Starting phenix.real_space_refine on Mon Aug 25 16:36:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8era_28551/08_2025/8era_28551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8era_28551/08_2025/8era_28551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8era_28551/08_2025/8era_28551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8era_28551/08_2025/8era_28551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8era_28551/08_2025/8era_28551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8era_28551/08_2025/8era_28551.map" } resolution = 2.86 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 189 5.16 5 C 18535 2.51 5 N 5065 2.21 5 O 5265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29054 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 17342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2177, 17342 Classifications: {'peptide': 2177} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 85, 'TRANS': 2091} Chain breaks: 19 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 5, 'PHE:plan': 2, 'ARG:plan': 4, 'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2395 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain breaks: 1 Chain: "Y" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'XZ9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'XYU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.52, per 1000 atoms: 0.26 Number of scatterers: 29054 At special positions: 0 Unit cell: (262.9, 148.5, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 189 16.00 O 5265 8.00 N 5065 7.00 C 18535 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: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 21 sheets defined 61.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.908A pdb=" N LEU A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.551A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 4.578A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.526A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.509A pdb=" N TRP A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.527A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.557A pdb=" N GLY A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.502A pdb=" N GLY A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 removed outlier: 4.551A pdb=" N GLY A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.477A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 361 through 376 removed outlier: 3.741A pdb=" N LEU A 365 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 403 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 412 through 425 removed outlier: 3.704A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 4.176A pdb=" N THR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.526A pdb=" N VAL A 455 " --> pdb=" O TYR A 451 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.758A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.802A pdb=" N LYS A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 516 through 528 Processing helix chain 'A' and resid 532 through 549 removed outlier: 4.028A pdb=" N HIS A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.603A pdb=" N ARG A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 removed outlier: 3.626A pdb=" N MET A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.692A pdb=" N CYS A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.624A pdb=" N LEU A 693 " --> pdb=" O GLN A 689 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 718 Processing helix chain 'A' and resid 722 through 743 removed outlier: 3.716A pdb=" N VAL A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.730A pdb=" N LEU A 767 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG A 769 " --> pdb=" O ARG A 766 " (cutoff:3.500A) Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.645A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 829 removed outlier: 3.555A pdb=" N LEU A 820 " --> pdb=" O TRP A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.711A pdb=" N ARG A 859 " --> pdb=" O VAL A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 871 removed outlier: 3.632A pdb=" N ASN A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 871 " --> pdb=" O VAL A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 877 through 892 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 942 through 959 Proline residue: A 948 - end of helix Processing helix chain 'A' and resid 963 through 983 removed outlier: 7.221A pdb=" N THR A 969 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N MET A 970 " --> pdb=" O HIS A 966 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 977 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 removed outlier: 3.528A pdb=" N GLN A 988 " --> pdb=" O LYS A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 989 through 1003 Proline residue: A 995 - end of helix removed outlier: 3.634A pdb=" N ASN A 999 " --> pdb=" O PRO A 995 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A1003 " --> pdb=" O ASN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1025 through 1029 removed outlier: 3.727A pdb=" N ARG A1028 " --> pdb=" O SER A1025 " (cutoff:3.500A) Proline residue: A1029 - end of helix No H-bonds generated for 'chain 'A' and resid 1025 through 1029' Processing helix chain 'A' and resid 1030 through 1041 Processing helix chain 'A' and resid 1045 through 1063 removed outlier: 3.751A pdb=" N GLN A1049 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A1050 " --> pdb=" O THR A1046 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1069 removed outlier: 3.837A pdb=" N PHE A1067 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A1068 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1084 removed outlier: 3.760A pdb=" N LEU A1074 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 3.684A pdb=" N ILE A1094 " --> pdb=" O ARG A1090 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1124 Proline residue: A1116 - end of helix removed outlier: 3.617A pdb=" N PHE A1122 " --> pdb=" O ILE A1118 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A1124 " --> pdb=" O LYS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1143 removed outlier: 3.570A pdb=" N ARG A1132 " --> pdb=" O PRO A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 Proline residue: A1158 - end of helix removed outlier: 3.809A pdb=" N ASP A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1183 removed outlier: 3.519A pdb=" N SER A1179 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1180 " --> pdb=" O THR A1176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1190 removed outlier: 3.704A pdb=" N LYS A1187 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1203 removed outlier: 3.806A pdb=" N VAL A1198 " --> pdb=" O MET A1194 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1219 Processing helix chain 'A' and resid 1262 through 1270 removed outlier: 3.511A pdb=" N GLN A1266 " --> pdb=" O THR A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1294 Processing helix chain 'A' and resid 1297 through 1302 removed outlier: 3.745A pdb=" N ARG A1301 " --> pdb=" O SER A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 4.023A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1329 removed outlier: 4.251A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1329 " --> pdb=" O CYS A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1348 removed outlier: 3.584A pdb=" N ASP A1335 " --> pdb=" O GLU A1331 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A1336 " --> pdb=" O ASP A1332 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A1348 " --> pdb=" O ALA A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1379 through 1391 removed outlier: 3.620A pdb=" N LYS A1389 " --> pdb=" O GLU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1407 Processing helix chain 'A' and resid 1409 through 1423 removed outlier: 3.653A pdb=" N LEU A1413 " --> pdb=" O THR A1409 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A1414 " --> pdb=" O PRO A1410 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A1415 " --> pdb=" O ALA A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.615A pdb=" N ALA A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 4.475A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1470 removed outlier: 3.517A pdb=" N THR A1469 " --> pdb=" O LYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1488 removed outlier: 3.659A pdb=" N LEU A1487 " --> pdb=" O CYS A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1500 Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 3.641A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1534 removed outlier: 3.701A pdb=" N MET A1529 " --> pdb=" O GLN A1525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A1530 " --> pdb=" O TRP A1526 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 Processing helix chain 'A' and resid 1556 through 1580 removed outlier: 4.594A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1585 No H-bonds generated for 'chain 'A' and resid 1583 through 1585' Processing helix chain 'A' and resid 1586 through 1603 removed outlier: 3.712A pdb=" N ILE A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1610 No H-bonds generated for 'chain 'A' and resid 1608 through 1610' Processing helix chain 'A' and resid 1611 through 1624 removed outlier: 3.667A pdb=" N ILE A1615 " --> pdb=" O ARG A1611 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A1624 " --> pdb=" O TRP A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1641 removed outlier: 3.762A pdb=" N TRP A1633 " --> pdb=" O ILE A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1663 removed outlier: 4.232A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A1663 " --> pdb=" O LEU A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 removed outlier: 3.516A pdb=" N ALA A1669 " --> pdb=" O ARG A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1707 Processing helix chain 'A' and resid 1709 through 1731 Processing helix chain 'A' and resid 1736 through 1759 removed outlier: 3.568A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A1753 " --> pdb=" O ARG A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1783 removed outlier: 3.559A pdb=" N ASP A1783 " --> pdb=" O ALA A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1810 removed outlier: 3.925A pdb=" N TRP A1790 " --> pdb=" O TRP A1786 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A1801 " --> pdb=" O ASN A1797 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1802 " --> pdb=" O PHE A1798 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A1805 " --> pdb=" O VAL A1801 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS A1806 " --> pdb=" O LEU A1802 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A1808 " --> pdb=" O TYR A1804 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1878 Processing helix chain 'A' and resid 1880 through 1894 Processing helix chain 'A' and resid 1899 through 1914 removed outlier: 3.541A pdb=" N ASP A1912 " --> pdb=" O THR A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1916 through 1930 removed outlier: 3.747A pdb=" N LYS A1928 " --> pdb=" O VAL A1924 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A1929 " --> pdb=" O GLU A1925 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1936 removed outlier: 3.625A pdb=" N TRP A1935 " --> pdb=" O ILE A1932 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A1936 " --> pdb=" O ASP A1933 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1932 through 1936' Processing helix chain 'A' and resid 1938 through 1944 removed outlier: 3.936A pdb=" N ALA A1944 " --> pdb=" O PRO A1940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1967 removed outlier: 4.150A pdb=" N GLY A1954 " --> pdb=" O ARG A1950 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG A1955 " --> pdb=" O PRO A1951 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A1967 " --> pdb=" O ASP A1963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1981 removed outlier: 3.655A pdb=" N LYS A1981 " --> pdb=" O THR A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 2000 removed outlier: 3.782A pdb=" N HIS A1988 " --> pdb=" O THR A1984 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2020 removed outlier: 3.697A pdb=" N ARG A2018 " --> pdb=" O GLU A2014 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A2020 " --> pdb=" O LEU A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2042 removed outlier: 4.181A pdb=" N GLU A2032 " --> pdb=" O HIS A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2060 Proline residue: A2053 - end of helix removed outlier: 3.644A pdb=" N MET A2058 " --> pdb=" O LEU A2054 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A2059 " --> pdb=" O HIS A2055 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A2060 " --> pdb=" O ALA A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2064 through 2092 removed outlier: 3.549A pdb=" N ASN A2071 " --> pdb=" O GLU A2067 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG A2076 " --> pdb=" O GLN A2072 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2115 removed outlier: 4.011A pdb=" N LEU A2097 " --> pdb=" O ASN A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2127 through 2133 removed outlier: 3.531A pdb=" N LEU A2131 " --> pdb=" O SER A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2193 through 2211 Processing helix chain 'A' and resid 2212 through 2217 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2279 through 2293 removed outlier: 3.562A pdb=" N GLU A2285 " --> pdb=" O MET A2281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A2286 " --> pdb=" O GLN A2282 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2306 Processing helix chain 'A' and resid 2310 through 2335 removed outlier: 3.939A pdb=" N PHE A2314 " --> pdb=" O SER A2310 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP A2315 " --> pdb=" O GLU A2311 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A2333 " --> pdb=" O MET A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2342 No H-bonds generated for 'chain 'A' and resid 2340 through 2342' Processing helix chain 'A' and resid 2380 through 2386 removed outlier: 3.529A pdb=" N ALA A2386 " --> pdb=" O MET A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 removed outlier: 3.676A pdb=" N ILE A2398 " --> pdb=" O GLY A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.813A pdb=" N VAL A2414 " --> pdb=" O HIS A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2433 removed outlier: 3.771A pdb=" N MET A2432 " --> pdb=" O ASN A2428 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A2433 " --> pdb=" O TRP A2429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2428 through 2433' Processing helix chain 'A' and resid 2493 through 2510 Processing helix chain 'A' and resid 2520 through 2533 removed outlier: 3.559A pdb=" N GLU A2526 " --> pdb=" O PRO A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2534 through 2540 removed outlier: 3.953A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2541 through 2546 removed outlier: 5.865A pdb=" N GLY A2544 " --> pdb=" O CYS A2541 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'Y' and resid 19 through 26 Processing helix chain 'Y' and resid 32 through 37 Processing helix chain 'Y' and resid 89 through 93 removed outlier: 3.558A pdb=" N SER Y 92 " --> pdb=" O ASP Y 89 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET Y 93 " --> pdb=" O PRO Y 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 89 through 93' Processing helix chain 'Y' and resid 94 through 112 Processing helix chain 'Y' and resid 126 through 142 Processing helix chain 'Y' and resid 179 through 186 Processing helix chain 'Y' and resid 199 through 216 removed outlier: 3.602A pdb=" N VAL Y 203 " --> pdb=" O ALA Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 238 No H-bonds generated for 'chain 'Y' and resid 236 through 238' Processing helix chain 'Y' and resid 261 through 269 Processing helix chain 'Y' and resid 269 through 279 removed outlier: 3.682A pdb=" N ILE Y 273 " --> pdb=" O THR Y 269 " (cutoff:3.500A) Processing helix chain 'Y' and resid 280 through 287 removed outlier: 6.645A pdb=" N CYS Y 283 " --> pdb=" O MET Y 280 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Y 284 " --> pdb=" O GLN Y 281 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER Y 285 " --> pdb=" O LYS Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 297 removed outlier: 3.632A pdb=" N LYS Y 297 " --> pdb=" O ASP Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 328 removed outlier: 3.575A pdb=" N GLU Y 311 " --> pdb=" O THR Y 307 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU Y 312 " --> pdb=" O PRO Y 308 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN Y 313 " --> pdb=" O LEU Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 329 through 338 removed outlier: 3.676A pdb=" N ARG Y 338 " --> pdb=" O GLN Y 334 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 359 removed outlier: 3.623A pdb=" N LEU Y 351 " --> pdb=" O PHE Y 347 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU Y 352 " --> pdb=" O ARG Y 348 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER Y 359 " --> pdb=" O ARG Y 355 " (cutoff:3.500A) Processing helix chain 'Y' and resid 377 through 390 removed outlier: 3.814A pdb=" N ALA Y 381 " --> pdb=" O ALA Y 377 " (cutoff:3.500A) Processing helix chain 'Y' and resid 392 through 399 Processing helix chain 'Y' and resid 407 through 423 removed outlier: 3.545A pdb=" N LEU Y 420 " --> pdb=" O PHE Y 416 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR Y 421 " --> pdb=" O GLN Y 417 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET Y 422 " --> pdb=" O VAL Y 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 438 Processing helix chain 'Y' and resid 445 through 458 removed outlier: 3.619A pdb=" N ASP Y 458 " --> pdb=" O GLY Y 454 " (cutoff:3.500A) Processing helix chain 'Y' and resid 460 through 470 Processing helix chain 'Y' and resid 472 through 480 removed outlier: 3.552A pdb=" N VAL Y 476 " --> pdb=" O ILE Y 472 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Y 479 " --> pdb=" O TYR Y 475 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU Y 480 " --> pdb=" O VAL Y 476 " (cutoff:3.500A) Processing helix chain 'Y' and resid 487 through 502 removed outlier: 3.904A pdb=" N VAL Y 501 " --> pdb=" O LYS Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 512 removed outlier: 3.831A pdb=" N ASP Y 512 " --> pdb=" O ASP Y 508 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 523 removed outlier: 3.868A pdb=" N PHE Y 518 " --> pdb=" O GLY Y 514 " (cutoff:3.500A) Processing helix chain 'Y' and resid 528 through 544 Processing helix chain 'Y' and resid 546 through 556 Processing helix chain 'Y' and resid 557 through 565 removed outlier: 4.113A pdb=" N ILE Y 561 " --> pdb=" O ASN Y 557 " (cutoff:3.500A) Processing helix chain 'Y' and resid 570 through 585 removed outlier: 3.985A pdb=" N TRP Y 585 " --> pdb=" O LEU Y 581 " (cutoff:3.500A) Processing helix chain 'Y' and resid 588 through 598 removed outlier: 3.588A pdb=" N ARG Y 592 " --> pdb=" O PHE Y 588 " (cutoff:3.500A) Processing helix chain 'Y' and resid 600 through 605 Processing helix chain 'Y' and resid 606 through 610 Processing helix chain 'Y' and resid 612 through 629 removed outlier: 3.529A pdb=" N ARG Y 616 " --> pdb=" O ILE Y 612 " (cutoff:3.500A) Processing helix chain 'Y' and resid 634 through 645 Processing helix chain 'Y' and resid 646 through 654 removed outlier: 4.044A pdb=" N ALA Y 649 " --> pdb=" O MET Y 646 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL Y 652 " --> pdb=" O ALA Y 649 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER Y 653 " --> pdb=" O GLN Y 650 " (cutoff:3.500A) Processing helix chain 'Y' and resid 656 through 672 Processing helix chain 'Y' and resid 674 through 686 removed outlier: 4.027A pdb=" N PHE Y 678 " --> pdb=" O TYR Y 674 " (cutoff:3.500A) Processing helix chain 'Y' and resid 807 through 820 Processing helix chain 'Y' and resid 823 through 839 removed outlier: 3.788A pdb=" N ASN Y 835 " --> pdb=" O MET Y 831 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER Y 836 " --> pdb=" O LYS Y 832 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE Y 837 " --> pdb=" O VAL Y 833 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Y 839 " --> pdb=" O ASN Y 835 " (cutoff:3.500A) Processing helix chain 'Y' and resid 958 through 965 Processing helix chain 'Y' and resid 966 through 969 Processing helix chain 'Y' and resid 975 through 979 Processing helix chain 'Y' and resid 982 through 1008 removed outlier: 3.717A pdb=" N ALA Y1002 " --> pdb=" O VAL Y 998 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN Y1003 " --> pdb=" O ARG Y 999 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN Y1004 " --> pdb=" O ARG Y1000 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS Y1008 " --> pdb=" O GLN Y1004 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 7.332A pdb=" N SER A2159 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR A2173 " --> pdb=" O SER A2159 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N THR A2173 " --> pdb=" O ILE A2156 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE A2156 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 7.332A pdb=" N SER A2159 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR A2173 " --> pdb=" O SER A2159 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.615A pdb=" N VAL B 5 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR B 76 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR B 7 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS B 74 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 24 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU B 107 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR B 22 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 31 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS B 36 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.615A pdb=" N VAL B 5 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR B 76 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR B 7 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS B 74 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 24 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU B 107 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR B 22 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 34 through 39 removed outlier: 4.341A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 25 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 47 through 50 removed outlier: 8.700A pdb=" N GLN C 63 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY C 83 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.803A pdb=" N ARG C 123 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 removed outlier: 3.782A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 173 through 178 removed outlier: 6.945A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE C 178 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR C 184 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 214 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 226 through 228 removed outlier: 6.106A pdb=" N CYS C 244 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU C 257 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 246 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 277 through 278 removed outlier: 6.438A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 118 through 123 removed outlier: 6.554A pdb=" N ARG Y 145 " --> pdb=" O THR Y 57 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER Y 59 " --> pdb=" O ARG Y 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 163 through 167 Processing sheet with id=AB6, first strand: chain 'Y' and resid 1015 through 1021 removed outlier: 5.764A pdb=" N GLN Y1016 " --> pdb=" O SER Y1329 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER Y1329 " --> pdb=" O GLN Y1016 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR Y1324 " --> pdb=" O SER Y1320 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 1028 through 1031 removed outlier: 6.896A pdb=" N ILE Y1046 " --> pdb=" O TYR Y1059 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR Y1059 " --> pdb=" O ILE Y1046 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE Y1048 " --> pdb=" O LEU Y1057 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 1070 through 1076 removed outlier: 3.810A pdb=" N ALA Y1072 " --> pdb=" O ALA Y1087 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE Y1093 " --> pdb=" O ALA Y1111 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA Y1111 " --> pdb=" O ILE Y1093 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL Y1095 " --> pdb=" O VAL Y1109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 1127 through 1132 removed outlier: 4.550A pdb=" N GLY Y1142 " --> pdb=" O ILE Y1146 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE Y1146 " --> pdb=" O GLY Y1142 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN Y1159 " --> pdb=" O ILE Y1149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 1169 through 1174 removed outlier: 6.867A pdb=" N GLY Y1184 " --> pdb=" O THR Y1170 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU Y1172 " --> pdb=" O VAL Y1182 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL Y1182 " --> pdb=" O LEU Y1172 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N CYS Y1174 " --> pdb=" O LEU Y1180 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU Y1180 " --> pdb=" O CYS Y1174 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE Y1190 " --> pdb=" O THR Y1206 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR Y1206 " --> pdb=" O ILE Y1190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL Y1192 " --> pdb=" O VAL Y1204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 1214 through 1220 removed outlier: 4.103A pdb=" N HIS Y1226 " --> pdb=" O GLN Y1220 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL Y1236 " --> pdb=" O VAL Y1249 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL Y1249 " --> pdb=" O VAL Y1236 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE Y1238 " --> pdb=" O VAL Y1247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 1259 through 1261 1574 hydrogen bonds defined for protein. 4593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.52 Time building geometry restraints manager: 3.92 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: 4788 1.32 - 1.44: 7754 1.44 - 1.57: 16830 1.57 - 1.69: 2 1.69 - 1.82: 305 Bond restraints: 29679 Sorted by residual: bond pdb=" N MET Y1205 " pdb=" CA MET Y1205 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.20e-02 6.94e+03 1.74e+01 bond pdb=" C ILE A1939 " pdb=" O ILE A1939 " ideal model delta sigma weight residual 1.240 1.192 0.048 1.26e-02 6.30e+03 1.45e+01 bond pdb=" N VAL Y 439 " pdb=" CA VAL Y 439 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.04e-02 9.25e+03 1.34e+01 bond pdb=" C MET Y1205 " pdb=" O MET Y1205 " ideal model delta sigma weight residual 1.234 1.192 0.042 1.15e-02 7.56e+03 1.34e+01 bond pdb=" N VAL B 25 " pdb=" CA VAL B 25 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.13e+01 ... (remaining 29674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 39498 2.62 - 5.24: 726 5.24 - 7.86: 32 7.86 - 10.48: 4 10.48 - 13.10: 4 Bond angle restraints: 40264 Sorted by residual: angle pdb=" C GLN A 962 " pdb=" CA GLN A 962 " pdb=" CB GLN A 962 " ideal model delta sigma weight residual 117.23 105.45 11.78 1.36e+00 5.41e-01 7.50e+01 angle pdb=" N PRO C 75 " pdb=" CA PRO C 75 " pdb=" C PRO C 75 " ideal model delta sigma weight residual 111.38 124.48 -13.10 1.59e+00 3.96e-01 6.79e+01 angle pdb=" C VAL A2422 " pdb=" N TYR A2423 " pdb=" CA TYR A2423 " ideal model delta sigma weight residual 122.54 112.05 10.49 1.65e+00 3.67e-01 4.04e+01 angle pdb=" CA GLY A2188 " pdb=" C GLY A2188 " pdb=" O GLY A2188 " ideal model delta sigma weight residual 121.57 117.25 4.32 8.70e-01 1.32e+00 2.46e+01 angle pdb=" C PRO C 75 " pdb=" CA PRO C 75 " pdb=" CB PRO C 75 " ideal model delta sigma weight residual 110.98 104.49 6.49 1.31e+00 5.83e-01 2.46e+01 ... (remaining 40259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15894 17.98 - 35.95: 1557 35.95 - 53.93: 387 53.93 - 71.91: 112 71.91 - 89.88: 35 Dihedral angle restraints: 17985 sinusoidal: 7326 harmonic: 10659 Sorted by residual: dihedral pdb=" N PHE A2421 " pdb=" C PHE A2421 " pdb=" CA PHE A2421 " pdb=" CB PHE A2421 " ideal model delta harmonic sigma weight residual 122.80 112.61 10.19 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" CA ALA A1105 " pdb=" C ALA A1105 " pdb=" N ASN A1106 " pdb=" CA ASN A1106 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU A1556 " pdb=" C LEU A1556 " pdb=" N PHE A1557 " pdb=" CA PHE A1557 " ideal model delta harmonic sigma weight residual 180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 17982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3771 0.060 - 0.119: 627 0.119 - 0.179: 133 0.179 - 0.238: 33 0.238 - 0.298: 5 Chirality restraints: 4569 Sorted by residual: chirality pdb=" CA PRO C 75 " pdb=" N PRO C 75 " pdb=" C PRO C 75 " pdb=" CB PRO C 75 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA TRP A2101 " pdb=" N TRP A2101 " pdb=" C TRP A2101 " pdb=" CB TRP A2101 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PHE A2421 " pdb=" N PHE A2421 " pdb=" C PHE A2421 " pdb=" CB PHE A2421 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 4566 not shown) Planarity restraints: 5126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 XZ9 A2601 " 0.085 2.00e-02 2.50e+03 6.84e-02 7.02e+01 pdb=" C25 XZ9 A2601 " 0.084 2.00e-02 2.50e+03 pdb=" C3 XZ9 A2601 " -0.006 2.00e-02 2.50e+03 pdb=" C4 XZ9 A2601 " -0.080 2.00e-02 2.50e+03 pdb=" N1 XZ9 A2601 " 0.002 2.00e-02 2.50e+03 pdb=" O3 XZ9 A2601 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Y1205 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.69e+01 pdb=" C MET Y1205 " 0.090 2.00e-02 2.50e+03 pdb=" O MET Y1205 " -0.034 2.00e-02 2.50e+03 pdb=" N THR Y1206 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1964 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ILE A1964 " 0.078 2.00e-02 2.50e+03 pdb=" O ILE A1964 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY A1965 " -0.026 2.00e-02 2.50e+03 ... (remaining 5123 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2680 2.74 - 3.28: 28735 3.28 - 3.82: 44380 3.82 - 4.36: 52165 4.36 - 4.90: 91241 Nonbonded interactions: 219201 Sorted by model distance: nonbonded pdb=" O GLU Y1132 " pdb=" N GLY Y1136 " model vdw 2.202 3.120 nonbonded pdb=" O VAL A 272 " pdb=" OG SER A 275 " model vdw 2.224 3.040 nonbonded pdb=" OG SER C 229 " pdb=" OD1 ASP C 231 " model vdw 2.229 3.040 nonbonded pdb=" O MET A1018 " pdb=" OG SER A1021 " model vdw 2.250 3.040 nonbonded pdb=" O GLN Y 114 " pdb=" OH TYR Y 119 " model vdw 2.271 3.040 ... (remaining 219196 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 5.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 32.370 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.005 0.064 29679 Z= 0.329 Angle : 0.766 13.098 40264 Z= 0.488 Chirality : 0.050 0.298 4569 Planarity : 0.006 0.122 5126 Dihedral : 16.121 89.883 11041 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.34 % Rotamer: Outliers : 1.11 % Allowed : 15.57 % Favored : 83.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.09 (0.15), residues: 3586 helix: 1.20 (0.12), residues: 1961 sheet: -0.51 (0.25), residues: 389 loop : -1.61 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2042 TYR 0.034 0.001 TYR A2104 PHE 0.026 0.001 PHE A2070 TRP 0.025 0.001 TRP A2101 HIS 0.009 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00484 (29679) covalent geometry : angle 0.76579 (40264) hydrogen bonds : bond 0.17356 ( 1556) hydrogen bonds : angle 6.14327 ( 4593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TYR cc_start: 0.1571 (OUTLIER) cc_final: 0.0993 (p90) REVERT: A 417 MET cc_start: 0.3170 (tmm) cc_final: 0.2627 (ptp) REVERT: A 740 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8061 (mm-30) REVERT: A 1726 GLN cc_start: 0.8608 (mt0) cc_final: 0.8380 (tm130) REVERT: A 1799 GLU cc_start: 0.8389 (tp30) cc_final: 0.8149 (tp30) REVERT: A 2047 MET cc_start: 0.7976 (ttp) cc_final: 0.7231 (tmm) REVERT: A 2153 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 2154 GLN cc_start: 0.8370 (tt0) cc_final: 0.8036 (tm-30) REVERT: B 4 GLN cc_start: 0.8973 (mt0) cc_final: 0.8736 (pp30) REVERT: B 27 TYR cc_start: 0.8680 (p90) cc_final: 0.8120 (p90) REVERT: B 74 LYS cc_start: 0.8705 (tttt) cc_final: 0.8461 (pttm) REVERT: B 102 VAL cc_start: 0.8700 (p) cc_final: 0.8121 (m) REVERT: C 142 GLU cc_start: 0.6755 (mp0) cc_final: 0.6379 (mp0) REVERT: C 257 GLU cc_start: 0.8147 (tt0) cc_final: 0.7768 (tm-30) REVERT: C 305 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7439 (tmtt) REVERT: Y 667 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8547 (mp) outliers start: 35 outliers final: 8 residues processed: 355 average time/residue: 0.7108 time to fit residues: 290.6034 Evaluate side-chains 265 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 1939 ILE Chi-restraints excluded: chain A residue 1967 TYR Chi-restraints excluded: chain A residue 2153 ILE Chi-restraints excluded: chain A residue 2165 SER Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain Y residue 439 VAL Chi-restraints excluded: chain Y residue 527 MET Chi-restraints excluded: chain Y residue 667 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 530 GLN ** A 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 ASN A1330 ASN A1509 GLN A1541 HIS A1594 HIS A1992 ASN A2189 HIS A2194 GLN C 73 ASN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS Y 67 ASN Y 198 ASN Y 506 GLN ** Y 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1022 ASN Y1262 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.174557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102392 restraints weight = 52508.992| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 4.44 r_work: 0.2942 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29679 Z= 0.169 Angle : 0.622 11.778 40264 Z= 0.325 Chirality : 0.043 0.335 4569 Planarity : 0.005 0.052 5126 Dihedral : 5.025 80.480 4088 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 2.55 % Allowed : 16.08 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.72 (0.14), residues: 3586 helix: 1.65 (0.12), residues: 2010 sheet: -0.11 (0.26), residues: 375 loop : -1.35 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 58 TYR 0.022 0.001 TYR A2105 PHE 0.026 0.001 PHE A 610 TRP 0.028 0.001 TRP A2101 HIS 0.016 0.001 HIS Y 669 Details of bonding type rmsd covalent geometry : bond 0.00392 (29679) covalent geometry : angle 0.62153 (40264) hydrogen bonds : bond 0.06023 ( 1556) hydrogen bonds : angle 4.48513 ( 4593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 279 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TYR cc_start: 0.1628 (OUTLIER) cc_final: 0.1363 (p90) REVERT: A 694 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8791 (mt0) REVERT: A 740 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7792 (mm-30) REVERT: A 821 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: A 856 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8635 (mm-30) REVERT: A 937 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7727 (t0) REVERT: A 1446 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: A 1726 GLN cc_start: 0.8680 (mt0) cc_final: 0.8323 (tm130) REVERT: A 1879 MET cc_start: 0.8962 (ptt) cc_final: 0.8750 (ptt) REVERT: A 2047 MET cc_start: 0.7817 (ttp) cc_final: 0.7268 (tmm) REVERT: A 2048 PHE cc_start: 0.8728 (m-80) cc_final: 0.8381 (m-80) REVERT: A 2049 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8889 (pt0) REVERT: A 2153 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 2154 GLN cc_start: 0.8518 (tt0) cc_final: 0.8225 (tt0) REVERT: A 2271 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7573 (tmt) REVERT: A 2357 ASP cc_start: 0.9065 (t0) cc_final: 0.8835 (t0) REVERT: A 2415 MET cc_start: 0.8857 (mmm) cc_final: 0.8573 (mmm) REVERT: B 4 GLN cc_start: 0.8932 (mt0) cc_final: 0.8642 (pp30) REVERT: B 27 TYR cc_start: 0.8711 (p90) cc_final: 0.8356 (p90) REVERT: B 50 MET cc_start: 0.7980 (ttm) cc_final: 0.7677 (tpp) REVERT: B 71 GLN cc_start: 0.6871 (tt0) cc_final: 0.6411 (tm130) REVERT: B 102 VAL cc_start: 0.8013 (p) cc_final: 0.7786 (m) REVERT: C 49 GLU cc_start: 0.8633 (tp30) cc_final: 0.8239 (tp30) REVERT: C 191 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9067 (p) REVERT: C 257 GLU cc_start: 0.8618 (tt0) cc_final: 0.8057 (tm-30) REVERT: C 307 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6909 (tm-30) REVERT: Y 100 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8477 (mm-30) REVERT: Y 298 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8905 (mm) REVERT: Y 340 ASP cc_start: 0.8306 (t0) cc_final: 0.8079 (t0) REVERT: Y 667 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8611 (mp) REVERT: Y 971 VAL cc_start: 0.9067 (t) cc_final: 0.8805 (m) REVERT: Y 1205 MET cc_start: 0.1939 (tmm) cc_final: 0.0302 (mmp) outliers start: 80 outliers final: 12 residues processed: 333 average time/residue: 0.7547 time to fit residues: 293.3323 Evaluate side-chains 270 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1446 GLN Chi-restraints excluded: chain A residue 2153 ILE Chi-restraints excluded: chain A residue 2271 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain Y residue 298 ILE Chi-restraints excluded: chain Y residue 563 LEU Chi-restraints excluded: chain Y residue 667 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 348 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 337 optimal weight: 9.9990 chunk 276 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 349 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN ** A 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 GLN A2063 GLN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 587 ASN ** Y 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1262 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.173627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101871 restraints weight = 52341.750| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.69 r_work: 0.2917 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29679 Z= 0.166 Angle : 0.596 8.802 40264 Z= 0.311 Chirality : 0.043 0.281 4569 Planarity : 0.004 0.056 5126 Dihedral : 4.521 36.099 4074 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 2.68 % Allowed : 17.42 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.94 (0.14), residues: 3586 helix: 1.81 (0.12), residues: 2005 sheet: 0.10 (0.26), residues: 374 loop : -1.27 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2060 TYR 0.030 0.001 TYR A 451 PHE 0.024 0.001 PHE A 610 TRP 0.027 0.001 TRP B 60 HIS 0.014 0.001 HIS Y 669 Details of bonding type rmsd covalent geometry : bond 0.00391 (29679) covalent geometry : angle 0.59575 (40264) hydrogen bonds : bond 0.05652 ( 1556) hydrogen bonds : angle 4.21464 ( 4593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 268 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TYR cc_start: 0.1282 (OUTLIER) cc_final: 0.0952 (p90) REVERT: A 821 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: A 829 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: A 856 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8665 (mm-30) REVERT: A 968 HIS cc_start: 0.6884 (m-70) cc_final: 0.6552 (m-70) REVERT: A 1031 MET cc_start: 0.8823 (mmm) cc_final: 0.8582 (mmm) REVERT: A 1348 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: A 1434 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: A 1437 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (mtt) REVERT: A 1446 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: A 1726 GLN cc_start: 0.8773 (mt0) cc_final: 0.8423 (tm130) REVERT: A 2047 MET cc_start: 0.7683 (ttp) cc_final: 0.7428 (tmm) REVERT: A 2048 PHE cc_start: 0.9008 (m-80) cc_final: 0.8481 (m-80) REVERT: A 2049 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8901 (pt0) REVERT: A 2057 MET cc_start: 0.8720 (ttp) cc_final: 0.8448 (ttm) REVERT: A 2113 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8307 (mmtm) REVERT: A 2153 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8327 (mt) REVERT: A 2154 GLN cc_start: 0.8585 (tt0) cc_final: 0.8290 (tt0) REVERT: A 2271 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7613 (tmt) REVERT: A 2357 ASP cc_start: 0.9160 (t0) cc_final: 0.8851 (t0) REVERT: A 2428 ASN cc_start: 0.7697 (m-40) cc_final: 0.7434 (m-40) REVERT: A 2516 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8103 (p0) REVERT: B 27 TYR cc_start: 0.8708 (p90) cc_final: 0.8446 (p90) REVERT: B 58 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7507 (mmm160) REVERT: B 67 MET cc_start: 0.5661 (tpp) cc_final: 0.5330 (tpp) REVERT: B 71 GLN cc_start: 0.7004 (tt0) cc_final: 0.6364 (tm130) REVERT: C 49 GLU cc_start: 0.8728 (tp30) cc_final: 0.8267 (tp30) REVERT: C 213 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8119 (ttmt) REVERT: C 257 GLU cc_start: 0.8837 (tt0) cc_final: 0.8257 (tm-30) REVERT: C 305 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7629 (tmtp) REVERT: C 307 GLU cc_start: 0.7300 (tm-30) cc_final: 0.7021 (tm-30) REVERT: Y 298 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8879 (mm) REVERT: Y 340 ASP cc_start: 0.8330 (t0) cc_final: 0.8039 (t0) REVERT: Y 669 HIS cc_start: 0.7634 (m-70) cc_final: 0.7354 (m90) REVERT: Y 1076 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6722 (pp) REVERT: Y 1205 MET cc_start: 0.1904 (tmm) cc_final: 0.0282 (mmp) REVERT: Y 1243 MET cc_start: 0.5773 (ppp) cc_final: 0.5528 (ppp) REVERT: Y 1323 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5605 (m-80) outliers start: 84 outliers final: 26 residues processed: 333 average time/residue: 0.7272 time to fit residues: 284.7571 Evaluate side-chains 294 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1348 GLN Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1446 GLN Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2153 ILE Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2271 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2364 VAL Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2516 ASP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain Y residue 298 ILE Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 527 MET Chi-restraints excluded: chain Y residue 543 VAL Chi-restraints excluded: chain Y residue 1076 LEU Chi-restraints excluded: chain Y residue 1323 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 143 optimal weight: 0.6980 chunk 314 optimal weight: 7.9990 chunk 324 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 358 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1604 GLN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 555 GLN Y 587 ASN ** Y 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101299 restraints weight = 52129.418| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.51 r_work: 0.2950 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29679 Z= 0.125 Angle : 0.563 7.956 40264 Z= 0.291 Chirality : 0.041 0.291 4569 Planarity : 0.004 0.055 5126 Dihedral : 4.355 34.523 4072 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.52 % Allowed : 18.15 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.21 (0.14), residues: 3586 helix: 2.05 (0.12), residues: 1992 sheet: 0.25 (0.26), residues: 375 loop : -1.16 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2060 TYR 0.022 0.001 TYR A 451 PHE 0.023 0.001 PHE A 610 TRP 0.029 0.001 TRP B 60 HIS 0.011 0.001 HIS Y 669 Details of bonding type rmsd covalent geometry : bond 0.00281 (29679) covalent geometry : angle 0.56264 (40264) hydrogen bonds : bond 0.04602 ( 1556) hydrogen bonds : angle 3.96965 ( 4593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 282 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.4005 (pmt) cc_final: 0.3024 (tpt) REVERT: A 412 TYR cc_start: 0.1349 (OUTLIER) cc_final: 0.1022 (p90) REVERT: A 821 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8586 (m-80) REVERT: A 856 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8678 (mm-30) REVERT: A 968 HIS cc_start: 0.6905 (m-70) cc_final: 0.6682 (m-70) REVERT: A 1031 MET cc_start: 0.8808 (mmm) cc_final: 0.8569 (mmm) REVERT: A 1437 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8606 (mtt) REVERT: A 1446 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: A 1649 ASP cc_start: 0.8903 (t0) cc_final: 0.8586 (t70) REVERT: A 1686 ASP cc_start: 0.8991 (m-30) cc_final: 0.8716 (p0) REVERT: A 1726 GLN cc_start: 0.8786 (mt0) cc_final: 0.8446 (tm130) REVERT: A 2047 MET cc_start: 0.7663 (ttp) cc_final: 0.7340 (tmm) REVERT: A 2049 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8910 (pt0) REVERT: A 2057 MET cc_start: 0.8723 (ttp) cc_final: 0.8402 (ttm) REVERT: A 2113 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8295 (mmtm) REVERT: A 2153 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8288 (mt) REVERT: A 2154 GLN cc_start: 0.8536 (tt0) cc_final: 0.8217 (tt0) REVERT: A 2271 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7597 (tmt) REVERT: A 2357 ASP cc_start: 0.9040 (t0) cc_final: 0.8745 (t0) REVERT: A 2428 ASN cc_start: 0.7777 (m-40) cc_final: 0.7446 (m-40) REVERT: A 2511 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8220 (mtp-110) REVERT: A 2516 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8064 (p0) REVERT: B 4 GLN cc_start: 0.8310 (mp10) cc_final: 0.8109 (mp10) REVERT: B 27 TYR cc_start: 0.8682 (p90) cc_final: 0.8448 (p90) REVERT: B 62 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7826 (mm-30) REVERT: B 67 MET cc_start: 0.5798 (tpp) cc_final: 0.5538 (tpp) REVERT: B 71 GLN cc_start: 0.7192 (tt0) cc_final: 0.6640 (tm130) REVERT: C 49 GLU cc_start: 0.8770 (tp30) cc_final: 0.8277 (tp30) REVERT: C 257 GLU cc_start: 0.8874 (tt0) cc_final: 0.8287 (tm-30) REVERT: C 307 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6998 (tm-30) REVERT: Y 261 ASP cc_start: 0.8264 (t0) cc_final: 0.7770 (t0) REVERT: Y 298 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8892 (mm) REVERT: Y 340 ASP cc_start: 0.8213 (t0) cc_final: 0.7878 (t0) REVERT: Y 555 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: Y 669 HIS cc_start: 0.7515 (m-70) cc_final: 0.7224 (m90) REVERT: Y 1205 MET cc_start: 0.2134 (tmm) cc_final: 0.0653 (mmt) REVERT: Y 1323 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5747 (m-80) outliers start: 79 outliers final: 23 residues processed: 335 average time/residue: 0.6394 time to fit residues: 250.9837 Evaluate side-chains 295 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1446 GLN Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1948 THR Chi-restraints excluded: chain A residue 2153 ILE Chi-restraints excluded: chain A residue 2164 THR Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2271 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2364 VAL Chi-restraints excluded: chain A residue 2511 ARG Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2516 ASP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain Y residue 294 LEU Chi-restraints excluded: chain Y residue 298 ILE Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 436 VAL Chi-restraints excluded: chain Y residue 543 VAL Chi-restraints excluded: chain Y residue 555 GLN Chi-restraints excluded: chain Y residue 1135 THR Chi-restraints excluded: chain Y residue 1323 TYR Chi-restraints excluded: chain Y residue 1328 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 0.9990 chunk 24 optimal weight: 50.0000 chunk 192 optimal weight: 1.9990 chunk 348 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 221 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 277 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN ** A 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1594 HIS B 88 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 587 ASN ** Y 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1262 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.175165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103344 restraints weight = 52269.822| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.92 r_work: 0.2933 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29679 Z= 0.122 Angle : 0.559 9.998 40264 Z= 0.288 Chirality : 0.041 0.244 4569 Planarity : 0.004 0.055 5126 Dihedral : 4.262 32.468 4072 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 2.32 % Allowed : 18.95 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.30 (0.14), residues: 3586 helix: 2.12 (0.12), residues: 1992 sheet: 0.36 (0.26), residues: 373 loop : -1.15 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2060 TYR 0.020 0.001 TYR A 451 PHE 0.023 0.001 PHE A 610 TRP 0.028 0.001 TRP B 60 HIS 0.009 0.001 HIS Y 669 Details of bonding type rmsd covalent geometry : bond 0.00277 (29679) covalent geometry : angle 0.55897 (40264) hydrogen bonds : bond 0.04461 ( 1556) hydrogen bonds : angle 3.87053 ( 4593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.4135 (pmt) cc_final: 0.3179 (tpt) REVERT: A 440 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.4886 (mm) REVERT: A 819 GLU cc_start: 0.7862 (pm20) cc_final: 0.7635 (pm20) REVERT: A 821 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: A 856 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 968 HIS cc_start: 0.6966 (m-70) cc_final: 0.6614 (m-70) REVERT: A 1031 MET cc_start: 0.8813 (mmm) cc_final: 0.8610 (mmm) REVERT: A 1437 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8610 (mtt) REVERT: A 1446 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: A 1649 ASP cc_start: 0.8922 (t0) cc_final: 0.8565 (t70) REVERT: A 1686 ASP cc_start: 0.9034 (m-30) cc_final: 0.8762 (p0) REVERT: A 1726 GLN cc_start: 0.8792 (mt0) cc_final: 0.8443 (tm130) REVERT: A 2033 GLU cc_start: 0.9031 (tp30) cc_final: 0.8762 (tp30) REVERT: A 2047 MET cc_start: 0.7662 (ttp) cc_final: 0.7371 (tmm) REVERT: A 2057 MET cc_start: 0.8657 (ttp) cc_final: 0.8376 (ttm) REVERT: A 2084 TRP cc_start: 0.7369 (m100) cc_final: 0.6658 (t-100) REVERT: A 2124 GLN cc_start: 0.8819 (pp30) cc_final: 0.8470 (pp30) REVERT: A 2154 GLN cc_start: 0.8545 (tt0) cc_final: 0.8263 (tt0) REVERT: A 2271 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7597 (tmt) REVERT: A 2357 ASP cc_start: 0.9022 (t0) cc_final: 0.8749 (t0) REVERT: A 2369 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 2370 LYS cc_start: 0.8068 (mppt) cc_final: 0.7815 (mmtt) REVERT: A 2428 ASN cc_start: 0.7847 (m-40) cc_final: 0.7491 (m-40) REVERT: A 2511 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8248 (mtp-110) REVERT: A 2516 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8070 (p0) REVERT: B 4 GLN cc_start: 0.8295 (mp10) cc_final: 0.7740 (pp30) REVERT: B 27 TYR cc_start: 0.8695 (p90) cc_final: 0.8421 (p90) REVERT: B 50 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7536 (ttm) REVERT: B 53 LYS cc_start: 0.6493 (mmpt) cc_final: 0.6291 (mmmt) REVERT: B 62 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 67 MET cc_start: 0.5862 (tpp) cc_final: 0.5622 (tpp) REVERT: B 71 GLN cc_start: 0.7185 (tt0) cc_final: 0.6640 (tm130) REVERT: C 49 GLU cc_start: 0.8759 (tp30) cc_final: 0.8257 (tp30) REVERT: C 213 LYS cc_start: 0.8243 (ttmt) cc_final: 0.8040 (ttmt) REVERT: C 257 GLU cc_start: 0.8876 (tt0) cc_final: 0.8279 (tm-30) REVERT: C 307 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6990 (tm-30) REVERT: Y 261 ASP cc_start: 0.8278 (t0) cc_final: 0.7778 (t0) REVERT: Y 340 ASP cc_start: 0.8317 (t0) cc_final: 0.7919 (t0) REVERT: Y 669 HIS cc_start: 0.7538 (m-70) cc_final: 0.7210 (m90) REVERT: Y 1073 MET cc_start: 0.2789 (OUTLIER) cc_final: 0.2364 (tmm) REVERT: Y 1323 TYR cc_start: 0.6017 (OUTLIER) cc_final: 0.5595 (m-80) outliers start: 73 outliers final: 30 residues processed: 328 average time/residue: 0.6555 time to fit residues: 251.8915 Evaluate side-chains 306 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 605 HIS Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1446 GLN Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1948 THR Chi-restraints excluded: chain A residue 2164 THR Chi-restraints excluded: chain A residue 2215 SER Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2271 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2364 VAL Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2511 ARG Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2516 ASP Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 401 THR Chi-restraints excluded: chain Y residue 436 VAL Chi-restraints excluded: chain Y residue 470 VAL Chi-restraints excluded: chain Y residue 527 MET Chi-restraints excluded: chain Y residue 543 VAL Chi-restraints excluded: chain Y residue 554 LEU Chi-restraints excluded: chain Y residue 1073 MET Chi-restraints excluded: chain Y residue 1135 THR Chi-restraints excluded: chain Y residue 1323 TYR Chi-restraints excluded: chain Y residue 1328 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 355 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 339 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 327 optimal weight: 7.9990 chunk 335 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN ** A 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 GLN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 587 ASN Y1275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.174864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101055 restraints weight = 52112.103| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.64 r_work: 0.2924 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29679 Z= 0.140 Angle : 0.571 11.003 40264 Z= 0.293 Chirality : 0.041 0.271 4569 Planarity : 0.004 0.055 5126 Dihedral : 4.191 23.331 4068 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 2.58 % Allowed : 19.27 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.33 (0.14), residues: 3586 helix: 2.14 (0.12), residues: 1986 sheet: 0.34 (0.27), residues: 374 loop : -1.11 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2060 TYR 0.030 0.001 TYR A 451 PHE 0.022 0.001 PHE A 610 TRP 0.035 0.001 TRP B 60 HIS 0.008 0.001 HIS A1988 Details of bonding type rmsd covalent geometry : bond 0.00328 (29679) covalent geometry : angle 0.57062 (40264) hydrogen bonds : bond 0.04913 ( 1556) hydrogen bonds : angle 3.86395 ( 4593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 274 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.3275 (pmt) cc_final: 0.2365 (tpt) REVERT: A 440 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.4920 (mm) REVERT: A 821 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: A 856 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8730 (mm-30) REVERT: A 937 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7693 (t0) REVERT: A 968 HIS cc_start: 0.6960 (m-70) cc_final: 0.6739 (m-70) REVERT: A 1078 MET cc_start: 0.9229 (mtm) cc_final: 0.8438 (mtm) REVERT: A 1083 MET cc_start: 0.7624 (ttp) cc_final: 0.7238 (ttm) REVERT: A 1165 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: A 1348 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: A 1437 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8614 (mtt) REVERT: A 1649 ASP cc_start: 0.8942 (t0) cc_final: 0.8560 (t70) REVERT: A 1686 ASP cc_start: 0.9070 (m-30) cc_final: 0.8841 (p0) REVERT: A 1726 GLN cc_start: 0.8808 (mt0) cc_final: 0.8428 (tm130) REVERT: A 1879 MET cc_start: 0.9034 (ptt) cc_final: 0.8816 (ptt) REVERT: A 2047 MET cc_start: 0.7688 (ttp) cc_final: 0.7340 (tmm) REVERT: A 2057 MET cc_start: 0.8659 (ttp) cc_final: 0.8389 (ttm) REVERT: A 2084 TRP cc_start: 0.7183 (m100) cc_final: 0.6608 (t-100) REVERT: A 2113 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8261 (mmtm) REVERT: A 2154 GLN cc_start: 0.8543 (tt0) cc_final: 0.8261 (tt0) REVERT: A 2271 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7577 (tmt) REVERT: A 2357 ASP cc_start: 0.9029 (t0) cc_final: 0.8707 (t0) REVERT: A 2511 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8247 (mtp-110) REVERT: A 2516 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8082 (p0) REVERT: B 4 GLN cc_start: 0.8364 (mp10) cc_final: 0.7802 (pp30) REVERT: B 27 TYR cc_start: 0.8773 (p90) cc_final: 0.8526 (p90) REVERT: B 50 MET cc_start: 0.7719 (ttp) cc_final: 0.7463 (tmm) REVERT: B 67 MET cc_start: 0.5949 (tpp) cc_final: 0.5707 (tpp) REVERT: B 71 GLN cc_start: 0.7227 (tt0) cc_final: 0.6609 (tm130) REVERT: C 49 GLU cc_start: 0.8714 (tp30) cc_final: 0.8165 (tp30) REVERT: C 257 GLU cc_start: 0.8860 (tt0) cc_final: 0.8248 (tm-30) REVERT: C 307 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7077 (tm-30) REVERT: Y 163 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: Y 261 ASP cc_start: 0.8270 (t0) cc_final: 0.7753 (t0) REVERT: Y 340 ASP cc_start: 0.8356 (t0) cc_final: 0.8121 (m-30) REVERT: Y 669 HIS cc_start: 0.7647 (m-70) cc_final: 0.7298 (m90) REVERT: Y 1073 MET cc_start: 0.2864 (OUTLIER) cc_final: 0.2392 (tmm) REVERT: Y 1205 MET cc_start: 0.2512 (tmm) cc_final: 0.0728 (mmp) REVERT: Y 1323 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5470 (m-80) outliers start: 81 outliers final: 38 residues processed: 333 average time/residue: 0.5734 time to fit residues: 224.6512 Evaluate side-chains 315 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1165 GLN Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1348 GLN Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1881 THR Chi-restraints excluded: chain A residue 1948 THR Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2164 THR Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2215 SER Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2271 MET Chi-restraints excluded: chain A residue 2274 ASP Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2364 VAL Chi-restraints excluded: chain A residue 2388 GLU Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2511 ARG Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2516 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 401 THR Chi-restraints excluded: chain Y residue 436 VAL Chi-restraints excluded: chain Y residue 470 VAL Chi-restraints excluded: chain Y residue 543 VAL Chi-restraints excluded: chain Y residue 554 LEU Chi-restraints excluded: chain Y residue 1073 MET Chi-restraints excluded: chain Y residue 1135 THR Chi-restraints excluded: chain Y residue 1323 TYR Chi-restraints excluded: chain Y residue 1328 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.2555 > 50: distance: 4 - 9: 14.749 distance: 9 - 10: 40.022 distance: 10 - 11: 28.407 distance: 11 - 12: 18.480 distance: 11 - 13: 23.342 distance: 13 - 14: 21.982 distance: 14 - 15: 19.054 distance: 14 - 17: 12.882 distance: 15 - 16: 13.007 distance: 15 - 21: 13.698 distance: 17 - 18: 17.359 distance: 18 - 19: 18.442 distance: 18 - 20: 10.833 distance: 21 - 22: 14.965 distance: 22 - 23: 10.854 distance: 23 - 24: 13.083 distance: 23 - 25: 18.030 distance: 25 - 26: 14.662 distance: 26 - 27: 19.236 distance: 26 - 29: 4.635 distance: 27 - 28: 10.209 distance: 27 - 36: 3.524 distance: 29 - 30: 17.732 distance: 30 - 31: 12.168 distance: 32 - 33: 7.595 distance: 33 - 34: 4.058 distance: 36 - 37: 11.894 distance: 37 - 38: 29.459 distance: 37 - 40: 30.097 distance: 38 - 39: 26.609 distance: 38 - 43: 18.102 distance: 40 - 41: 28.667 distance: 40 - 42: 10.745 distance: 43 - 44: 9.494 distance: 44 - 45: 30.937 distance: 44 - 47: 10.338 distance: 45 - 46: 29.461 distance: 45 - 54: 26.095 distance: 47 - 48: 14.036 distance: 48 - 49: 38.457 distance: 48 - 50: 14.821 distance: 49 - 51: 7.167 distance: 50 - 52: 14.698 distance: 52 - 53: 20.048 distance: 54 - 55: 9.532 distance: 54 - 60: 17.630 distance: 55 - 56: 31.620 distance: 55 - 58: 15.175 distance: 56 - 57: 35.917 distance: 56 - 61: 15.724 distance: 58 - 59: 33.075 distance: 59 - 60: 23.310 distance: 61 - 62: 7.068 distance: 62 - 63: 7.179 distance: 62 - 65: 22.435 distance: 63 - 64: 4.575 distance: 63 - 70: 39.276 distance: 65 - 66: 12.023 distance: 66 - 67: 16.049 distance: 67 - 68: 31.299 distance: 68 - 69: 40.197 distance: 70 - 71: 5.333 distance: 71 - 72: 23.229 distance: 71 - 74: 15.126 distance: 72 - 73: 5.252 distance: 72 - 81: 19.940 distance: 74 - 75: 36.430 distance: 75 - 76: 13.510 distance: 76 - 77: 8.364 distance: 77 - 78: 23.461 distance: 78 - 79: 4.954 distance: 78 - 80: 14.927 distance: 82 - 83: 4.264 distance: 83 - 84: 4.393 distance: 83 - 85: 30.762