Starting phenix.real_space_refine on Fri May 23 13:03:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhz_36301/05_2025/8jhz_36301_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhz_36301/05_2025/8jhz_36301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jhz_36301/05_2025/8jhz_36301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhz_36301/05_2025/8jhz_36301.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhz_36301/05_2025/8jhz_36301_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhz_36301/05_2025/8jhz_36301_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1 5.49 5 S 64 5.16 5 C 15245 2.51 5 N 3887 2.21 5 O 4616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 345 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23814 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 21144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2615, 21144 Classifications: {'peptide': 2615} Link IDs: {'PTRANS': 66, 'TRANS': 2548} Chain: "B" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2669 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5709 SG CYS A 700 64.591 77.034 278.461 1.00 54.87 S Time building chain proxies: 16.69, per 1000 atoms: 0.70 Number of scatterers: 23814 At special positions: 0 Unit cell: (116.309, 209.791, 311.969, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 64 16.00 P 1 15.00 O 4616 8.00 N 3887 7.00 C 15245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" NE2 HIS A 759 " pdb="ZN ZN A3000 " - pdb=" ND1 HIS A 655 " pdb="ZN ZN A3000 " - pdb=" SG CYS A 700 " 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5552 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 56 sheets defined 27.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 20 through 35 Processing helix chain 'A' and resid 40 through 62 removed outlier: 3.817A pdb=" N LYS A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 87 removed outlier: 3.757A pdb=" N ILE A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.589A pdb=" N TRP A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 156 Processing helix chain 'A' and resid 166 through 194 removed outlier: 4.061A pdb=" N PHE A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 243 removed outlier: 3.746A pdb=" N ASN A 243 " --> pdb=" O ARG A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 307 through 324 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.603A pdb=" N SER A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.738A pdb=" N ASN A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) Proline residue: A 415 - end of helix removed outlier: 3.857A pdb=" N LEU A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.598A pdb=" N VAL A 455 " --> pdb=" O TYR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 4.375A pdb=" N SER A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 482 removed outlier: 3.928A pdb=" N TYR A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 511 through 519 Processing helix chain 'A' and resid 522 through 539 removed outlier: 3.861A pdb=" N LYS A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 589 through 603 removed outlier: 4.208A pdb=" N ASN A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.989A pdb=" N ALA A 618 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.529A pdb=" N LEU A 642 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 685 removed outlier: 3.664A pdb=" N ILE A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 712 through 729 removed outlier: 5.099A pdb=" N ASP A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 766 through 776 Processing helix chain 'A' and resid 795 through 812 Processing helix chain 'A' and resid 816 through 840 Processing helix chain 'A' and resid 848 through 878 removed outlier: 3.550A pdb=" N LEU A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 935 removed outlier: 3.632A pdb=" N ASN A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 973 removed outlier: 3.970A pdb=" N VAL A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.659A pdb=" N SER A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 988 " --> pdb=" O ARG A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1003 removed outlier: 3.723A pdb=" N THR A1002 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1043 through 1051 Processing helix chain 'A' and resid 1055 through 1066 Processing helix chain 'A' and resid 1074 through 1092 removed outlier: 3.550A pdb=" N GLU A1090 " --> pdb=" O GLY A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 removed outlier: 4.277A pdb=" N SER A1132 " --> pdb=" O HIS A1128 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS A1134 " --> pdb=" O SER A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1247 through 1260 Processing helix chain 'A' and resid 1306 through 1312 Processing helix chain 'A' and resid 1349 through 1353 removed outlier: 3.657A pdb=" N VAL A1353 " --> pdb=" O ILE A1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1349 through 1353' Processing helix chain 'A' and resid 1433 through 1440 Processing helix chain 'A' and resid 1440 through 1451 Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1578 through 1589 removed outlier: 3.881A pdb=" N ILE A1582 " --> pdb=" O THR A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1595 Processing helix chain 'A' and resid 1648 through 1650 No H-bonds generated for 'chain 'A' and resid 1648 through 1650' Processing helix chain 'A' and resid 1733 through 1735 No H-bonds generated for 'chain 'A' and resid 1733 through 1735' Processing helix chain 'A' and resid 1771 through 1777 Processing helix chain 'A' and resid 1790 through 1797 Processing helix chain 'A' and resid 1804 through 1808 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.589A pdb=" N GLY B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.616A pdb=" N LYS B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 225' Processing helix chain 'B' and resid 294 through 299 removed outlier: 4.013A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 477 through 492 removed outlier: 4.795A pdb=" N ASP B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TRP B 483 " --> pdb=" O VAL B 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 238 removed outlier: 7.242A pdb=" N VAL A 237 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL A 128 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 97 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TRP A 129 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A 99 " --> pdb=" O TRP A 129 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL A 100 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLN A 384 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N LYS A 373 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.754A pdb=" N LEU A 289 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 630 through 633 removed outlier: 4.956A pdb=" N LEU A 623 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N SER A 607 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL A 608 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS A 581 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 610 " --> pdb=" O HIS A 581 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 583 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 648 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN A 696 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 650 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 698 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 652 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE A 737 " --> pdb=" O PHE A 782 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE A 782 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 746 through 748 removed outlier: 4.042A pdb=" N LEU A 764 " --> pdb=" O LEU A 756 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 894 removed outlier: 4.871A pdb=" N ARG A 901 " --> pdb=" O SER A 887 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N GLU A 889 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N THR A 899 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ILE A 891 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N THR A 897 " --> pdb=" O ILE A 891 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 938 through 939 removed outlier: 3.937A pdb=" N ILE A 947 " --> pdb=" O ILE A 939 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1037 through 1038 Processing sheet with id=AA9, first strand: chain 'A' and resid 1138 through 1141 Processing sheet with id=AB1, first strand: chain 'A' and resid 1163 through 1166 removed outlier: 6.913A pdb=" N SER A1163 " --> pdb=" O ILE A1157 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE A1157 " --> pdb=" O SER A1163 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS A1165 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A1155 " --> pdb=" O LYS A1289 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS A1291 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A1157 " --> pdb=" O LYS A1291 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER A1334 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A1335 " --> pdb=" O ILE A1389 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1181 through 1183 removed outlier: 6.500A pdb=" N ASP A1187 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A1235 " --> pdb=" O THR A1277 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A1279 " --> pdb=" O TRP A1233 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP A1233 " --> pdb=" O LEU A1279 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A1231 " --> pdb=" O PRO A1281 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP A1170 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TRP A1234 " --> pdb=" O ASP A1170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1174 through 1175 Processing sheet with id=AB4, first strand: chain 'A' and resid 1221 through 1223 removed outlier: 6.550A pdb=" N ARG A1297 " --> pdb=" O SER A1325 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU A1327 " --> pdb=" O ARG A1297 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A1299 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP A1345 " --> pdb=" O TYR A1402 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N TYR A1426 " --> pdb=" O ASN A1457 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N SER A1459 " --> pdb=" O TYR A1426 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A1428 " --> pdb=" O SER A1459 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN A1461 " --> pdb=" O LEU A1428 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A1430 " --> pdb=" O ASN A1461 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR A1463 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS A1469 " --> pdb=" O LYS A1486 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A1486 " --> pdb=" O LYS A1469 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A1480 " --> pdb=" O SER A1475 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A1493 " --> pdb=" O SER A1505 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A1503 " --> pdb=" O LEU A1495 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN A1497 " --> pdb=" O LEU A1501 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1501 " --> pdb=" O ASN A1497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1354 through 1359 removed outlier: 4.652A pdb=" N GLU A1355 " --> pdb=" O GLY A1366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1511 through 1517 removed outlier: 5.674A pdb=" N ASP A1512 " --> pdb=" O LYS A1527 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS A1527 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN A1522 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A1544 " --> pdb=" O ASN A1522 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A1543 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A1552 " --> pdb=" O SER A1543 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A1545 " --> pdb=" O VAL A1550 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL A1550 " --> pdb=" O ILE A1545 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N LYS A1549 " --> pdb=" O VAL A1603 " (cutoff:3.500A) removed outlier: 11.498A pdb=" N ASP A1605 " --> pdb=" O LYS A1549 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N LYS A1551 " --> pdb=" O ASP A1605 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N TYR A1607 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASN A1553 " --> pdb=" O TYR A1607 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1609 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE A1608 " --> pdb=" O CYS A1623 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A1618 " --> pdb=" O GLY A1634 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY A1634 " --> pdb=" O TYR A1618 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A1620 " --> pdb=" O TYR A1632 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A1653 " --> pdb=" O LEU A1689 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A1688 " --> pdb=" O ILE A1715 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A1714 " --> pdb=" O ARG A1764 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1671 through 1674 removed outlier: 6.470A pdb=" N VAL A1699 " --> pdb=" O ASN A1729 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL A1726 " --> pdb=" O MET A1779 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP A1781 " --> pdb=" O VAL A1726 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A1728 " --> pdb=" O ASP A1781 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1813 through 1816 removed outlier: 3.672A pdb=" N LYS A1819 " --> pdb=" O ILE A1816 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1832 through 1836 removed outlier: 3.836A pdb=" N PHE A1843 " --> pdb=" O GLY A1832 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1853 through 1857 Processing sheet with id=AC2, first strand: chain 'A' and resid 1874 through 1878 Processing sheet with id=AC3, first strand: chain 'A' and resid 1894 through 1898 removed outlier: 3.965A pdb=" N GLN A1918 " --> pdb=" O ALA A1906 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1925 through 1929 removed outlier: 3.755A pdb=" N LYS A1925 " --> pdb=" O PHE A1936 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A1936 " --> pdb=" O LYS A1925 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1945 through 1949 Processing sheet with id=AC6, first strand: chain 'A' and resid 1966 through 1970 Processing sheet with id=AC7, first strand: chain 'A' and resid 1987 through 1991 Processing sheet with id=AC8, first strand: chain 'A' and resid 2008 through 2012 Processing sheet with id=AC9, first strand: chain 'A' and resid 2028 through 2032 removed outlier: 3.875A pdb=" N GLN A2052 " --> pdb=" O ALA A2040 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2059 through 2062 Processing sheet with id=AD2, first strand: chain 'A' and resid 2079 through 2083 Processing sheet with id=AD3, first strand: chain 'A' and resid 2100 through 2104 removed outlier: 3.592A pdb=" N PHE A2111 " --> pdb=" O GLY A2100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 2121 through 2125 Processing sheet with id=AD5, first strand: chain 'A' and resid 2142 through 2146 removed outlier: 3.630A pdb=" N PHE A2151 " --> pdb=" O THR A2144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2162 through 2166 removed outlier: 3.529A pdb=" N GLN A2186 " --> pdb=" O ALA A2174 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2193 through 2197 Processing sheet with id=AD8, first strand: chain 'A' and resid 2213 through 2217 Processing sheet with id=AD9, first strand: chain 'A' and resid 2235 through 2238 Processing sheet with id=AE1, first strand: chain 'A' and resid 2254 through 2258 Processing sheet with id=AE2, first strand: chain 'A' and resid 2276 through 2280 Processing sheet with id=AE3, first strand: chain 'A' and resid 2308 through 2311 Processing sheet with id=AE4, first strand: chain 'A' and resid 2327 through 2331 Processing sheet with id=AE5, first strand: chain 'A' and resid 2348 through 2352 Processing sheet with id=AE6, first strand: chain 'A' and resid 2369 through 2373 Processing sheet with id=AE7, first strand: chain 'A' and resid 2390 through 2394 Processing sheet with id=AE8, first strand: chain 'A' and resid 2411 through 2415 Processing sheet with id=AE9, first strand: chain 'A' and resid 2431 through 2435 Processing sheet with id=AF1, first strand: chain 'A' and resid 2462 through 2466 removed outlier: 3.641A pdb=" N LYS A2462 " --> pdb=" O PHE A2473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 2484 through 2486 Processing sheet with id=AF3, first strand: chain 'A' and resid 2502 through 2507 removed outlier: 3.504A pdb=" N LYS A2505 " --> pdb=" O PHE A2512 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A2512 " --> pdb=" O LYS A2505 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 2522 through 2523 Processing sheet with id=AF5, first strand: chain 'A' and resid 2553 through 2557 removed outlier: 3.854A pdb=" N LYS A2553 " --> pdb=" O PHE A2564 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A2564 " --> pdb=" O LYS A2553 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 2573 through 2577 Processing sheet with id=AF7, first strand: chain 'A' and resid 2595 through 2597 removed outlier: 3.689A pdb=" N PHE A2606 " --> pdb=" O GLY A2595 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A2605 " --> pdb=" O GLN A2613 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AF9, first strand: chain 'B' and resid 196 through 201 Processing sheet with id=AG1, first strand: chain 'B' and resid 279 through 282 removed outlier: 3.672A pdb=" N CYS B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 379 through 383 removed outlier: 3.526A pdb=" N GLY B 383 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN B 398 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 473 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2538 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: 17.27 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 73 1.20 - 1.35: 7624 1.35 - 1.51: 8091 1.51 - 1.66: 8456 1.66 - 1.81: 107 Bond restraints: 24351 Sorted by residual: bond pdb=" C SER A1833 " pdb=" O SER A1833 " ideal model delta sigma weight residual 1.234 1.045 0.189 1.27e-02 6.20e+03 2.22e+02 bond pdb=" C PHE A1471 " pdb=" O PHE A1471 " ideal model delta sigma weight residual 1.234 1.057 0.177 1.26e-02 6.30e+03 1.97e+02 bond pdb=" C TYR A1710 " pdb=" O TYR A1710 " ideal model delta sigma weight residual 1.236 1.075 0.161 1.20e-02 6.94e+03 1.79e+02 bond pdb=" C ASN B 304 " pdb=" O ASN B 304 " ideal model delta sigma weight residual 1.235 1.044 0.191 1.45e-02 4.76e+03 1.73e+02 bond pdb=" C PHE A 408 " pdb=" O PHE A 408 " ideal model delta sigma weight residual 1.236 1.082 0.154 1.26e-02 6.30e+03 1.49e+02 ... (remaining 24346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.70: 32836 5.70 - 11.40: 133 11.40 - 17.10: 24 17.10 - 22.80: 5 22.80 - 28.50: 1 Bond angle restraints: 32999 Sorted by residual: angle pdb=" C PHE A 408 " pdb=" CA PHE A 408 " pdb=" CB PHE A 408 " ideal model delta sigma weight residual 110.67 82.17 28.50 1.92e+00 2.71e-01 2.20e+02 angle pdb=" C PHE A1711 " pdb=" N PRO A1712 " pdb=" CA PRO A1712 " ideal model delta sigma weight residual 119.78 134.57 -14.79 1.03e+00 9.43e-01 2.06e+02 angle pdb=" N TYR B 414 " pdb=" CA TYR B 414 " pdb=" C TYR B 414 " ideal model delta sigma weight residual 114.16 93.44 20.72 1.48e+00 4.57e-01 1.96e+02 angle pdb=" CA THR A 960 " pdb=" CB THR A 960 " pdb=" OG1 THR A 960 " ideal model delta sigma weight residual 109.60 90.19 19.41 1.50e+00 4.44e-01 1.67e+02 angle pdb=" C ASN A 959 " pdb=" CA ASN A 959 " pdb=" CB ASN A 959 " ideal model delta sigma weight residual 110.79 89.80 20.99 1.66e+00 3.63e-01 1.60e+02 ... (remaining 32994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 12879 17.66 - 35.33: 1191 35.33 - 52.99: 264 52.99 - 70.66: 75 70.66 - 88.32: 22 Dihedral angle restraints: 14431 sinusoidal: 5752 harmonic: 8679 Sorted by residual: dihedral pdb=" C PHE A 408 " pdb=" N PHE A 408 " pdb=" CA PHE A 408 " pdb=" CB PHE A 408 " ideal model delta harmonic sigma weight residual -122.60 -90.85 -31.75 0 2.50e+00 1.60e-01 1.61e+02 dihedral pdb=" C ILE A2608 " pdb=" N ILE A2608 " pdb=" CA ILE A2608 " pdb=" CB ILE A2608 " ideal model delta harmonic sigma weight residual -122.00 -148.01 26.01 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" C LYS B 342 " pdb=" N LYS B 342 " pdb=" CA LYS B 342 " pdb=" CB LYS B 342 " ideal model delta harmonic sigma weight residual -122.60 -145.95 23.35 0 2.50e+00 1.60e-01 8.73e+01 ... (remaining 14428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 3554 0.202 - 0.404: 31 0.404 - 0.606: 4 0.606 - 0.809: 1 0.809 - 1.011: 2 Chirality restraints: 3592 Sorted by residual: chirality pdb=" CA LYS B 342 " pdb=" N LYS B 342 " pdb=" C LYS B 342 " pdb=" CB LYS B 342 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA ILE A2608 " pdb=" N ILE A2608 " pdb=" C ILE A2608 " pdb=" CB ILE A2608 " both_signs ideal model delta sigma weight residual False 2.43 1.61 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA ARG B 413 " pdb=" N ARG B 413 " pdb=" C ARG B 413 " pdb=" CB ARG B 413 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 3589 not shown) Planarity restraints: 4261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2080 " 0.153 2.00e-02 2.50e+03 8.30e-02 1.72e+02 pdb=" CG TRP A2080 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A2080 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A2080 " -0.077 2.00e-02 2.50e+03 pdb=" NE1 TRP A2080 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TRP A2080 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP A2080 " -0.093 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2080 " 0.126 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2080 " -0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP A2080 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 306 " 0.032 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C TRP B 306 " -0.119 2.00e-02 2.50e+03 pdb=" O TRP B 306 " 0.047 2.00e-02 2.50e+03 pdb=" N HIS B 307 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1833 " -0.030 2.00e-02 2.50e+03 6.45e-02 4.16e+01 pdb=" C SER A1833 " 0.111 2.00e-02 2.50e+03 pdb=" O SER A1833 " -0.043 2.00e-02 2.50e+03 pdb=" N ILE A1834 " -0.039 2.00e-02 2.50e+03 ... (remaining 4258 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 90 2.38 - 3.01: 14082 3.01 - 3.64: 33184 3.64 - 4.27: 52225 4.27 - 4.90: 89634 Nonbonded interactions: 189215 Sorted by model distance: nonbonded pdb=" OG1 THR A2326 " pdb=" CA PRO A2340 " model vdw 1.755 3.470 nonbonded pdb=" O THR A2099 " pdb=" NE2 HIS A2102 " model vdw 1.816 3.120 nonbonded pdb=" O TYR A1675 " pdb=" OD1 ASN A1708 " model vdw 1.896 3.040 nonbonded pdb=" OH TYR B 416 " pdb=" O PRO B 471 " model vdw 1.906 3.040 nonbonded pdb=" OG1 THR A2326 " pdb=" N PRO A2340 " model vdw 1.950 3.120 ... (remaining 189210 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 69.650 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.011 0.528 24359 Z= 0.593 Angle : 1.037 28.502 33009 Z= 0.643 Chirality : 0.065 1.011 3592 Planarity : 0.006 0.083 4261 Dihedral : 15.002 88.319 8864 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.85 % Favored : 94.91 % Rotamer: Outliers : 3.67 % Allowed : 13.06 % Favored : 83.27 % Cbeta Deviations : 1.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 2947 helix: 0.09 (0.18), residues: 715 sheet: -0.95 (0.19), residues: 689 loop : -1.08 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.153 0.004 TRP A2080 HIS 0.015 0.002 HIS A 759 PHE 0.025 0.002 PHE A1711 TYR 0.062 0.002 TYR A1705 ARG 0.006 0.001 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.18188 ( 955) hydrogen bonds : angle 7.64183 ( 2538) metal coordination : bond 0.39367 ( 3) SS BOND : bond 0.00202 ( 5) SS BOND : angle 0.89698 ( 10) covalent geometry : bond 0.00986 (24351) covalent geometry : angle 1.03702 (32999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 229 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.8677 (mmt) cc_final: 0.8289 (mmt) REVERT: A 458 MET cc_start: 0.9029 (mtp) cc_final: 0.8768 (mtp) REVERT: A 515 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8587 (mt) REVERT: A 1416 MET cc_start: 0.7336 (mtp) cc_final: 0.7120 (mtp) REVERT: A 1709 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8460 (tttp) REVERT: A 1913 ASN cc_start: 0.8204 (m110) cc_final: 0.7968 (t0) REVERT: A 2125 ILE cc_start: 0.8185 (mt) cc_final: 0.7579 (mt) REVERT: A 2273 MET cc_start: 0.8175 (ttp) cc_final: 0.7786 (tmm) REVERT: B 146 ASN cc_start: 0.0669 (OUTLIER) cc_final: -0.0330 (t0) REVERT: B 333 SER cc_start: -0.1386 (OUTLIER) cc_final: -0.1811 (p) REVERT: B 372 MET cc_start: -0.0014 (mpt) cc_final: -0.0454 (ptt) outliers start: 97 outliers final: 49 residues processed: 317 average time/residue: 0.3567 time to fit residues: 176.7672 Evaluate side-chains 201 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1659 TYR Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1705 TYR Chi-restraints excluded: chain A residue 1709 LYS Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 2063 ILE Chi-restraints excluded: chain A residue 2072 ASN Chi-restraints excluded: chain A residue 2077 VAL Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 0.0470 chunk 223 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 267 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 529 GLN A 606 ASN A 765 ASN A 814 ASN A 852 ASN A 859 ASN A 879 ASN A 926 HIS A 937 ASN A1188 HIS A1198 ASN ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 HIS A1792 HIS A1835 ASN A1868 ASN A1909 ASN A1959 ASN A1971 ASN A1992 ASN A1993 ASN A2022 ASN A2047 ASN A2058 ASN A2160 GLN A2294 ASN A2461 ASN B 431 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.162614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102446 restraints weight = 44471.245| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.62 r_work: 0.3140 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24359 Z= 0.134 Angle : 0.548 10.351 33009 Z= 0.301 Chirality : 0.046 0.232 3592 Planarity : 0.004 0.069 4261 Dihedral : 6.701 97.238 3291 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 2.88 % Allowed : 14.35 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2947 helix: 1.47 (0.19), residues: 728 sheet: -0.61 (0.19), residues: 676 loop : -0.61 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 453 HIS 0.010 0.001 HIS A 926 PHE 0.020 0.001 PHE A1597 TYR 0.016 0.001 TYR A 973 ARG 0.007 0.001 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 955) hydrogen bonds : angle 5.22343 ( 2538) metal coordination : bond 0.00172 ( 3) SS BOND : bond 0.01094 ( 5) SS BOND : angle 1.02478 ( 10) covalent geometry : bond 0.00298 (24351) covalent geometry : angle 0.54744 (32999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 154 time to evaluate : 2.726 Fit side-chains REVERT: A 175 MET cc_start: 0.8661 (tpt) cc_final: 0.8383 (tpp) REVERT: A 320 MET cc_start: 0.8382 (mmt) cc_final: 0.8103 (mmt) REVERT: A 458 MET cc_start: 0.9164 (mtp) cc_final: 0.8963 (mtp) REVERT: A 514 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: A 515 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7895 (mt) REVERT: A 549 ASP cc_start: 0.8666 (m-30) cc_final: 0.8273 (p0) REVERT: A 1289 LYS cc_start: 0.8905 (mttt) cc_final: 0.8588 (mtmm) REVERT: A 1301 MET cc_start: 0.8762 (mtp) cc_final: 0.8202 (ttm) REVERT: A 1757 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7668 (ttp80) REVERT: A 1971 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7193 (t0) REVERT: A 2031 LYS cc_start: 0.8453 (tttt) cc_final: 0.7931 (tppt) REVERT: A 2081 HIS cc_start: 0.7758 (m90) cc_final: 0.7295 (m170) REVERT: A 2123 HIS cc_start: 0.7068 (m-70) cc_final: 0.6437 (m-70) REVERT: A 2273 MET cc_start: 0.8387 (ttp) cc_final: 0.8027 (tmm) REVERT: A 2359 PHE cc_start: 0.5783 (m-80) cc_final: 0.5391 (m-80) REVERT: B 320 MET cc_start: 0.1392 (mtt) cc_final: 0.0783 (mmm) REVERT: B 349 MET cc_start: -0.1589 (mmt) cc_final: -0.3104 (mtt) REVERT: B 371 MET cc_start: -0.0693 (ttt) cc_final: -0.2370 (ttt) outliers start: 76 outliers final: 33 residues processed: 224 average time/residue: 0.3414 time to fit residues: 125.9795 Evaluate side-chains 164 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 2063 ILE Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 220 optimal weight: 7.9990 chunk 191 optimal weight: 0.4980 chunk 250 optimal weight: 8.9990 chunk 216 optimal weight: 0.0570 chunk 154 optimal weight: 0.6980 chunk 275 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 692 ASN A 851 HIS ** A1196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 ASN A1993 ASN A2047 ASN ** A2123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2520 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.161529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101409 restraints weight = 43979.352| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.00 r_work: 0.3086 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24359 Z= 0.201 Angle : 0.570 10.318 33009 Z= 0.310 Chirality : 0.047 0.211 3592 Planarity : 0.004 0.045 4261 Dihedral : 5.879 52.303 3230 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 3.07 % Allowed : 15.56 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2947 helix: 1.60 (0.19), residues: 733 sheet: -0.56 (0.19), residues: 722 loop : -0.54 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1636 HIS 0.005 0.001 HIS B 296 PHE 0.019 0.001 PHE A1597 TYR 0.017 0.001 TYR A 973 ARG 0.012 0.001 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.05131 ( 955) hydrogen bonds : angle 5.07831 ( 2538) metal coordination : bond 0.00486 ( 3) SS BOND : bond 0.00413 ( 5) SS BOND : angle 0.76783 ( 10) covalent geometry : bond 0.00482 (24351) covalent geometry : angle 0.56967 (32999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 141 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8717 (tpt) cc_final: 0.8409 (tpp) REVERT: A 340 GLN cc_start: 0.7940 (mp10) cc_final: 0.7608 (mp10) REVERT: A 514 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 515 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7918 (mt) REVERT: A 753 ARG cc_start: 0.6015 (mmm160) cc_final: 0.5731 (mmm160) REVERT: A 771 MET cc_start: 0.7931 (mmt) cc_final: 0.7594 (mtt) REVERT: A 923 TYR cc_start: 0.7640 (t80) cc_final: 0.7433 (t80) REVERT: A 1073 MET cc_start: 0.8576 (mtt) cc_final: 0.8285 (mtt) REVERT: A 1174 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8525 (mtp) REVERT: A 1289 LYS cc_start: 0.8888 (mttt) cc_final: 0.8532 (mtmm) REVERT: A 1546 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7091 (m) REVERT: A 1689 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8955 (mp) REVERT: A 1992 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7495 (p0) REVERT: A 2030 PHE cc_start: 0.7645 (m-80) cc_final: 0.7116 (m-80) REVERT: A 2031 LYS cc_start: 0.8317 (tttt) cc_final: 0.7776 (tppt) REVERT: A 2063 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 2081 HIS cc_start: 0.7850 (m90) cc_final: 0.7278 (m90) REVERT: A 2123 HIS cc_start: 0.6936 (m-70) cc_final: 0.6346 (m-70) REVERT: A 2262 ASN cc_start: 0.8033 (m-40) cc_final: 0.7453 (m-40) REVERT: A 2273 MET cc_start: 0.8393 (ttp) cc_final: 0.7810 (tmm) REVERT: A 2318 PHE cc_start: 0.6911 (m-80) cc_final: 0.6524 (m-80) REVERT: A 2347 MET cc_start: 0.4433 (mmm) cc_final: 0.4196 (mmm) REVERT: B 164 GLN cc_start: 0.2410 (OUTLIER) cc_final: 0.2091 (mp10) REVERT: B 349 MET cc_start: -0.2007 (mmt) cc_final: -0.3405 (mtt) REVERT: B 371 MET cc_start: 0.0750 (ttt) cc_final: -0.0473 (ttt) outliers start: 81 outliers final: 47 residues processed: 213 average time/residue: 0.3321 time to fit residues: 117.2054 Evaluate side-chains 183 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1435 ASP Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1546 SER Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1646 PHE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1784 ASP Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 1992 ASN Chi-restraints excluded: chain A residue 2063 ILE Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 40 optimal weight: 0.6980 chunk 294 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 ASN ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1993 ASN A2123 HIS ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.161574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100389 restraints weight = 43628.597| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.67 r_work: 0.3108 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24359 Z= 0.151 Angle : 0.515 10.004 33009 Z= 0.280 Chirality : 0.045 0.289 3592 Planarity : 0.003 0.043 4261 Dihedral : 5.542 59.092 3226 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 3.03 % Allowed : 15.86 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2947 helix: 1.85 (0.20), residues: 732 sheet: -0.44 (0.20), residues: 686 loop : -0.44 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1636 HIS 0.006 0.001 HIS B 296 PHE 0.017 0.001 PHE A1597 TYR 0.016 0.001 TYR A 973 ARG 0.008 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 955) hydrogen bonds : angle 4.77345 ( 2538) metal coordination : bond 0.00345 ( 3) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.50545 ( 10) covalent geometry : bond 0.00357 (24351) covalent geometry : angle 0.51509 (32999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 140 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.7393 (mp10) cc_final: 0.6332 (pp30) REVERT: A 175 MET cc_start: 0.8648 (tpt) cc_final: 0.8335 (tpp) REVERT: A 285 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: A 320 MET cc_start: 0.8264 (mmt) cc_final: 0.7971 (mmt) REVERT: A 340 GLN cc_start: 0.8015 (mp10) cc_final: 0.7772 (mp10) REVERT: A 349 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7275 (mm) REVERT: A 514 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: A 515 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7694 (mt) REVERT: A 771 MET cc_start: 0.8008 (mmt) cc_final: 0.7643 (mtt) REVERT: A 1073 MET cc_start: 0.8659 (mtt) cc_final: 0.8342 (mtt) REVERT: A 1174 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8538 (mtp) REVERT: A 1289 LYS cc_start: 0.8886 (mttt) cc_final: 0.8572 (mtmm) REVERT: A 1301 MET cc_start: 0.8723 (mtp) cc_final: 0.8158 (ttm) REVERT: A 1992 ASN cc_start: 0.7972 (m110) cc_final: 0.7590 (p0) REVERT: A 2030 PHE cc_start: 0.7752 (m-80) cc_final: 0.7210 (m-80) REVERT: A 2031 LYS cc_start: 0.8414 (tttt) cc_final: 0.7887 (tppt) REVERT: A 2081 HIS cc_start: 0.7781 (m90) cc_final: 0.7229 (m90) REVERT: A 2123 HIS cc_start: 0.6905 (m170) cc_final: 0.6400 (m-70) REVERT: A 2242 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7217 (mtmt) REVERT: A 2273 MET cc_start: 0.8353 (ttp) cc_final: 0.7794 (tmm) REVERT: A 2318 PHE cc_start: 0.6884 (m-80) cc_final: 0.6616 (m-80) REVERT: A 2531 GLU cc_start: 0.0649 (OUTLIER) cc_final: 0.0433 (pp20) REVERT: B 164 GLN cc_start: 0.2274 (OUTLIER) cc_final: 0.1973 (mp10) REVERT: B 290 TRP cc_start: 0.4199 (m100) cc_final: 0.3641 (m100) REVERT: B 349 MET cc_start: -0.2102 (mmp) cc_final: -0.2320 (mmt) REVERT: B 371 MET cc_start: -0.0255 (ttt) cc_final: -0.0560 (mtp) REVERT: B 460 SER cc_start: -0.1427 (OUTLIER) cc_final: -0.1670 (p) REVERT: B 478 MET cc_start: 0.1442 (ptp) cc_final: 0.0249 (ttp) outliers start: 80 outliers final: 49 residues processed: 212 average time/residue: 0.3241 time to fit residues: 115.6174 Evaluate side-chains 180 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 122 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2242 LYS Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2292 THR Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2531 GLU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 152 optimal weight: 0.6980 chunk 167 optimal weight: 0.5980 chunk 221 optimal weight: 6.9990 chunk 267 optimal weight: 0.0030 chunk 275 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 191 optimal weight: 0.3980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 ASN ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.162788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102261 restraints weight = 43411.874| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.83 r_work: 0.3140 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 24359 Z= 0.105 Angle : 0.480 9.629 33009 Z= 0.261 Chirality : 0.044 0.242 3592 Planarity : 0.003 0.042 4261 Dihedral : 5.185 52.196 3221 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.61 % Allowed : 16.50 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2947 helix: 2.11 (0.20), residues: 732 sheet: -0.26 (0.20), residues: 686 loop : -0.32 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1636 HIS 0.005 0.001 HIS B 296 PHE 0.018 0.001 PHE A1597 TYR 0.014 0.001 TYR A 973 ARG 0.006 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 955) hydrogen bonds : angle 4.54934 ( 2538) metal coordination : bond 0.00192 ( 3) SS BOND : bond 0.00251 ( 5) SS BOND : angle 0.42970 ( 10) covalent geometry : bond 0.00236 (24351) covalent geometry : angle 0.47983 (32999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.7362 (mp10) cc_final: 0.6430 (pp30) REVERT: A 175 MET cc_start: 0.8579 (tpt) cc_final: 0.8264 (tpp) REVERT: A 285 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: A 320 MET cc_start: 0.8207 (mmt) cc_final: 0.7953 (mmt) REVERT: A 349 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7110 (mm) REVERT: A 514 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: A 515 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7717 (mt) REVERT: A 771 MET cc_start: 0.8001 (mmt) cc_final: 0.7677 (mtt) REVERT: A 1073 MET cc_start: 0.8628 (mtt) cc_final: 0.8245 (mtt) REVERT: A 1289 LYS cc_start: 0.8869 (mttt) cc_final: 0.8594 (mtpp) REVERT: A 1301 MET cc_start: 0.8717 (mtp) cc_final: 0.8189 (ttm) REVERT: A 1493 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8824 (tt) REVERT: A 2030 PHE cc_start: 0.7761 (m-80) cc_final: 0.7174 (m-80) REVERT: A 2031 LYS cc_start: 0.8333 (tttt) cc_final: 0.7838 (tppt) REVERT: A 2081 HIS cc_start: 0.7796 (m90) cc_final: 0.7310 (m90) REVERT: A 2123 HIS cc_start: 0.7034 (m170) cc_final: 0.6819 (m-70) REVERT: A 2242 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7179 (mtmt) REVERT: A 2273 MET cc_start: 0.8378 (ttp) cc_final: 0.7820 (tmm) REVERT: A 2531 GLU cc_start: 0.1001 (OUTLIER) cc_final: 0.0703 (pp20) REVERT: B 164 GLN cc_start: 0.2308 (OUTLIER) cc_final: 0.2028 (mp10) REVERT: B 371 MET cc_start: 0.0033 (ttt) cc_final: -0.0189 (mtp) outliers start: 69 outliers final: 45 residues processed: 201 average time/residue: 0.3331 time to fit residues: 110.2972 Evaluate side-chains 180 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1435 ASP Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1909 ASN Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2242 LYS Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2292 THR Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2531 GLU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 174 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 102 optimal weight: 0.0030 chunk 224 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.163188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102751 restraints weight = 42922.009| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.79 r_work: 0.3145 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 24359 Z= 0.107 Angle : 0.473 9.520 33009 Z= 0.257 Chirality : 0.044 0.211 3592 Planarity : 0.003 0.045 4261 Dihedral : 5.040 46.641 3220 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 2.50 % Allowed : 16.50 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2947 helix: 2.18 (0.20), residues: 734 sheet: -0.16 (0.20), residues: 705 loop : -0.25 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 290 HIS 0.005 0.001 HIS B 296 PHE 0.018 0.001 PHE A1597 TYR 0.014 0.001 TYR A2243 ARG 0.005 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 955) hydrogen bonds : angle 4.46417 ( 2538) metal coordination : bond 0.00204 ( 3) SS BOND : bond 0.00231 ( 5) SS BOND : angle 0.42940 ( 10) covalent geometry : bond 0.00243 (24351) covalent geometry : angle 0.47299 (32999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 132 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.7264 (mp10) cc_final: 0.6461 (pp30) REVERT: A 175 MET cc_start: 0.8550 (tpt) cc_final: 0.8236 (tpp) REVERT: A 285 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8533 (m-30) REVERT: A 320 MET cc_start: 0.8281 (mmt) cc_final: 0.8010 (mmt) REVERT: A 349 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7207 (mm) REVERT: A 515 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 771 MET cc_start: 0.7968 (mmt) cc_final: 0.7647 (mtt) REVERT: A 1073 MET cc_start: 0.8607 (mtt) cc_final: 0.8238 (mtt) REVERT: A 1289 LYS cc_start: 0.8881 (mttt) cc_final: 0.8604 (mtpp) REVERT: A 1301 MET cc_start: 0.8723 (mtp) cc_final: 0.8221 (ttm) REVERT: A 1493 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8878 (tt) REVERT: A 1630 ASP cc_start: 0.8124 (t0) cc_final: 0.7576 (m-30) REVERT: A 1720 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8199 (t0) REVERT: A 1969 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 2030 PHE cc_start: 0.7855 (m-80) cc_final: 0.7274 (m-80) REVERT: A 2031 LYS cc_start: 0.8297 (tttt) cc_final: 0.7794 (tppt) REVERT: A 2081 HIS cc_start: 0.7746 (m90) cc_final: 0.7246 (m90) REVERT: A 2123 HIS cc_start: 0.7081 (m170) cc_final: 0.6676 (m-70) REVERT: A 2164 PHE cc_start: 0.7777 (m-80) cc_final: 0.7322 (m-80) REVERT: A 2242 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7190 (mtmt) REVERT: A 2273 MET cc_start: 0.8391 (ttp) cc_final: 0.7861 (tmm) REVERT: A 2318 PHE cc_start: 0.6974 (m-80) cc_final: 0.6570 (m-80) REVERT: A 2531 GLU cc_start: 0.0932 (OUTLIER) cc_final: 0.0580 (pp20) REVERT: B 164 GLN cc_start: 0.2396 (OUTLIER) cc_final: 0.2085 (mp10) REVERT: B 478 MET cc_start: 0.1458 (ptp) cc_final: 0.0122 (ttp) REVERT: B 488 MET cc_start: -0.0961 (mmt) cc_final: -0.1491 (mtp) outliers start: 66 outliers final: 49 residues processed: 194 average time/residue: 0.3318 time to fit residues: 108.8861 Evaluate side-chains 182 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1969 ILE Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2242 LYS Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2292 THR Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2531 GLU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 122 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 ASN ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2026 GLN ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.160222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100234 restraints weight = 43406.182| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.90 r_work: 0.3081 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24359 Z= 0.174 Angle : 0.517 9.801 33009 Z= 0.281 Chirality : 0.046 0.327 3592 Planarity : 0.003 0.049 4261 Dihedral : 5.099 50.380 3211 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 3.07 % Allowed : 16.20 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2947 helix: 1.95 (0.19), residues: 735 sheet: -0.23 (0.20), residues: 667 loop : -0.35 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 290 HIS 0.005 0.001 HIS A 98 PHE 0.021 0.001 PHE A1597 TYR 0.014 0.001 TYR A1996 ARG 0.005 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 955) hydrogen bonds : angle 4.63426 ( 2538) metal coordination : bond 0.00422 ( 3) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.45491 ( 10) covalent geometry : bond 0.00413 (24351) covalent geometry : angle 0.51752 (32999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 130 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.7210 (mp10) cc_final: 0.6513 (pp30) REVERT: A 175 MET cc_start: 0.8637 (tpt) cc_final: 0.8320 (tpp) REVERT: A 285 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8573 (m-30) REVERT: A 320 MET cc_start: 0.8282 (mmt) cc_final: 0.8002 (mmt) REVERT: A 349 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7147 (mm) REVERT: A 1073 MET cc_start: 0.8639 (mtt) cc_final: 0.8281 (mtt) REVERT: A 1289 LYS cc_start: 0.8857 (mttt) cc_final: 0.8575 (mtpp) REVERT: A 1301 MET cc_start: 0.8768 (mtp) cc_final: 0.8184 (ttm) REVERT: A 1720 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8216 (t0) REVERT: A 1969 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 2030 PHE cc_start: 0.7916 (m-80) cc_final: 0.7372 (m-80) REVERT: A 2031 LYS cc_start: 0.8410 (tttt) cc_final: 0.7944 (tppt) REVERT: A 2081 HIS cc_start: 0.7753 (m90) cc_final: 0.7237 (m90) REVERT: A 2115 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8735 (t) REVERT: A 2123 HIS cc_start: 0.7115 (m170) cc_final: 0.6694 (m-70) REVERT: A 2164 PHE cc_start: 0.8041 (m-80) cc_final: 0.7624 (m-80) REVERT: A 2273 MET cc_start: 0.8431 (ttp) cc_final: 0.7769 (tmm) REVERT: A 2318 PHE cc_start: 0.7067 (m-80) cc_final: 0.6712 (m-80) REVERT: A 2531 GLU cc_start: 0.0981 (OUTLIER) cc_final: 0.0760 (pp20) REVERT: B 164 GLN cc_start: 0.2423 (OUTLIER) cc_final: 0.2087 (mp10) REVERT: B 460 SER cc_start: -0.0951 (OUTLIER) cc_final: -0.1308 (p) outliers start: 81 outliers final: 60 residues processed: 200 average time/residue: 0.3080 time to fit residues: 105.1425 Evaluate side-chains 189 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1435 ASP Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1644 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1845 THR Chi-restraints excluded: chain A residue 1909 ASN Chi-restraints excluded: chain A residue 1969 ILE Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2292 THR Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2531 GLU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 92 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 264 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 269 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 ASN ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.160736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101319 restraints weight = 43399.772| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.66 r_work: 0.3109 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24359 Z= 0.139 Angle : 0.490 9.722 33009 Z= 0.266 Chirality : 0.045 0.173 3592 Planarity : 0.003 0.050 4261 Dihedral : 4.959 54.339 3209 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 2.76 % Allowed : 16.77 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2947 helix: 2.04 (0.19), residues: 734 sheet: -0.20 (0.20), residues: 673 loop : -0.34 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 290 HIS 0.005 0.001 HIS B 296 PHE 0.019 0.001 PHE A1597 TYR 0.014 0.001 TYR A 973 ARG 0.005 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 955) hydrogen bonds : angle 4.52122 ( 2538) metal coordination : bond 0.00325 ( 3) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.40224 ( 10) covalent geometry : bond 0.00327 (24351) covalent geometry : angle 0.49007 (32999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.7070 (mp10) cc_final: 0.6441 (pp30) REVERT: A 175 MET cc_start: 0.8650 (tpt) cc_final: 0.8339 (tpp) REVERT: A 285 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: A 320 MET cc_start: 0.8311 (mmt) cc_final: 0.8038 (mmt) REVERT: A 349 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7196 (mm) REVERT: A 1073 MET cc_start: 0.8570 (mtt) cc_final: 0.8235 (mtt) REVERT: A 1289 LYS cc_start: 0.8844 (mttt) cc_final: 0.8561 (mtpp) REVERT: A 1301 MET cc_start: 0.8718 (mtp) cc_final: 0.8138 (ttm) REVERT: A 1720 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8313 (t0) REVERT: A 2030 PHE cc_start: 0.7831 (m-80) cc_final: 0.7261 (m-80) REVERT: A 2031 LYS cc_start: 0.8425 (tttt) cc_final: 0.7932 (tppt) REVERT: A 2081 HIS cc_start: 0.7673 (m90) cc_final: 0.7218 (m90) REVERT: A 2115 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (t) REVERT: A 2123 HIS cc_start: 0.7229 (m170) cc_final: 0.6830 (m-70) REVERT: A 2164 PHE cc_start: 0.7879 (m-80) cc_final: 0.7450 (m-80) REVERT: A 2273 MET cc_start: 0.8502 (ttp) cc_final: 0.7940 (tmm) REVERT: A 2318 PHE cc_start: 0.6963 (m-80) cc_final: 0.6613 (m-80) REVERT: A 2531 GLU cc_start: 0.1073 (OUTLIER) cc_final: 0.0846 (pp20) REVERT: B 227 HIS cc_start: 0.0762 (OUTLIER) cc_final: -0.0315 (p-80) outliers start: 73 outliers final: 58 residues processed: 192 average time/residue: 0.3343 time to fit residues: 110.4223 Evaluate side-chains 187 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 123 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 973 TYR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1435 ASP Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1644 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1948 ILE Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2168 ASP Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2292 THR Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2531 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 10 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 ASN ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.161043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102226 restraints weight = 43525.336| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.62 r_work: 0.3149 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24359 Z= 0.116 Angle : 0.476 9.500 33009 Z= 0.257 Chirality : 0.044 0.187 3592 Planarity : 0.003 0.049 4261 Dihedral : 4.786 55.483 3209 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.61 % Allowed : 16.99 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 2947 helix: 2.20 (0.20), residues: 735 sheet: -0.07 (0.20), residues: 698 loop : -0.27 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1636 HIS 0.005 0.001 HIS B 296 PHE 0.018 0.001 PHE A1597 TYR 0.012 0.001 TYR A 973 ARG 0.006 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 955) hydrogen bonds : angle 4.39009 ( 2538) metal coordination : bond 0.00249 ( 3) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.39537 ( 10) covalent geometry : bond 0.00266 (24351) covalent geometry : angle 0.47630 (32999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 139 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.6916 (mp10) cc_final: 0.6369 (pp30) REVERT: A 175 MET cc_start: 0.8635 (tpt) cc_final: 0.8319 (tpp) REVERT: A 285 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8500 (m-30) REVERT: A 320 MET cc_start: 0.8257 (mmt) cc_final: 0.7953 (mmt) REVERT: A 771 MET cc_start: 0.8068 (mmt) cc_final: 0.7710 (mtt) REVERT: A 1143 ASP cc_start: 0.8006 (t70) cc_final: 0.7690 (t0) REVERT: A 1289 LYS cc_start: 0.8826 (mttt) cc_final: 0.8540 (mtpp) REVERT: A 1301 MET cc_start: 0.8689 (mtp) cc_final: 0.8182 (ttm) REVERT: A 1341 LYS cc_start: 0.8025 (tttt) cc_final: 0.7635 (tptp) REVERT: A 1547 LYS cc_start: 0.8030 (tttt) cc_final: 0.7767 (tppt) REVERT: A 1720 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8221 (t0) REVERT: A 2030 PHE cc_start: 0.7947 (m-80) cc_final: 0.7365 (m-80) REVERT: A 2031 LYS cc_start: 0.8430 (tttt) cc_final: 0.7929 (tppt) REVERT: A 2081 HIS cc_start: 0.7715 (m90) cc_final: 0.7183 (m90) REVERT: A 2115 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8705 (t) REVERT: A 2123 HIS cc_start: 0.7223 (m170) cc_final: 0.6827 (m-70) REVERT: A 2164 PHE cc_start: 0.8077 (m-80) cc_final: 0.7651 (m-80) REVERT: A 2273 MET cc_start: 0.8472 (ttp) cc_final: 0.7938 (tmm) REVERT: A 2318 PHE cc_start: 0.7083 (m-80) cc_final: 0.6717 (m-80) REVERT: A 2531 GLU cc_start: 0.1075 (OUTLIER) cc_final: 0.0815 (pp20) REVERT: B 227 HIS cc_start: 0.0438 (OUTLIER) cc_final: -0.0464 (t70) REVERT: B 329 GLU cc_start: -0.0070 (pt0) cc_final: -0.0288 (pt0) REVERT: B 406 GLU cc_start: 0.0504 (mt-10) cc_final: 0.0299 (mm-30) REVERT: B 460 SER cc_start: -0.2143 (OUTLIER) cc_final: -0.2605 (p) outliers start: 69 outliers final: 55 residues processed: 199 average time/residue: 0.3062 time to fit residues: 103.9659 Evaluate side-chains 197 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 973 TYR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1435 ASP Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1909 ASN Chi-restraints excluded: chain A residue 1948 ILE Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2531 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 40 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 217 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 258 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 ASN ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.161296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102397 restraints weight = 43549.528| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.96 r_work: 0.3110 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24359 Z= 0.119 Angle : 0.481 9.536 33009 Z= 0.260 Chirality : 0.044 0.180 3592 Planarity : 0.003 0.049 4261 Dihedral : 4.618 46.156 3204 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 2.46 % Allowed : 17.18 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2947 helix: 2.16 (0.19), residues: 742 sheet: -0.05 (0.20), residues: 685 loop : -0.28 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.018 0.001 PHE A1597 TYR 0.012 0.001 TYR A 973 ARG 0.004 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 955) hydrogen bonds : angle 4.38306 ( 2538) metal coordination : bond 0.00255 ( 3) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.36390 ( 10) covalent geometry : bond 0.00273 (24351) covalent geometry : angle 0.48107 (32999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.6884 (mp10) cc_final: 0.6584 (pp30) REVERT: A 175 MET cc_start: 0.8626 (tpt) cc_final: 0.8319 (tpp) REVERT: A 285 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8507 (m-30) REVERT: A 320 MET cc_start: 0.8318 (mmt) cc_final: 0.8032 (mmt) REVERT: A 771 MET cc_start: 0.8086 (mmt) cc_final: 0.7742 (mtt) REVERT: A 1143 ASP cc_start: 0.7995 (t70) cc_final: 0.7682 (t0) REVERT: A 1289 LYS cc_start: 0.8826 (mttt) cc_final: 0.8540 (mtpp) REVERT: A 1301 MET cc_start: 0.8722 (mtp) cc_final: 0.8203 (ttm) REVERT: A 1341 LYS cc_start: 0.8025 (tttt) cc_final: 0.7636 (tptp) REVERT: A 1720 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8241 (t0) REVERT: A 2030 PHE cc_start: 0.8034 (m-80) cc_final: 0.7472 (m-80) REVERT: A 2031 LYS cc_start: 0.8468 (tttt) cc_final: 0.7999 (tppt) REVERT: A 2081 HIS cc_start: 0.7735 (m90) cc_final: 0.7166 (m90) REVERT: A 2115 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8721 (t) REVERT: A 2164 PHE cc_start: 0.8147 (m-80) cc_final: 0.7728 (m-80) REVERT: A 2273 MET cc_start: 0.8497 (ttp) cc_final: 0.7971 (tmm) REVERT: A 2318 PHE cc_start: 0.6969 (m-80) cc_final: 0.6631 (m-80) REVERT: A 2531 GLU cc_start: 0.1032 (OUTLIER) cc_final: 0.0816 (pp20) REVERT: B 145 GLU cc_start: 0.2775 (tp30) cc_final: 0.2456 (mp0) REVERT: B 350 LYS cc_start: 0.4684 (tptp) cc_final: 0.4364 (tttt) outliers start: 65 outliers final: 56 residues processed: 195 average time/residue: 0.3545 time to fit residues: 117.7960 Evaluate side-chains 196 residues out of total 2642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 973 TYR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1080 MET Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1435 ASP Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1641 THR Chi-restraints excluded: chain A residue 1643 ASN Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1909 ASN Chi-restraints excluded: chain A residue 1948 ILE Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2124 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2277 VAL Chi-restraints excluded: chain A residue 2292 THR Chi-restraints excluded: chain A residue 2304 TYR Chi-restraints excluded: chain A residue 2531 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 243 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 270 optimal weight: 0.6980 chunk 246 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1214 ASN A1548 ASN A1599 ASN ** A1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.160215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101086 restraints weight = 43425.117| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.54 r_work: 0.3143 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24359 Z= 0.146 Angle : 0.506 9.627 33009 Z= 0.272 Chirality : 0.045 0.182 3592 Planarity : 0.003 0.048 4261 Dihedral : 4.681 45.973 3204 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 2.42 % Allowed : 17.45 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2947 helix: 2.11 (0.19), residues: 735 sheet: -0.09 (0.20), residues: 696 loop : -0.31 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 290 HIS 0.004 0.001 HIS B 296 PHE 0.019 0.001 PHE A1597 TYR 0.013 0.001 TYR A 973 ARG 0.004 0.000 ARG A1651 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 955) hydrogen bonds : angle 4.45911 ( 2538) metal coordination : bond 0.00341 ( 3) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.37232 ( 10) covalent geometry : bond 0.00344 (24351) covalent geometry : angle 0.50631 (32999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18736.73 seconds wall clock time: 324 minutes 54.51 seconds (19494.51 seconds total)