Starting phenix.real_space_refine (version: dev) on Sat Feb 25 23:55:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvz_24059/02_2023/7mvz_24059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvz_24059/02_2023/7mvz_24059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvz_24059/02_2023/7mvz_24059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvz_24059/02_2023/7mvz_24059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvz_24059/02_2023/7mvz_24059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvz_24059/02_2023/7mvz_24059.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.002 sd= 0.053 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 Process input model Symmetric amino acids flipped Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A GLU 905": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1308": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1836": "OE1" <-> "OE2" Residue "B ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 706": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26733 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 25701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1641, 25701 Classifications: {'peptide': 1641} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1570} Chain breaks: 14 Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 854 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "C" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 178 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Time building chain proxies: 12.72, per 1000 atoms: 0.48 Number of scatterers: 26733 At special positions: 0 Unit cell: (80.352, 110.16, 186.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 2443 8.00 N 2291 7.00 C 8522 6.00 H 13421 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 23.27 Conformation dependent library (CDL) restraints added in 2.4 seconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 1 sheets defined 76.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.710A pdb=" N VAL A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 205 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 242 through 249 removed outlier: 4.089A pdb=" N THR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.911A pdb=" N ASP A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.816A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 332 through 352 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 375 through 393 removed outlier: 3.554A pdb=" N GLY A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 418 removed outlier: 4.806A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.839A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.176A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.630A pdb=" N ASP A 557 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 558' Processing helix chain 'A' and resid 564 through 577 removed outlier: 3.565A pdb=" N ASN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.541A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'A' and resid 595 through 610 removed outlier: 4.207A pdb=" N PHE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.852A pdb=" N ALA A 617 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.199A pdb=" N ARG A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 Processing helix chain 'A' and resid 731 through 755 removed outlier: 3.599A pdb=" N THR A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 800 through 819 removed outlier: 4.164A pdb=" N ALA A 819 " --> pdb=" O HIS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 830 Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.654A pdb=" N ARG A 846 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 847 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 848 " --> pdb=" O SER A 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 848' Processing helix chain 'A' and resid 854 through 877 removed outlier: 4.581A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 863 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 926 Processing helix chain 'A' and resid 933 through 957 removed outlier: 4.221A pdb=" N ARG A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.648A pdb=" N THR A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 979 removed outlier: 3.521A pdb=" N THR A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 Processing helix chain 'A' and resid 1008 through 1035 Processing helix chain 'A' and resid 1042 through 1055 removed outlier: 4.291A pdb=" N HIS A1046 " --> pdb=" O PRO A1042 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A1053 " --> pdb=" O GLN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1081 Processing helix chain 'A' and resid 1091 through 1097 removed outlier: 3.859A pdb=" N TYR A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1118 through 1134 Processing helix chain 'A' and resid 1137 through 1146 Processing helix chain 'A' and resid 1169 through 1179 removed outlier: 3.723A pdb=" N ALA A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1203 removed outlier: 3.817A pdb=" N ALA A1191 " --> pdb=" O GLN A1187 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A1202 " --> pdb=" O SER A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 removed outlier: 3.512A pdb=" N ILE A1207 " --> pdb=" O TRP A1203 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A1209 " --> pdb=" O TRP A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1228 removed outlier: 3.751A pdb=" N ASP A1218 " --> pdb=" O LYS A1214 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1267 removed outlier: 3.911A pdb=" N PHE A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1277 Processing helix chain 'A' and resid 1280 through 1287 Processing helix chain 'A' and resid 1294 through 1309 removed outlier: 3.682A pdb=" N HIS A1298 " --> pdb=" O ASN A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.570A pdb=" N PHE A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1342 removed outlier: 4.384A pdb=" N GLN A1340 " --> pdb=" O GLU A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1354 removed outlier: 4.002A pdb=" N GLN A1353 " --> pdb=" O GLY A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1391 removed outlier: 4.020A pdb=" N GLU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 3.559A pdb=" N GLN A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1447 removed outlier: 3.974A pdb=" N ALA A1436 " --> pdb=" O ARG A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1466 removed outlier: 3.756A pdb=" N LEU A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A1459 " --> pdb=" O HIS A1455 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1496 removed outlier: 3.741A pdb=" N GLY A1496 " --> pdb=" O ALA A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1518 removed outlier: 4.477A pdb=" N THR A1513 " --> pdb=" O GLN A1509 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A1515 " --> pdb=" O VAL A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1531 removed outlier: 3.564A pdb=" N HIS A1531 " --> pdb=" O ALA A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1559 Processing helix chain 'A' and resid 1561 through 1565 Processing helix chain 'A' and resid 1567 through 1578 removed outlier: 4.106A pdb=" N ASN A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A1574 " --> pdb=" O GLN A1570 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS A1578 " --> pdb=" O ILE A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 removed outlier: 3.905A pdb=" N VAL A1583 " --> pdb=" O ASP A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1632 Processing helix chain 'A' and resid 1634 through 1643 Processing helix chain 'A' and resid 1643 through 1653 removed outlier: 4.211A pdb=" N LEU A1647 " --> pdb=" O CYS A1643 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1661 removed outlier: 3.639A pdb=" N ARG A1661 " --> pdb=" O GLY A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1683 removed outlier: 3.543A pdb=" N CYS A1683 " --> pdb=" O ILE A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1695 removed outlier: 3.595A pdb=" N ALA A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1695 " --> pdb=" O ILE A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1710 Processing helix chain 'A' and resid 1710 through 1721 removed outlier: 4.370A pdb=" N LEU A1714 " --> pdb=" O PHE A1710 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A1721 " --> pdb=" O SER A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1766 removed outlier: 3.520A pdb=" N GLU A1750 " --> pdb=" O LEU A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1779 through 1789 Processing helix chain 'A' and resid 1794 through 1800 removed outlier: 3.967A pdb=" N ARG A1799 " --> pdb=" O LEU A1796 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A1800 " --> pdb=" O ARG A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1849 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 259 through 299 removed outlier: 4.001A pdb=" N MET B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 630 through 632 removed outlier: 3.757A pdb=" N VAL A 632 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 688 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 654 " --> pdb=" O GLY A 688 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2469 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: 11.00 Time building geometry restraints manager: 23.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13397 1.03 - 1.23: 26 1.23 - 1.42: 5593 1.42 - 1.62: 7889 1.62 - 1.81: 88 Bond restraints: 26993 Sorted by residual: bond pdb=" N ARG A 530 " pdb=" H ARG A 530 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" N ALA A 532 " pdb=" H ALA A 532 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" N SER A 531 " pdb=" CA SER A 531 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.92e+00 bond pdb=" N SER A 531 " pdb=" H SER A 531 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.33e-02 5.65e+03 4.15e+00 ... (remaining 26988 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 654 107.16 - 113.86: 32145 113.86 - 120.57: 9393 120.57 - 127.27: 6503 127.27 - 133.98: 159 Bond angle restraints: 48854 Sorted by residual: angle pdb=" CA LYS A 529 " pdb=" C LYS A 529 " pdb=" N ARG A 530 " ideal model delta sigma weight residual 117.30 113.32 3.98 1.16e+00 7.43e-01 1.18e+01 angle pdb=" O LYS A 529 " pdb=" C LYS A 529 " pdb=" N ARG A 530 " ideal model delta sigma weight residual 122.12 125.09 -2.97 1.06e+00 8.90e-01 7.83e+00 angle pdb=" N VAL A1165 " pdb=" CA VAL A1165 " pdb=" C VAL A1165 " ideal model delta sigma weight residual 111.00 103.35 7.65 2.80e+00 1.28e-01 7.46e+00 angle pdb=" C LYS A 529 " pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta sigma weight residual 121.14 125.77 -4.63 1.75e+00 3.27e-01 7.01e+00 angle pdb=" N ALA A 532 " pdb=" CA ALA A 532 " pdb=" C ALA A 532 " ideal model delta sigma weight residual 111.03 108.19 2.84 1.11e+00 8.12e-01 6.56e+00 ... (remaining 48849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 10539 17.78 - 35.56: 207 35.56 - 53.34: 70 53.34 - 71.12: 17 71.12 - 88.90: 2 Dihedral angle restraints: 10835 sinusoidal: 5037 harmonic: 5798 Sorted by residual: dihedral pdb=" CA CYS A 821 " pdb=" CB CYS A 821 " pdb=" SG CYS A 821 " pdb=" HG CYS A 821 " ideal model delta sinusoidal sigma weight residual 60.00 0.60 59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 759 " pdb=" CB ASP A 759 " pdb=" CG ASP A 759 " pdb=" OD1 ASP A 759 " ideal model delta sinusoidal sigma weight residual -30.00 -79.74 49.74 1 2.00e+01 2.50e-03 8.49e+00 dihedral pdb=" N LEU A 774 " pdb=" CA LEU A 774 " pdb=" CB LEU A 774 " pdb=" CG LEU A 774 " ideal model delta sinusoidal sigma weight residual -60.00 -104.84 44.84 3 1.50e+01 4.44e-03 8.07e+00 ... (remaining 10832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1655 0.033 - 0.066: 379 0.066 - 0.099: 110 0.099 - 0.132: 20 0.132 - 0.165: 3 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CA ILE A 535 " pdb=" N ILE A 535 " pdb=" C ILE A 535 " pdb=" CB ILE A 535 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA VAL A1165 " pdb=" N VAL A1165 " pdb=" C VAL A1165 " pdb=" CB VAL A1165 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE A 682 " pdb=" N ILE A 682 " pdb=" C ILE A 682 " pdb=" CB ILE A 682 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2164 not shown) Planarity restraints: 3975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 530 " -0.129 9.50e-02 1.11e+02 6.40e-02 5.21e+01 pdb=" NE ARG A 530 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 530 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 530 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 530 " -0.009 2.00e-02 2.50e+03 pdb="HH11 ARG A 530 " -0.017 2.00e-02 2.50e+03 pdb="HH12 ARG A 530 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 530 " 0.084 2.00e-02 2.50e+03 pdb="HH22 ARG A 530 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1670 " -0.022 2.00e-02 2.50e+03 3.67e-02 2.02e+01 pdb=" CG ASN A1670 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A1670 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A1670 " -0.063 2.00e-02 2.50e+03 pdb="HD21 ASN A1670 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN A1670 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1397 " -0.018 2.00e-02 2.50e+03 3.12e-02 1.46e+01 pdb=" CG ASN A1397 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A1397 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A1397 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN A1397 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN A1397 " 0.034 2.00e-02 2.50e+03 ... (remaining 3972 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 2002 2.23 - 2.82: 59597 2.82 - 3.41: 71758 3.41 - 4.01: 91023 4.01 - 4.60: 145388 Nonbonded interactions: 369768 Sorted by model distance: nonbonded pdb=" O MET A1659 " pdb="HD21 ASN A1712 " model vdw 1.633 1.850 nonbonded pdb=" OE1 GLU A 905 " pdb=" H GLU A 905 " model vdw 1.636 1.850 nonbonded pdb=" HE1 TRP A 638 " pdb=" O SER A 725 " model vdw 1.641 1.850 nonbonded pdb=" O PHE A 581 " pdb=" HG1 THR A 585 " model vdw 1.646 1.850 nonbonded pdb=" OE1 GLU A1336 " pdb=" H GLU A1336 " model vdw 1.647 1.850 ... (remaining 369763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 8522 2.51 5 N 2291 2.21 5 O 2443 1.98 5 H 13421 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.81 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.390 Extract box with map and model: 5.890 Check model and map are aligned: 0.400 Process input model: 86.170 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.220 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13572 Z= 0.133 Angle : 0.478 7.646 18446 Z= 0.254 Chirality : 0.032 0.165 2167 Planarity : 0.004 0.048 2354 Dihedral : 7.604 85.418 4902 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1673 helix: -0.10 (0.15), residues: 1132 sheet: -2.50 (1.41), residues: 9 loop : -1.93 (0.27), residues: 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 397 average time/residue: 2.3498 time to fit residues: 1039.0777 Evaluate side-chains 200 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 2.0008 time to fit residues: 5.0814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 492 GLN A1510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 13572 Z= 0.251 Angle : 0.593 7.095 18446 Z= 0.307 Chirality : 0.035 0.151 2167 Planarity : 0.005 0.094 2354 Dihedral : 2.999 12.996 1838 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.24 (0.21), residues: 1673 helix: 0.89 (0.15), residues: 1156 sheet: -2.67 (1.25), residues: 9 loop : -1.39 (0.28), residues: 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 17 residues processed: 219 average time/residue: 2.3568 time to fit residues: 577.4998 Evaluate side-chains 165 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 2.286 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 3 average time/residue: 0.3473 time to fit residues: 4.7486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 chunk 153 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS A 377 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 13572 Z= 0.349 Angle : 0.647 8.600 18446 Z= 0.340 Chirality : 0.037 0.173 2167 Planarity : 0.005 0.055 2354 Dihedral : 3.608 15.410 1838 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.30 (0.20), residues: 1673 helix: 0.96 (0.15), residues: 1172 sheet: None (None), residues: 0 loop : -1.58 (0.27), residues: 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 160 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 26 residues processed: 207 average time/residue: 2.3535 time to fit residues: 546.4426 Evaluate side-chains 160 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.9485 time to fit residues: 8.6741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 352 ASN A 377 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS ** A1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 13572 Z= 0.349 Angle : 0.647 7.400 18446 Z= 0.339 Chirality : 0.038 0.177 2167 Planarity : 0.005 0.060 2354 Dihedral : 3.908 17.875 1838 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.23 (0.20), residues: 1673 helix: 0.87 (0.15), residues: 1166 sheet: -3.03 (1.46), residues: 9 loop : -1.43 (0.27), residues: 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 144 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 28 residues processed: 194 average time/residue: 2.1670 time to fit residues: 475.5496 Evaluate side-chains 156 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 2.545 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 1.5248 time to fit residues: 10.1526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13572 Z= 0.186 Angle : 0.553 6.841 18446 Z= 0.278 Chirality : 0.034 0.165 2167 Planarity : 0.004 0.063 2354 Dihedral : 3.612 17.727 1838 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.76 (0.21), residues: 1673 helix: 1.32 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.39 (0.27), residues: 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 179 average time/residue: 1.9645 time to fit residues: 402.2698 Evaluate side-chains 147 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 0.3960 time to fit residues: 3.3321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 0.0170 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 13572 Z= 0.277 Angle : 0.592 8.259 18446 Z= 0.305 Chirality : 0.036 0.176 2167 Planarity : 0.004 0.059 2354 Dihedral : 3.717 17.915 1838 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.67 (0.21), residues: 1673 helix: 1.24 (0.15), residues: 1158 sheet: -2.41 (1.61), residues: 9 loop : -1.31 (0.27), residues: 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 130 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 177 average time/residue: 2.1324 time to fit residues: 429.7105 Evaluate side-chains 150 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 2.112 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 3 average time/residue: 0.8635 time to fit residues: 6.1076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.7824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 13572 Z= 0.236 Angle : 0.579 7.786 18446 Z= 0.294 Chirality : 0.035 0.172 2167 Planarity : 0.004 0.053 2354 Dihedral : 3.680 17.868 1838 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.78 (0.21), residues: 1673 helix: 1.34 (0.15), residues: 1157 sheet: -3.03 (1.62), residues: 9 loop : -1.31 (0.27), residues: 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 28 residues processed: 171 average time/residue: 2.0989 time to fit residues: 406.6095 Evaluate side-chains 150 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 1.7405 time to fit residues: 4.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 13572 Z= 0.238 Angle : 0.581 9.010 18446 Z= 0.295 Chirality : 0.035 0.182 2167 Planarity : 0.004 0.062 2354 Dihedral : 3.683 17.546 1838 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1673 helix: 1.44 (0.15), residues: 1157 sheet: -3.15 (1.55), residues: 9 loop : -1.29 (0.27), residues: 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 171 average time/residue: 2.0640 time to fit residues: 401.3029 Evaluate side-chains 148 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 3 average time/residue: 0.8660 time to fit residues: 6.1002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.8344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 13572 Z= 0.277 Angle : 0.611 8.748 18446 Z= 0.314 Chirality : 0.036 0.184 2167 Planarity : 0.004 0.057 2354 Dihedral : 3.790 17.793 1838 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.71 (0.21), residues: 1673 helix: 1.27 (0.15), residues: 1166 sheet: -3.06 (1.47), residues: 9 loop : -1.34 (0.27), residues: 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 164 average time/residue: 1.9570 time to fit residues: 369.3676 Evaluate side-chains 139 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 2.7843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0170 chunk 76 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.8391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13572 Z= 0.201 Angle : 0.597 8.856 18446 Z= 0.297 Chirality : 0.035 0.190 2167 Planarity : 0.004 0.064 2354 Dihedral : 3.691 19.467 1838 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.98 (0.21), residues: 1673 helix: 1.46 (0.15), residues: 1166 sheet: -2.88 (1.61), residues: 9 loop : -1.22 (0.27), residues: 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 150 average time/residue: 2.1412 time to fit residues: 364.7962 Evaluate side-chains 143 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 2.113 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.4510 time to fit residues: 3.2772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 471 GLN ** 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 = 0.4203 r_free = 0.4203 target = 0.107949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.090939 restraints weight = 127770.195| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.78 r_work: 0.3765 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4203 r_free = 0.4203 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4202 r_free = 0.4202 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.8549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 13572 Z= 0.249 Angle : 0.604 8.495 18446 Z= 0.306 Chirality : 0.035 0.192 2167 Planarity : 0.004 0.053 2354 Dihedral : 3.735 20.651 1838 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.86 (0.21), residues: 1673 helix: 1.37 (0.15), residues: 1170 sheet: -2.54 (1.01), residues: 19 loop : -1.25 (0.28), residues: 484 =============================================================================== Job complete usr+sys time: 8802.77 seconds wall clock time: 155 minutes 57.72 seconds (9357.72 seconds total)