Starting phenix.real_space_refine on Wed Mar 20 05:25:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/03_2024/7mvy_24058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/03_2024/7mvy_24058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/03_2024/7mvy_24058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/03_2024/7mvy_24058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/03_2024/7mvy_24058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/03_2024/7mvy_24058.pdb" } resolution = 2.39 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 8464 2.51 5 N 2276 2.21 5 O 2422 1.98 5 H 13337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 "B ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26555 Number of models: 1 Model: "" Number of chains: 2 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} Time building chain proxies: 11.34, per 1000 atoms: 0.43 Number of scatterers: 26555 At special positions: 0 Unit cell: (79.704, 109.836, 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 2422 8.00 N 2276 7.00 C 8464 6.00 H 13337 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: 20.20 Conformation dependent library (CDL) restraints added in 2.6 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3236 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 1 sheets defined 76.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 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 66 removed outlier: 3.855A pdb=" N VAL A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' 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 260 removed outlier: 4.131A pdb=" N THR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 3.845A 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: 3.765A 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: 3.530A pdb=" N GLY A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 removed outlier: 4.792A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 4.011A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.647A 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 531 removed outlier: 4.061A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 Processing helix chain 'A' and resid 564 through 577 removed outlier: 3.606A pdb=" N ASN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 583 Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'A' and resid 595 through 610 removed outlier: 4.073A pdb=" N PHE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.796A 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: 4.158A 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: 3.602A pdb=" N THR A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.720A 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 821 removed outlier: 4.076A pdb=" N ALA A 819 " --> pdb=" O HIS A 815 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 830 removed outlier: 3.588A pdb=" N VAL A 825 " --> pdb=" O CYS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.656A pdb=" N ARG A 846 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 847 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.889A 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: 4.686A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 863 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.726A 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: 4.213A pdb=" N ARG A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.641A pdb=" N THR A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 979 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: 4.283A pdb=" N HIS A1046 " --> pdb=" O PRO A1042 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.881A 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 1145 Processing helix chain 'A' and resid 1169 through 1179 removed outlier: 3.816A pdb=" N ALA A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1203 removed outlier: 3.835A pdb=" N ALA A1191 " --> pdb=" O GLN A1187 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A1202 " --> pdb=" O SER A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 removed outlier: 3.888A pdb=" N ALA A1209 " --> pdb=" O TRP A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1228 removed outlier: 3.804A pdb=" N ASP A1218 " --> pdb=" O LYS A1214 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1266 removed outlier: 3.962A 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: 3.674A pdb=" N HIS A1298 " --> pdb=" O ASN A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.575A pdb=" N PHE A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1342 removed outlier: 4.521A pdb=" N GLN A1340 " --> pdb=" O GLU A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1391 removed outlier: 4.014A pdb=" N GLU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 3.504A pdb=" N PHE A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1447 removed outlier: 4.075A pdb=" N ALA A1436 " --> pdb=" O ARG A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1466 removed outlier: 3.770A pdb=" N LEU A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A1459 " --> pdb=" O HIS A1455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1495 removed outlier: 3.639A pdb=" N PHE A1479 " --> pdb=" O ASP A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1517 removed outlier: 4.600A pdb=" N THR A1513 " --> pdb=" O GLN A1509 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1515 " --> pdb=" O VAL A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1531 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 1577 removed outlier: 4.278A pdb=" N ASN A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE A1574 " --> pdb=" O GLN A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 removed outlier: 4.123A 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: 4.292A pdb=" N LEU A1647 " --> pdb=" O CYS A1643 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A1648 " --> pdb=" O ASP A1644 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1661 removed outlier: 3.803A pdb=" N ARG A1661 " --> pdb=" O GLY A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1683 Processing helix chain 'A' and resid 1683 through 1695 removed outlier: 3.546A pdb=" N ALA A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) removed outlier: 3.765A 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: 4.387A pdb=" N LEU A1714 " --> pdb=" O PHE A1710 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A1721 " --> pdb=" O SER A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1766 removed outlier: 3.540A 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: 3.989A pdb=" N ARG A1799 " --> pdb=" O LEU A1796 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A1800 " --> pdb=" O ARG A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1850 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.993A pdb=" N MET B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 299 removed outlier: 3.964A pdb=" N GLU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.147A 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: 3.743A pdb=" N VAL A 632 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 698 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 655 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2475 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: 10.35 Time building geometry restraints manager: 20.96 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: 13313 1.03 - 1.23: 24 1.23 - 1.42: 5554 1.42 - 1.61: 7835 1.61 - 1.81: 88 Bond restraints: 26814 Sorted by residual: bond pdb=" N SER A 531 " pdb=" CA SER A 531 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.22e-02 6.72e+03 8.35e+00 bond pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.33e-02 5.65e+03 8.35e+00 bond pdb=" N ARG A 530 " pdb=" H ARG A 530 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" N ALA A 532 " pdb=" H ALA A 532 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" N SER A 531 " pdb=" H SER A 531 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.08e+00 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 1046 107.46 - 114.09: 31854 114.09 - 120.73: 9640 120.73 - 127.36: 5840 127.36 - 133.99: 153 Bond angle restraints: 48533 Sorted by residual: angle pdb=" N ALA A 532 " pdb=" CA ALA A 532 " pdb=" C ALA A 532 " ideal model delta sigma weight residual 112.45 108.10 4.35 1.39e+00 5.18e-01 9.81e+00 angle pdb=" N SER A 531 " pdb=" CA SER A 531 " pdb=" C SER A 531 " ideal model delta sigma weight residual 112.88 109.79 3.09 1.29e+00 6.01e-01 5.72e+00 angle pdb=" CA SER A 531 " pdb=" C SER A 531 " pdb=" O SER A 531 " ideal model delta sigma weight residual 119.59 117.03 2.56 1.18e+00 7.18e-01 4.72e+00 angle pdb=" N ILE A1001 " pdb=" CA ILE A1001 " pdb=" C ILE A1001 " ideal model delta sigma weight residual 111.88 109.79 2.09 1.06e+00 8.90e-01 3.87e+00 angle pdb=" N ARG A 530 " pdb=" CA ARG A 530 " pdb=" C ARG A 530 " ideal model delta sigma weight residual 112.89 110.60 2.29 1.24e+00 6.50e-01 3.40e+00 ... (remaining 48528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12141 17.91 - 35.81: 258 35.81 - 53.72: 114 53.72 - 71.63: 36 71.63 - 89.54: 1 Dihedral angle restraints: 12550 sinusoidal: 6793 harmonic: 5757 Sorted by residual: dihedral pdb=" N GLU A 67 " pdb=" CA GLU A 67 " pdb=" CB GLU A 67 " pdb=" CG GLU A 67 " ideal model delta sinusoidal sigma weight residual -180.00 -130.46 -49.54 3 1.50e+01 4.44e-03 8.79e+00 dihedral pdb=" CA LEU A1457 " pdb=" CB LEU A1457 " pdb=" CG LEU A1457 " pdb=" CD1 LEU A1457 " ideal model delta sinusoidal sigma weight residual 180.00 140.16 39.84 3 1.50e+01 4.44e-03 7.08e+00 dihedral pdb=" CA LEU A 844 " pdb=" CB LEU A 844 " pdb=" CG LEU A 844 " pdb=" CD1 LEU A 844 " ideal model delta sinusoidal sigma weight residual 180.00 140.18 39.82 3 1.50e+01 4.44e-03 7.07e+00 ... (remaining 12547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1620 0.028 - 0.056: 342 0.056 - 0.085: 134 0.085 - 0.113: 47 0.113 - 0.141: 10 Chirality restraints: 2153 Sorted by residual: 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 4.96e-01 chirality pdb=" CA ILE A 681 " pdb=" N ILE A 681 " pdb=" C ILE A 681 " pdb=" CB ILE A 681 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL A1561 " pdb=" N VAL A1561 " pdb=" C VAL A1561 " pdb=" CB VAL A1561 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 2150 not shown) Planarity restraints: 3946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 529 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C LYS A 529 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS A 529 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A 530 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 532 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" N TYR A 533 " -0.033 2.00e-02 2.50e+03 pdb=" CA TYR A 533 " 0.008 2.00e-02 2.50e+03 pdb=" H TYR A 533 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1700 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A1701 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1701 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1701 " 0.027 5.00e-02 4.00e+02 ... (remaining 3943 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1863 2.23 - 2.83: 61114 2.83 - 3.42: 69655 3.42 - 4.01: 90016 4.01 - 4.60: 143330 Nonbonded interactions: 365978 Sorted by model distance: nonbonded pdb=" OE1 GLU A1336 " pdb=" H GLU A1336 " model vdw 1.643 1.850 nonbonded pdb=" OE1 GLN A1509 " pdb=" H GLN A1509 " model vdw 1.646 1.850 nonbonded pdb=" OE1 GLU A1669 " pdb=" H GLU A1669 " model vdw 1.650 1.850 nonbonded pdb=" O MET A1659 " pdb="HD21 ASN A1712 " model vdw 1.661 1.850 nonbonded pdb=" HE1 TRP A 638 " pdb=" O SER A 725 " model vdw 1.688 1.850 ... (remaining 365973 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.420 Extract box with map and model: 9.560 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 80.390 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 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 0.038 13477 Z= 0.112 Angle : 0.392 5.046 18318 Z= 0.220 Chirality : 0.031 0.141 2153 Planarity : 0.002 0.048 2336 Dihedral : 6.612 89.537 4869 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.54 (0.20), residues: 1662 helix: 0.40 (0.15), residues: 1154 sheet: -1.72 (1.93), residues: 9 loop : -2.05 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 313 HIS 0.002 0.000 HIS A 211 PHE 0.005 0.000 PHE A1344 TYR 0.007 0.000 TYR A1251 ARG 0.002 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 381 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 2.195 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: A 1479 PHE cc_start: 0.6209 (t80) cc_final: 0.5880 (t80) REVERT: A 1513 THR cc_start: 0.6685 (t) cc_final: 0.6459 (t) REVERT: A 1574 ILE cc_start: 0.7733 (pp) cc_final: 0.7500 (pt) outliers start: 0 outliers final: 1 residues processed: 381 average time/residue: 2.3407 time to fit residues: 991.3539 Evaluate side-chains 208 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1796 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.0030 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13477 Z= 0.240 Angle : 0.578 9.124 18318 Z= 0.294 Chirality : 0.035 0.160 2153 Planarity : 0.005 0.082 2336 Dihedral : 2.888 15.776 1828 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.86 % Allowed : 12.30 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 0.65 (0.21), residues: 1662 helix: 1.19 (0.15), residues: 1165 sheet: -0.31 (1.95), residues: 9 loop : -1.35 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1203 HIS 0.008 0.001 HIS A 125 PHE 0.024 0.002 PHE A1581 TYR 0.019 0.002 TYR A1008 ARG 0.010 0.001 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 1.935 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: A 542 VAL cc_start: 0.7345 (OUTLIER) cc_final: 0.7036 (t) REVERT: A 1035 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5537 (m-80) REVERT: A 1575 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.5167 (tpt) outliers start: 40 outliers final: 14 residues processed: 241 average time/residue: 2.1680 time to fit residues: 585.8799 Evaluate side-chains 185 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 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 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1120 HIS A1268 GLN A1378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 13477 Z= 0.324 Angle : 0.616 9.445 18318 Z= 0.316 Chirality : 0.037 0.249 2153 Planarity : 0.005 0.058 2336 Dihedral : 3.503 16.271 1826 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.36 % Allowed : 15.02 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 0.72 (0.21), residues: 1662 helix: 1.16 (0.15), residues: 1166 sheet: -0.08 (1.32), residues: 19 loop : -1.13 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1203 HIS 0.009 0.002 HIS A 704 PHE 0.060 0.003 PHE A 543 TYR 0.017 0.002 TYR A1333 ARG 0.009 0.001 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 1.773 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: A 522 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7376 (mm) REVERT: A 542 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7013 (t) REVERT: A 905 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: A 1408 VAL cc_start: 0.4512 (OUTLIER) cc_final: 0.4088 (t) REVERT: A 1575 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5233 (tpt) outliers start: 47 outliers final: 16 residues processed: 218 average time/residue: 2.0994 time to fit residues: 514.4404 Evaluate side-chains 168 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain A residue 1465 HIS Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 264 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13477 Z= 0.307 Angle : 0.617 10.453 18318 Z= 0.313 Chirality : 0.037 0.187 2153 Planarity : 0.005 0.093 2336 Dihedral : 3.723 20.631 1826 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.00 % Allowed : 16.52 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 0.87 (0.21), residues: 1662 helix: 1.27 (0.15), residues: 1163 sheet: -0.02 (1.30), residues: 19 loop : -1.05 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1203 HIS 0.007 0.002 HIS A 288 PHE 0.022 0.002 PHE A 654 TYR 0.017 0.002 TYR A1223 ARG 0.010 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.924 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: A 285 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 387 THR cc_start: 0.7884 (m) cc_final: 0.7644 (p) REVERT: A 522 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7542 (mm) REVERT: A 539 ASP cc_start: 0.6444 (t0) cc_final: 0.5356 (t0) REVERT: A 542 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7583 (t) REVERT: A 1183 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 1408 VAL cc_start: 0.4825 (OUTLIER) cc_final: 0.4537 (t) REVERT: A 1575 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5341 (tpt) outliers start: 42 outliers final: 16 residues processed: 192 average time/residue: 2.2108 time to fit residues: 477.3548 Evaluate side-chains 161 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 264 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN A1447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13477 Z= 0.254 Angle : 0.562 7.338 18318 Z= 0.289 Chirality : 0.035 0.169 2153 Planarity : 0.004 0.056 2336 Dihedral : 3.619 20.363 1826 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.08 % Allowed : 17.17 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 0.99 (0.21), residues: 1662 helix: 1.40 (0.15), residues: 1172 sheet: -0.17 (1.26), residues: 19 loop : -1.16 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1203 HIS 0.008 0.001 HIS A1262 PHE 0.034 0.002 PHE A1208 TYR 0.015 0.002 TYR A 415 ARG 0.009 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 2.042 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: A 252 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: A 387 THR cc_start: 0.7946 (m) cc_final: 0.7738 (p) REVERT: A 522 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7553 (mm) REVERT: A 542 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7556 (t) REVERT: A 701 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6748 (pp20) REVERT: A 1175 MET cc_start: 0.7421 (mpt) cc_final: 0.6586 (mpt) REVERT: A 1382 TYR cc_start: 0.7486 (m-10) cc_final: 0.7193 (m-10) REVERT: A 1406 GLN cc_start: 0.7123 (tt0) cc_final: 0.6532 (mp10) REVERT: A 1575 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5336 (tpt) outliers start: 43 outliers final: 14 residues processed: 180 average time/residue: 2.0599 time to fit residues: 417.8323 Evaluate side-chains 161 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.8165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13477 Z= 0.270 Angle : 0.573 7.683 18318 Z= 0.296 Chirality : 0.035 0.156 2153 Planarity : 0.004 0.056 2336 Dihedral : 3.720 21.982 1826 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.93 % Allowed : 17.31 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.02 (0.21), residues: 1662 helix: 1.39 (0.15), residues: 1174 sheet: -0.08 (1.27), residues: 19 loop : -1.07 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1203 HIS 0.006 0.001 HIS A 125 PHE 0.038 0.002 PHE A1208 TYR 0.021 0.002 TYR A 415 ARG 0.005 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 2.080 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: A 387 THR cc_start: 0.8024 (m) cc_final: 0.7789 (p) REVERT: A 542 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7413 (t) REVERT: A 701 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6846 (pp20) REVERT: A 1314 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7901 (t) REVERT: A 1575 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5229 (tpt) REVERT: A 1627 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: B 269 GLU cc_start: 0.7238 (mp0) cc_final: 0.6647 (tm-30) outliers start: 41 outliers final: 21 residues processed: 185 average time/residue: 2.1584 time to fit residues: 455.5408 Evaluate side-chains 170 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1627 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 162 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 482 GLN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.8315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13477 Z= 0.198 Angle : 0.546 6.607 18318 Z= 0.278 Chirality : 0.034 0.165 2153 Planarity : 0.004 0.059 2336 Dihedral : 3.592 20.980 1826 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.79 % Allowed : 18.10 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.24 (0.21), residues: 1662 helix: 1.57 (0.15), residues: 1181 sheet: -0.14 (1.22), residues: 19 loop : -1.05 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1203 HIS 0.013 0.001 HIS A1262 PHE 0.046 0.002 PHE A 543 TYR 0.014 0.001 TYR A 415 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 2.249 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: A 387 THR cc_start: 0.8004 (m) cc_final: 0.7784 (p) REVERT: A 542 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7436 (t) REVERT: A 701 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6762 (pp20) REVERT: A 1386 GLU cc_start: 0.5753 (pt0) cc_final: 0.5513 (pt0) REVERT: A 1575 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.5192 (tpt) REVERT: A 1627 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: B 252 LEU cc_start: 0.1544 (OUTLIER) cc_final: 0.1132 (mt) REVERT: B 269 GLU cc_start: 0.7287 (mp0) cc_final: 0.6801 (tm-30) outliers start: 39 outliers final: 22 residues processed: 177 average time/residue: 2.2169 time to fit residues: 440.8821 Evaluate side-chains 171 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1627 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 103 optimal weight: 0.0470 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 482 GLN A 538 GLN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.8435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13477 Z= 0.224 Angle : 0.556 7.660 18318 Z= 0.282 Chirality : 0.034 0.159 2153 Planarity : 0.004 0.060 2336 Dihedral : 3.627 21.272 1826 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.65 % Allowed : 18.17 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.29 (0.21), residues: 1662 helix: 1.60 (0.15), residues: 1183 sheet: -0.18 (1.20), residues: 19 loop : -1.02 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1203 HIS 0.014 0.001 HIS A1262 PHE 0.037 0.002 PHE A 543 TYR 0.014 0.001 TYR A 415 ARG 0.007 0.000 ARG A1285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 1.979 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: A 387 THR cc_start: 0.8009 (m) cc_final: 0.7785 (p) REVERT: A 701 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: A 1386 GLU cc_start: 0.5827 (pt0) cc_final: 0.5586 (pt0) REVERT: A 1416 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: A 1575 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5144 (tpt) REVERT: A 1710 PHE cc_start: 0.2497 (m-80) cc_final: 0.1887 (m-10) REVERT: B 252 LEU cc_start: 0.1690 (OUTLIER) cc_final: 0.1262 (mt) REVERT: B 269 GLU cc_start: 0.7239 (mp0) cc_final: 0.6800 (tm-30) outliers start: 37 outliers final: 24 residues processed: 177 average time/residue: 2.2498 time to fit residues: 445.9928 Evaluate side-chains 173 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 chunk 160 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 409 HIS A 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.8524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13477 Z= 0.196 Angle : 0.551 10.863 18318 Z= 0.276 Chirality : 0.034 0.164 2153 Planarity : 0.004 0.060 2336 Dihedral : 3.571 20.885 1826 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.36 % Allowed : 18.74 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.42 (0.21), residues: 1662 helix: 1.70 (0.15), residues: 1182 sheet: -0.16 (1.19), residues: 19 loop : -0.97 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1203 HIS 0.013 0.001 HIS A1262 PHE 0.033 0.002 PHE A 543 TYR 0.016 0.001 TYR A 415 ARG 0.004 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 2.129 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: A 387 THR cc_start: 0.8033 (m) cc_final: 0.7797 (p) REVERT: A 701 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6733 (pp20) REVERT: A 1386 GLU cc_start: 0.5798 (pt0) cc_final: 0.5554 (pt0) REVERT: A 1406 GLN cc_start: 0.7406 (tt0) cc_final: 0.7090 (mp10) REVERT: A 1575 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5022 (tpt) REVERT: A 1710 PHE cc_start: 0.2532 (m-80) cc_final: 0.1925 (m-10) REVERT: B 252 LEU cc_start: 0.1779 (OUTLIER) cc_final: 0.1362 (mt) REVERT: B 269 GLU cc_start: 0.7262 (mp0) cc_final: 0.6865 (tm-30) outliers start: 33 outliers final: 20 residues processed: 168 average time/residue: 2.2713 time to fit residues: 429.1262 Evaluate side-chains 162 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 482 GLN A 538 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.8704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13477 Z= 0.232 Angle : 0.567 9.586 18318 Z= 0.288 Chirality : 0.034 0.155 2153 Planarity : 0.004 0.065 2336 Dihedral : 3.649 21.496 1826 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.86 % Allowed : 19.17 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.35 (0.21), residues: 1662 helix: 1.65 (0.15), residues: 1183 sheet: -0.22 (1.16), residues: 19 loop : -1.02 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1203 HIS 0.016 0.001 HIS A1262 PHE 0.045 0.002 PHE A 543 TYR 0.018 0.002 TYR A 415 ARG 0.015 0.000 ARG A 689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 2.171 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: A 387 THR cc_start: 0.8038 (m) cc_final: 0.7798 (p) REVERT: A 526 ASP cc_start: 0.6895 (m-30) cc_final: 0.6440 (m-30) REVERT: A 701 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6775 (pp20) REVERT: A 1289 MET cc_start: 0.6319 (mtm) cc_final: 0.5896 (mtm) REVERT: A 1406 GLN cc_start: 0.7390 (tt0) cc_final: 0.7107 (mp10) REVERT: A 1575 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5033 (tpt) REVERT: B 252 LEU cc_start: 0.1656 (OUTLIER) cc_final: 0.1235 (mt) REVERT: B 269 GLU cc_start: 0.7309 (mp0) cc_final: 0.6912 (tm-30) outliers start: 26 outliers final: 21 residues processed: 163 average time/residue: 2.3710 time to fit residues: 430.7510 Evaluate side-chains 165 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1575 MET Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.150024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.117863 restraints weight = 65723.812| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.77 r_work: 0.3724 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13477 Z= 0.289 Angle : 0.592 9.664 18318 Z= 0.304 Chirality : 0.036 0.184 2153 Planarity : 0.005 0.060 2336 Dihedral : 3.751 22.385 1826 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.29 % Allowed : 18.60 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.21 (0.21), residues: 1662 helix: 1.54 (0.15), residues: 1183 sheet: -0.29 (1.15), residues: 19 loop : -1.04 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1203 HIS 0.018 0.001 HIS A1262 PHE 0.024 0.002 PHE A1208 TYR 0.020 0.002 TYR A 415 ARG 0.011 0.000 ARG A 689 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10069.88 seconds wall clock time: 176 minutes 0.07 seconds (10560.07 seconds total)