0.4901 (t) REVERT: Z 46 PHE cc_start: 0.4885 (OUTLIER) cc_final: 0.4472 (t80) REVERT: Z 49 MET cc_start: 0.4626 (mmm) cc_final: 0.4270 (tmt) outliers start: 124 outliers final: 53 residues processed: 380 average time/residue: 0.7611 time to fit residues: 338.8821 Evaluate side-chains 349 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 277 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 1008 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 46 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 259 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 chunk 357 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 186 ASN I 83 GLN I 628 HIS ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1038 GLN I1264 GLN J 430 HIS J 817 HIS K 43 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103361 restraints weight = 40964.734| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.89 r_work: 0.3084 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33273 Z= 0.157 Angle : 0.585 12.319 45449 Z= 0.309 Chirality : 0.043 0.335 5196 Planarity : 0.005 0.133 5512 Dihedral : 16.387 128.660 5694 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 3.77 % Allowed : 18.28 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.14), residues: 3797 helix: 1.71 (0.13), residues: 1537 sheet: 0.21 (0.25), residues: 406 loop : -1.31 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1206 TYR 0.019 0.001 TYR I 47 PHE 0.021 0.001 PHE I 545 TRP 0.025 0.001 TRP J1193 HIS 0.008 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (33265) covalent geometry : angle 0.58240 / 0.31 (45437) hydrogen bonds : bond 0.05267 / 3.57 ( 1395) hydrogen bonds : angle 3.98689 / 2.77 ( 3919) metal coordination : bond 0.00688 / 0.36 ( 8) metal coordination : angle 3.63081 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 286 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6155 (p-80) REVERT: G 226 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: H 6 THR cc_start: 0.7357 (m) cc_final: 0.7042 (p) REVERT: H 12 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6235 (ptp-170) REVERT: H 30 PRO cc_start: 0.8353 (Cg_exo) cc_final: 0.8094 (Cg_endo) REVERT: H 76 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: H 104 LYS cc_start: 0.7425 (tptp) cc_final: 0.7208 (tptt) REVERT: H 107 ILE cc_start: 0.7766 (tp) cc_final: 0.7452 (tp) REVERT: H 143 ARG cc_start: 0.7604 (mtp180) cc_final: 0.7287 (mtp180) REVERT: H 218 ARG cc_start: 0.7174 (mtp-110) cc_final: 0.6826 (mtt180) REVERT: H 219 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7261 (mtp85) REVERT: I 119 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7415 (mm-30) REVERT: I 255 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.6047 (pp) REVERT: I 334 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7387 (pt0) REVERT: I 545 PHE cc_start: 0.7196 (t80) cc_final: 0.6429 (m-80) REVERT: I 583 GLU cc_start: 0.8300 (tt0) cc_final: 0.8067 (tt0) REVERT: I 681 MET cc_start: 0.9004 (mtp) cc_final: 0.8724 (mtt) REVERT: I 742 TYR cc_start: 0.7468 (m-80) cc_final: 0.7126 (m-10) REVERT: I 799 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7915 (p0) REVERT: I 854 ILE cc_start: 0.8274 (mm) cc_final: 0.8013 (mp) REVERT: I 867 GLU cc_start: 0.8281 (pp20) cc_final: 0.7993 (pm20) REVERT: I 955 GLN cc_start: 0.7573 (tp40) cc_final: 0.7242 (mm110) REVERT: I 958 LYS cc_start: 0.7858 (tttt) cc_final: 0.7540 (ttmm) REVERT: I 1008 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.5998 (tp40) REVERT: I 1211 ARG cc_start: 0.8688 (ttm170) cc_final: 0.7948 (mmt180) REVERT: I 1321 GLU cc_start: 0.7536 (tp30) cc_final: 0.7265 (tp30) REVERT: J 60 ARG cc_start: 0.8166 (ttt90) cc_final: 0.7816 (ttp80) REVERT: J 81 ARG cc_start: 0.8356 (tmm-80) cc_final: 0.7400 (ttt-90) REVERT: J 126 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7941 (tt) REVERT: J 183 GLU cc_start: 0.8128 (tt0) cc_final: 0.7410 (mp0) REVERT: J 227 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7784 (t80) REVERT: J 314 ARG cc_start: 0.8438 (ptp-170) cc_final: 0.7408 (ptm-80) REVERT: J 322 ARG cc_start: 0.8203 (mtp85) cc_final: 0.6911 (mtm-85) REVERT: J 340 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7970 (tp-100) REVERT: J 474 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8373 (mp) REVERT: J 562 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6675 (tp30) REVERT: J 603 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7795 (mmpt) REVERT: J 664 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6135 (mm) REVERT: J 802 ASP cc_start: 0.8204 (t0) cc_final: 0.7818 (m-30) REVERT: J 1152 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6833 (pm20) REVERT: J 1169 THR cc_start: 0.5262 (OUTLIER) cc_final: 0.4679 (p) REVERT: J 1177 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6495 (mp) REVERT: K 11 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7156 (mt-10) REVERT: K 55 GLU cc_start: 0.7684 (tt0) cc_final: 0.7458 (mt-10) REVERT: L 259 PHE cc_start: 0.6835 (m-10) cc_final: 0.6515 (m-80) REVERT: L 265 GLN cc_start: 0.7496 (mm110) cc_final: 0.7121 (mm-40) REVERT: L 277 MET cc_start: 0.5824 (tpp) cc_final: 0.5353 (tpp) REVERT: L 322 MET cc_start: 0.2193 (ptt) cc_final: 0.1602 (ttp) REVERT: L 344 LEU cc_start: 0.3192 (pp) cc_final: 0.2664 (tt) REVERT: L 482 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7803 (mt-10) REVERT: L 524 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: L 561 MET cc_start: 0.6575 (mmt) cc_final: 0.5924 (ttm) REVERT: L 582 VAL cc_start: 0.4956 (t) cc_final: 0.4596 (m) REVERT: R 316 MET cc_start: 0.2302 (pp-130) cc_final: 0.0863 (pmm) REVERT: Z 20 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5830 (tp30) REVERT: Z 44 VAL cc_start: 0.5459 (OUTLIER) cc_final: 0.5038 (t) REVERT: Z 49 MET cc_start: 0.4670 (mmm) cc_final: 0.4260 (tmt) outliers start: 123 outliers final: 56 residues processed: 382 average time/residue: 0.7546 time to fit residues: 337.2646 Evaluate side-chains 346 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 272 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1008 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 174 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 295 optimal weight: 8.9990 chunk 332 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 83 GLN I1010 GLN I1038 GLN J 430 HIS J 817 HIS J1126 GLN K 43 ASN Z 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.173752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102335 restraints weight = 41090.920| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.91 r_work: 0.3060 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33273 Z= 0.174 Angle : 0.609 12.549 45449 Z= 0.319 Chirality : 0.044 0.274 5196 Planarity : 0.005 0.133 5512 Dihedral : 16.411 130.446 5694 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 4.23 % Allowed : 18.16 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % 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: 0.14 (0.14), residues: 3797 helix: 1.65 (0.13), residues: 1536 sheet: 0.22 (0.26), residues: 405 loop : -1.33 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1206 TYR 0.020 0.002 TYR I 47 PHE 0.023 0.002 PHE I 337 TRP 0.029 0.001 TRP J1193 HIS 0.008 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (33265) covalent geometry : angle 0.60542 / 0.32 (45437) hydrogen bonds : bond 0.05507 / 3.74 ( 1395) hydrogen bonds : angle 4.01724 / 2.79 ( 3919) metal coordination : bond 0.00744 / 0.39 ( 8) metal coordination : angle 3.81210 / 2.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 277 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6185 (p-80) REVERT: G 188 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: G 226 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: H 6 THR cc_start: 0.7352 (m) cc_final: 0.7068 (p) REVERT: H 12 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6293 (ptp-170) REVERT: H 30 PRO cc_start: 0.8316 (Cg_exo) cc_final: 0.8054 (Cg_endo) REVERT: H 76 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: H 95 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7314 (mtpp) REVERT: H 120 ASP cc_start: 0.6479 (OUTLIER) cc_final: 0.5373 (p0) REVERT: H 143 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7298 (mtp180) REVERT: H 218 ARG cc_start: 0.7165 (mtp-110) cc_final: 0.6834 (mtt180) REVERT: I 119 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7277 (mm-30) REVERT: I 334 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: I 545 PHE cc_start: 0.7320 (t80) cc_final: 0.6565 (m-80) REVERT: I 583 GLU cc_start: 0.8344 (tt0) cc_final: 0.8091 (tt0) REVERT: I 681 MET cc_start: 0.9002 (mtp) cc_final: 0.8724 (mtt) REVERT: I 738 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: I 742 TYR cc_start: 0.7480 (m-80) cc_final: 0.7264 (m-10) REVERT: I 799 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.7950 (p0) REVERT: I 854 ILE cc_start: 0.8086 (mm) cc_final: 0.7876 (mp) REVERT: I 958 LYS cc_start: 0.7886 (tttt) cc_final: 0.7564 (ttmm) REVERT: I 1008 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6101 (tp40) REVERT: I 1143 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: I 1211 ARG cc_start: 0.8698 (ttm170) cc_final: 0.7970 (mmt180) REVERT: I 1321 GLU cc_start: 0.7590 (tp30) cc_final: 0.7339 (tp30) REVERT: J 60 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7826 (ttp80) REVERT: J 81 ARG cc_start: 0.8370 (tmm-80) cc_final: 0.7383 (ttt-90) REVERT: J 126 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7992 (tt) REVERT: J 227 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7760 (t80) REVERT: J 314 ARG cc_start: 0.8450 (ptp-170) cc_final: 0.7407 (ptm-80) REVERT: J 322 ARG cc_start: 0.8215 (mtp85) cc_final: 0.6945 (mtm-85) REVERT: J 340 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7947 (tp-100) REVERT: J 474 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8346 (mp) REVERT: J 562 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6638 (tp30) REVERT: J 603 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7798 (mmpt) REVERT: J 664 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6178 (mm) REVERT: J 708 ASN cc_start: 0.9005 (p0) cc_final: 0.8667 (p0) REVERT: J 802 ASP cc_start: 0.8252 (t0) cc_final: 0.7846 (m-30) REVERT: J 1152 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6793 (pm20) REVERT: J 1169 THR cc_start: 0.5205 (OUTLIER) cc_final: 0.4662 (p) REVERT: J 1177 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6396 (mp) REVERT: K 11 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7160 (mt-10) REVERT: K 12 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.6929 (mptp) REVERT: K 55 GLU cc_start: 0.7658 (tt0) cc_final: 0.7415 (mt-10) REVERT: K 56 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: L 259 PHE cc_start: 0.6885 (m-10) cc_final: 0.6555 (m-80) REVERT: L 277 MET cc_start: 0.5448 (tpp) cc_final: 0.5166 (tpp) REVERT: L 322 MET cc_start: 0.2262 (ptt) cc_final: 0.1620 (ttp) REVERT: L 344 LEU cc_start: 0.3305 (pp) cc_final: 0.2722 (tt) REVERT: L 425 TYR cc_start: 0.8354 (m-80) cc_final: 0.8041 (m-80) REVERT: L 482 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7880 (mt-10) REVERT: L 524 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7989 (pp20) REVERT: L 561 MET cc_start: 0.6570 (mmt) cc_final: 0.5910 (ttm) REVERT: L 582 VAL cc_start: 0.5052 (t) cc_final: 0.4684 (m) REVERT: L 608 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6507 (mtt90) REVERT: R 260 LEU cc_start: 0.4881 (mm) cc_final: 0.4645 (mm) REVERT: R 316 MET cc_start: 0.2413 (pp-130) cc_final: 0.0883 (pmm) REVERT: Z 44 VAL cc_start: 0.5470 (OUTLIER) cc_final: 0.5201 (t) REVERT: Z 49 MET cc_start: 0.4668 (mmm) cc_final: 0.4297 (tmt) outliers start: 138 outliers final: 72 residues processed: 386 average time/residue: 0.7499 time to fit residues: 338.3043 Evaluate side-chains 364 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 270 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 738 GLU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1008 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 37 TRP Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 331 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 287 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 186 ASN I 83 GLN I 955 GLN I1038 GLN J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103524 restraints weight = 40953.931| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.89 r_work: 0.3094 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33273 Z= 0.135 Angle : 0.568 14.033 45449 Z= 0.298 Chirality : 0.042 0.218 5196 Planarity : 0.005 0.130 5512 Dihedral : 16.355 132.304 5694 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 3.09 % Allowed : 19.32 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % 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: 0.26 (0.14), residues: 3797 helix: 1.77 (0.13), residues: 1536 sheet: 0.40 (0.26), residues: 389 loop : -1.30 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 33 TYR 0.017 0.001 TYR G 177 PHE 0.022 0.001 PHE I 337 TRP 0.035 0.001 TRP J1193 HIS 0.006 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (33265) covalent geometry : angle 0.56205 / 0.30 (45437) hydrogen bonds : bond 0.04935 / 3.36 ( 1395) hydrogen bonds : angle 3.93709 / 2.73 ( 3919) metal coordination : bond 0.00969 / 0.51 ( 8) metal coordination : angle 4.92792 / 3.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 280 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7755 (tpp-160) REVERT: G 117 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6110 (p-80) REVERT: H 6 THR cc_start: 0.7315 (m) cc_final: 0.6996 (p) REVERT: H 12 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.6197 (ptp-170) REVERT: H 30 PRO cc_start: 0.8293 (Cg_exo) cc_final: 0.8037 (Cg_endo) REVERT: H 51 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8286 (mmm) REVERT: H 76 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: H 143 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7300 (mtp180) REVERT: H 218 ARG cc_start: 0.7114 (mtp-110) cc_final: 0.6803 (mtt180) REVERT: I 119 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7277 (mm-30) REVERT: I 334 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: I 392 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7582 (mp0) REVERT: I 542 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6528 (tpt170) REVERT: I 545 PHE cc_start: 0.7299 (t80) cc_final: 0.6507 (m-80) REVERT: I 583 GLU cc_start: 0.8308 (tt0) cc_final: 0.8041 (tt0) REVERT: I 681 MET cc_start: 0.8957 (mtp) cc_final: 0.8683 (mtt) REVERT: I 742 TYR cc_start: 0.7425 (m-80) cc_final: 0.7222 (m-10) REVERT: I 799 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7762 (p0) REVERT: I 958 LYS cc_start: 0.7876 (tttt) cc_final: 0.7547 (ttmm) REVERT: I 1008 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6061 (tp40) REVERT: I 1143 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: I 1211 ARG cc_start: 0.8679 (ttm170) cc_final: 0.7921 (mmt180) REVERT: I 1321 GLU cc_start: 0.7541 (tp30) cc_final: 0.7284 (tp30) REVERT: J 60 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7792 (ttp80) REVERT: J 81 ARG cc_start: 0.8356 (tmm-80) cc_final: 0.7400 (ttt-90) REVERT: J 126 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8028 (tt) REVERT: J 183 GLU cc_start: 0.8080 (tt0) cc_final: 0.7360 (mp0) REVERT: J 227 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7682 (t80) REVERT: J 314 ARG cc_start: 0.8433 (ptp-170) cc_final: 0.7390 (ptm-80) REVERT: J 322 ARG cc_start: 0.8176 (mtp85) cc_final: 0.6901 (mtm-85) REVERT: J 340 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7895 (tp-100) REVERT: J 562 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6621 (tp30) REVERT: J 603 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7783 (mmpt) REVERT: J 664 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.6130 (mm) REVERT: J 802 ASP cc_start: 0.8211 (t0) cc_final: 0.7803 (m-30) REVERT: J 1152 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6775 (pm20) REVERT: J 1169 THR cc_start: 0.5314 (OUTLIER) cc_final: 0.4808 (p) REVERT: J 1177 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6460 (mp) REVERT: K 11 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7133 (mt-10) REVERT: K 12 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6899 (mptp) REVERT: K 55 GLU cc_start: 0.7659 (tt0) cc_final: 0.7445 (mt-10) REVERT: K 56 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: L 259 PHE cc_start: 0.6876 (m-10) cc_final: 0.6558 (m-80) REVERT: L 277 MET cc_start: 0.5632 (tpp) cc_final: 0.5391 (tpp) REVERT: L 322 MET cc_start: 0.2099 (ptt) cc_final: 0.1434 (ttp) REVERT: L 344 LEU cc_start: 0.3311 (pp) cc_final: 0.2725 (tt) REVERT: L 425 TYR cc_start: 0.8412 (m-80) cc_final: 0.8159 (m-80) REVERT: L 482 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7960 (mt-10) REVERT: L 524 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7947 (pp20) REVERT: L 561 MET cc_start: 0.6557 (mmt) cc_final: 0.5920 (ttm) REVERT: L 582 VAL cc_start: 0.4963 (t) cc_final: 0.4592 (m) REVERT: R 260 LEU cc_start: 0.4885 (mm) cc_final: 0.4647 (mm) REVERT: R 316 MET cc_start: 0.2459 (pp-130) cc_final: 0.0986 (pmm) REVERT: Z 20 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5869 (tp30) REVERT: Z 44 VAL cc_start: 0.5542 (OUTLIER) cc_final: 0.5280 (t) REVERT: Z 49 MET cc_start: 0.4558 (mmm) cc_final: 0.4231 (tmt) outliers start: 101 outliers final: 52 residues processed: 360 average time/residue: 0.8086 time to fit residues: 338.2879 Evaluate side-chains 338 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 266 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1008 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 37 TRP Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 280 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 351 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 251 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 83 GLN I 799 ASN I 955 GLN I1038 GLN J 430 HIS J 708 ASN J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105613 restraints weight = 40857.624| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.89 r_work: 0.3124 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 33273 Z= 0.113 Angle : 0.541 10.524 45449 Z= 0.285 Chirality : 0.041 0.217 5196 Planarity : 0.004 0.127 5512 Dihedral : 16.271 134.115 5694 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 2.48 % Allowed : 20.24 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.38 (0.14), residues: 3797 helix: 1.89 (0.13), residues: 1536 sheet: 0.38 (0.26), residues: 399 loop : -1.24 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 599 TYR 0.015 0.001 TYR G 177 PHE 0.013 0.001 PHE I 337 TRP 0.042 0.001 TRP J1193 HIS 0.005 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (33265) covalent geometry : angle 0.53772 / 0.28 (45437) hydrogen bonds : bond 0.04303 / 2.93 ( 1395) hydrogen bonds : angle 3.83799 / 2.66 ( 3919) metal coordination : bond 0.00766 / 0.40 ( 8) metal coordination : angle 3.78189 / 2.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6047 (p-80) REVERT: H 6 THR cc_start: 0.7311 (m) cc_final: 0.6994 (p) REVERT: H 12 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6220 (ptp-170) REVERT: H 30 PRO cc_start: 0.8295 (Cg_exo) cc_final: 0.8062 (Cg_endo) REVERT: H 51 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8348 (mmm) REVERT: H 76 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: H 104 LYS cc_start: 0.7429 (tptt) cc_final: 0.7188 (tttt) REVERT: H 120 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.5463 (p0) REVERT: H 143 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7293 (mtp180) REVERT: H 183 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8126 (mt) REVERT: H 218 ARG cc_start: 0.6953 (mtp-110) cc_final: 0.6677 (mtt180) REVERT: I 119 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7322 (mm-30) REVERT: I 334 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: I 392 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7556 (mp0) REVERT: I 545 PHE cc_start: 0.7316 (t80) cc_final: 0.6525 (m-80) REVERT: I 583 GLU cc_start: 0.8235 (tt0) cc_final: 0.8018 (tt0) REVERT: I 681 MET cc_start: 0.8931 (mtp) cc_final: 0.8698 (mtt) REVERT: I 742 TYR cc_start: 0.7387 (m-80) cc_final: 0.7174 (m-10) REVERT: I 867 GLU cc_start: 0.8262 (pp20) cc_final: 0.7913 (pm20) REVERT: I 958 LYS cc_start: 0.7852 (tttt) cc_final: 0.7524 (ttmm) REVERT: I 1008 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6110 (tp40) REVERT: I 1211 ARG cc_start: 0.8643 (ttm170) cc_final: 0.7910 (mmt180) REVERT: I 1321 GLU cc_start: 0.7447 (tp30) cc_final: 0.7186 (tp30) REVERT: J 60 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7784 (ttp80) REVERT: J 81 ARG cc_start: 0.8361 (tmm-80) cc_final: 0.7397 (ttt-90) REVERT: J 126 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8005 (tt) REVERT: J 227 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7666 (t80) REVERT: J 314 ARG cc_start: 0.8427 (ptp-170) cc_final: 0.7407 (ptm-80) REVERT: J 322 ARG cc_start: 0.8144 (mtp85) cc_final: 0.6871 (mtm-85) REVERT: J 340 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7889 (tp-100) REVERT: J 562 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6572 (tp30) REVERT: J 603 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7747 (mmpt) REVERT: J 664 ILE cc_start: 0.6403 (OUTLIER) cc_final: 0.6057 (mm) REVERT: J 802 ASP cc_start: 0.8205 (t0) cc_final: 0.7800 (m-30) REVERT: J 1152 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6747 (pm20) REVERT: J 1169 THR cc_start: 0.5371 (OUTLIER) cc_final: 0.4861 (p) REVERT: J 1177 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6473 (mp) REVERT: K 11 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7122 (mt-10) REVERT: K 55 GLU cc_start: 0.7625 (tt0) cc_final: 0.7418 (mt-10) REVERT: L 259 PHE cc_start: 0.6844 (m-10) cc_final: 0.6557 (m-80) REVERT: L 265 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6938 (mp10) REVERT: L 277 MET cc_start: 0.5585 (tpp) cc_final: 0.5323 (tpp) REVERT: L 284 GLU cc_start: 0.4092 (OUTLIER) cc_final: 0.3696 (pt0) REVERT: L 322 MET cc_start: 0.2204 (ptt) cc_final: 0.1478 (ttp) REVERT: L 344 LEU cc_start: 0.3258 (pp) cc_final: 0.2712 (tt) REVERT: L 425 TYR cc_start: 0.8460 (m-80) cc_final: 0.8211 (m-80) REVERT: L 482 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7985 (mt-10) REVERT: L 524 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7985 (pp20) REVERT: L 561 MET cc_start: 0.6448 (mmt) cc_final: 0.5766 (ttm) REVERT: L 582 VAL cc_start: 0.4929 (t) cc_final: 0.4578 (m) REVERT: L 608 ARG cc_start: 0.7142 (tpp80) cc_final: 0.6540 (mtt90) REVERT: R 316 MET cc_start: 0.2236 (pp-130) cc_final: 0.0816 (pmm) REVERT: Z 20 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5932 (tp30) REVERT: Z 44 VAL cc_start: 0.5533 (OUTLIER) cc_final: 0.5288 (t) REVERT: Z 49 MET cc_start: 0.4540 (mmm) cc_final: 0.4222 (tmt) outliers start: 81 outliers final: 46 residues processed: 346 average time/residue: 0.7387 time to fit residues: 298.5857 Evaluate side-chains 331 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1008 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 37 TRP Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 83 GLN I 955 GLN I1038 GLN I1312 ASN J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102234 restraints weight = 41040.817| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.89 r_work: 0.3039 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33273 Z= 0.198 Angle : 0.628 13.774 45449 Z= 0.326 Chirality : 0.045 0.274 5196 Planarity : 0.005 0.130 5512 Dihedral : 16.353 133.094 5694 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 2.63 % Allowed : 20.39 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % 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: 0.21 (0.14), residues: 3797 helix: 1.70 (0.13), residues: 1536 sheet: 0.40 (0.26), residues: 389 loop : -1.32 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 214 TYR 0.020 0.002 TYR I 47 PHE 0.018 0.002 PHE I 337 TRP 0.046 0.002 TRP J1193 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (33265) covalent geometry : angle 0.62308 / 0.33 (45437) hydrogen bonds : bond 0.05640 / 3.82 ( 1395) hydrogen bonds : angle 3.96976 / 2.76 ( 3919) metal coordination : bond 0.01057 / 0.56 ( 8) metal coordination : angle 4.69775 / 2.96 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 262 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.7120 (OUTLIER) cc_final: 0.6136 (p-80) REVERT: H 6 THR cc_start: 0.7306 (m) cc_final: 0.6968 (p) REVERT: H 12 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.6274 (ptp-170) REVERT: H 30 PRO cc_start: 0.8334 (Cg_exo) cc_final: 0.8059 (Cg_endo) REVERT: H 51 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: H 76 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: H 143 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7223 (mtp180) REVERT: H 218 ARG cc_start: 0.7027 (mtp-110) cc_final: 0.6741 (mtt180) REVERT: I 119 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7256 (mm-30) REVERT: I 334 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: I 392 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7582 (mp0) REVERT: I 542 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6509 (tpt170) REVERT: I 583 GLU cc_start: 0.8316 (tt0) cc_final: 0.8092 (tt0) REVERT: I 681 MET cc_start: 0.8971 (mtp) cc_final: 0.8710 (mtt) REVERT: I 958 LYS cc_start: 0.7890 (tttt) cc_final: 0.7540 (ttmm) REVERT: I 1008 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6149 (tp40) REVERT: I 1211 ARG cc_start: 0.8685 (ttm170) cc_final: 0.7949 (mmt180) REVERT: I 1321 GLU cc_start: 0.7549 (tp30) cc_final: 0.7273 (tp30) REVERT: J 81 ARG cc_start: 0.8348 (tmm-80) cc_final: 0.7383 (ttt-90) REVERT: J 126 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8033 (tt) REVERT: J 227 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7708 (t80) REVERT: J 314 ARG cc_start: 0.8455 (ptp-170) cc_final: 0.7389 (ptm-80) REVERT: J 322 ARG cc_start: 0.8173 (mtp85) cc_final: 0.6891 (mtm-85) REVERT: J 340 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7914 (tp-100) REVERT: J 562 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6615 (tp30) REVERT: J 664 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.6107 (mm) REVERT: J 736 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: J 802 ASP cc_start: 0.8260 (t0) cc_final: 0.7811 (m-30) REVERT: J 1040 MET cc_start: 0.2719 (ptp) cc_final: 0.1419 (mpt) REVERT: J 1152 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6768 (pm20) REVERT: J 1169 THR cc_start: 0.5345 (OUTLIER) cc_final: 0.4843 (p) REVERT: J 1177 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6487 (mp) REVERT: K 11 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7104 (mt-10) REVERT: K 12 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.6892 (mptp) REVERT: K 56 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: L 259 PHE cc_start: 0.6859 (m-10) cc_final: 0.6549 (m-80) REVERT: L 265 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6860 (mp10) REVERT: L 277 MET cc_start: 0.5720 (tpp) cc_final: 0.5482 (tpp) REVERT: L 322 MET cc_start: 0.2276 (ptt) cc_final: 0.1503 (ttp) REVERT: L 344 LEU cc_start: 0.3319 (pp) cc_final: 0.2734 (tt) REVERT: L 485 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: L 524 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8015 (pp20) REVERT: L 561 MET cc_start: 0.6544 (mmt) cc_final: 0.5897 (ttm) REVERT: L 582 VAL cc_start: 0.5027 (t) cc_final: 0.4651 (m) REVERT: R 316 MET cc_start: 0.2451 (pp-130) cc_final: 0.0964 (pmm) REVERT: Z 44 VAL cc_start: 0.5642 (OUTLIER) cc_final: 0.5375 (t) REVERT: Z 49 MET cc_start: 0.4662 (mmm) cc_final: 0.4364 (tmt) outliers start: 86 outliers final: 52 residues processed: 330 average time/residue: 0.7727 time to fit residues: 297.9001 Evaluate side-chains 324 residues out of total 3277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 254 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1008 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 736 GLN Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 169 optimal weight: 0.8980 chunk 327 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 276 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 83 GLN I1038 GLN J 158 GLN J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104073 restraints weight = 41036.985| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.88 r_work: 0.3097 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33273 Z= 0.131 Angle : 0.565 11.593 45449 Z= 0.296 Chirality : 0.042 0.218 5196 Planarity : 0.004 0.127 5512 Dihedral : 16.296 135.035 5694 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 2.42 % Allowed : 20.70 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % 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: 0.31 (0.14), residues: 3797 helix: 1.81 (0.13), residues: 1533 sheet: 0.36 (0.26), residues: 396 loop : -1.26 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 599 TYR 0.016 0.001 TYR G 177 PHE 0.015 0.001 PHE I 337 TRP 0.049 0.001 TRP J1193 HIS 0.004 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (33265) covalent geometry : angle 0.56098 / 0.30 (45437) hydrogen bonds : bond 0.04781 / 3.25 ( 1395) hydrogen bonds : angle 3.88882 / 2.70 ( 3919) metal coordination : bond 0.00773 / 0.41 ( 8) metal coordination : angle 4.06321 / 2.60 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17388.12 seconds wall clock time: 294 minutes 34.24 seconds (17674.24 seconds total)