Starting phenix.real_space_refine on Sat Jul 27 05:24:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/07_2024/7oim_12932_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/07_2024/7oim_12932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/07_2024/7oim_12932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/07_2024/7oim_12932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/07_2024/7oim_12932_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/07_2024/7oim_12932_neut.cif" } resolution = 4.0 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= 0.001 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 8 5.49 5 Mg 1 5.21 5 S 211 5.16 5 C 22671 2.51 5 N 6108 2.21 5 O 6596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3993": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 1.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 35597 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 35505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4426, 35505 Classifications: {'peptide': 4426} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 183, 'TRANS': 4242} Chain breaks: 15 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1, 'AGS': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26526 SG CYS A3962 90.965 134.860 220.574 1.00156.31 S ATOM 26690 SG CYS A3982 88.838 133.051 223.422 1.00148.05 S ATOM 26715 SG CYS A3985 92.641 133.384 223.408 1.00156.00 S ATOM 26416 SG CYS A3947 81.021 128.628 219.242 1.00126.19 S ATOM 26441 SG CYS A3950 78.901 125.352 217.540 1.00126.72 S ATOM 26569 SG CYS A3967 78.504 127.837 215.770 1.00139.40 S Time building chain proxies: 17.60, per 1000 atoms: 0.49 Number of scatterers: 35597 At special positions: 0 Unit cell: (129.519, 155.844, 244.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 211 16.00 P 8 15.00 Mg 1 11.99 O 6596 8.00 N 6108 7.00 C 22671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " distance=2.03 Simple disulfide: pdb=" SG CYS A2605 " - pdb=" SG CYS A2653 " distance=2.03 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: 14.32 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 3 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8472 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 15 sheets defined 60.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 492 through 512 removed outlier: 3.545A pdb=" N VAL A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 535 removed outlier: 3.761A pdb=" N SER A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 removed outlier: 3.938A pdb=" N VAL A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.902A pdb=" N CYS A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.626A pdb=" N HIS A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.666A pdb=" N ILE A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 removed outlier: 4.180A pdb=" N LEU A 665 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.512A pdb=" N LEU A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 694 removed outlier: 4.006A pdb=" N TRP A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 4.122A pdb=" N GLU A 702 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 720 removed outlier: 3.934A pdb=" N GLN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 4.441A pdb=" N ARG A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.552A pdb=" N TYR A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.771A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 removed outlier: 4.082A pdb=" N ASP A 763 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 801 removed outlier: 3.789A pdb=" N LYS A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 827 Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.817A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 889 removed outlier: 3.500A pdb=" N SER A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 917 Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.914A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 982 Processing helix chain 'A' and resid 994 through 1010 Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1032 through 1044 removed outlier: 3.960A pdb=" N GLN A1036 " --> pdb=" O PRO A1032 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 removed outlier: 4.080A pdb=" N ILE A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1044 through 1049' Processing helix chain 'A' and resid 1053 through 1072 Processing helix chain 'A' and resid 1079 through 1089 Processing helix chain 'A' and resid 1089 through 1102 removed outlier: 3.767A pdb=" N ARG A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1143 Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.553A pdb=" N ILE A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1171 removed outlier: 3.642A pdb=" N ALA A1171 " --> pdb=" O LEU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1203 removed outlier: 3.883A pdb=" N ARG A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1234 through 1241 removed outlier: 3.903A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1257 removed outlier: 4.044A pdb=" N CYS A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 removed outlier: 3.674A pdb=" N VAL A1266 " --> pdb=" O THR A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1274 removed outlier: 4.192A pdb=" N VAL A1274 " --> pdb=" O LYS A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1271 through 1274' Processing helix chain 'A' and resid 1277 through 1289 Processing helix chain 'A' and resid 1298 through 1329 removed outlier: 3.926A pdb=" N ARG A1302 " --> pdb=" O TRP A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1346 removed outlier: 3.766A pdb=" N LEU A1342 " --> pdb=" O LEU A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1368 Processing helix chain 'A' and resid 1369 through 1371 No H-bonds generated for 'chain 'A' and resid 1369 through 1371' Processing helix chain 'A' and resid 1377 through 1387 Processing helix chain 'A' and resid 1388 through 1398 removed outlier: 3.551A pdb=" N LEU A1398 " --> pdb=" O LEU A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1402 No H-bonds generated for 'chain 'A' and resid 1400 through 1402' Processing helix chain 'A' and resid 1403 through 1415 removed outlier: 4.090A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1440 removed outlier: 4.592A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1464 removed outlier: 3.682A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A1464 " --> pdb=" O ARG A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1477 Processing helix chain 'A' and resid 1478 through 1487 removed outlier: 4.554A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A1487 " --> pdb=" O LYS A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1507 Processing helix chain 'A' and resid 1544 through 1557 removed outlier: 3.839A pdb=" N LEU A1557 " --> pdb=" O ASN A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1594 removed outlier: 4.049A pdb=" N ASN A1567 " --> pdb=" O ASP A1563 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A1594 " --> pdb=" O LEU A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1658 removed outlier: 3.887A pdb=" N LEU A1634 " --> pdb=" O ASP A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1665 removed outlier: 3.691A pdb=" N PHE A1665 " --> pdb=" O TYR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1678 Processing helix chain 'A' and resid 1684 through 1691 Processing helix chain 'A' and resid 1699 through 1709 removed outlier: 3.673A pdb=" N ALA A1709 " --> pdb=" O GLN A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1713 through 1726 removed outlier: 3.564A pdb=" N TYR A1717 " --> pdb=" O LYS A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1729 through 1733 removed outlier: 3.513A pdb=" N SER A1732 " --> pdb=" O GLN A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1736 through 1750 Processing helix chain 'A' and resid 1760 through 1775 Processing helix chain 'A' and resid 1798 through 1801 Processing helix chain 'A' and resid 1802 through 1811 removed outlier: 3.631A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1844 removed outlier: 4.052A pdb=" N VAL A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A1844 " --> pdb=" O LEU A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1862 removed outlier: 3.620A pdb=" N LEU A1862 " --> pdb=" O ALA A1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1859 through 1862' Processing helix chain 'A' and resid 1863 through 1881 Processing helix chain 'A' and resid 1900 through 1905 Processing helix chain 'A' and resid 1906 through 1909 removed outlier: 3.549A pdb=" N LYS A1909 " --> pdb=" O SER A1906 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1906 through 1909' Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1938 through 1942 removed outlier: 4.040A pdb=" N VAL A1941 " --> pdb=" O ALA A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1974 Processing helix chain 'A' and resid 1993 through 2002 removed outlier: 4.139A pdb=" N VAL A1997 " --> pdb=" O ASP A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2037 removed outlier: 3.815A pdb=" N PHE A2031 " --> pdb=" O GLY A2027 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2081 through 2085 Processing helix chain 'A' and resid 2116 through 2121 Processing helix chain 'A' and resid 2122 through 2137 Proline residue: A2128 - end of helix removed outlier: 4.137A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A2137 " --> pdb=" O LYS A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2165 Processing helix chain 'A' and resid 2172 through 2193 removed outlier: 3.915A pdb=" N LEU A2176 " --> pdb=" O SER A2172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A2193 " --> pdb=" O ASP A2189 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2203 Processing helix chain 'A' and resid 2207 through 2224 removed outlier: 3.823A pdb=" N PHE A2211 " --> pdb=" O GLY A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2255 removed outlier: 3.721A pdb=" N LEU A2255 " --> pdb=" O ALA A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2319 removed outlier: 4.206A pdb=" N PHE A2312 " --> pdb=" O THR A2308 " (cutoff:3.500A) Processing helix chain 'A' and resid 2330 through 2343 Processing helix chain 'A' and resid 2358 through 2374 removed outlier: 4.083A pdb=" N ILE A2364 " --> pdb=" O ASN A2360 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A2374 " --> pdb=" O ARG A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2400 Processing helix chain 'A' and resid 2417 through 2439 removed outlier: 3.843A pdb=" N ILE A2421 " --> pdb=" O THR A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2464 removed outlier: 3.813A pdb=" N LEU A2463 " --> pdb=" O ILE A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2500 Processing helix chain 'A' and resid 2521 through 2525 removed outlier: 3.699A pdb=" N GLN A2524 " --> pdb=" O PRO A2521 " (cutoff:3.500A) Processing helix chain 'A' and resid 2536 through 2540 removed outlier: 3.853A pdb=" N VAL A2540 " --> pdb=" O ILE A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2550 through 2563 Processing helix chain 'A' and resid 2571 through 2589 removed outlier: 4.071A pdb=" N VAL A2575 " --> pdb=" O SER A2571 " (cutoff:3.500A) Processing helix chain 'A' and resid 2605 through 2615 Processing helix chain 'A' and resid 2618 through 2630 Processing helix chain 'A' and resid 2642 through 2654 Processing helix chain 'A' and resid 2660 through 2669 Processing helix chain 'A' and resid 2673 through 2677 removed outlier: 3.586A pdb=" N ASN A2677 " --> pdb=" O LYS A2674 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2696 removed outlier: 3.738A pdb=" N ILE A2682 " --> pdb=" O SER A2678 " (cutoff:3.500A) Processing helix chain 'A' and resid 2706 through 2722 removed outlier: 3.558A pdb=" N LYS A2710 " --> pdb=" O ASN A2706 " (cutoff:3.500A) Processing helix chain 'A' and resid 2736 through 2747 Processing helix chain 'A' and resid 2756 through 2760 Processing helix chain 'A' and resid 2775 through 2791 removed outlier: 4.004A pdb=" N ILE A2779 " --> pdb=" O THR A2775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2816 through 2819 removed outlier: 3.916A pdb=" N LYS A2819 " --> pdb=" O MET A2816 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2816 through 2819' Processing helix chain 'A' and resid 2820 through 2825 removed outlier: 3.721A pdb=" N LEU A2824 " --> pdb=" O THR A2820 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2878 Processing helix chain 'A' and resid 2883 through 2889 removed outlier: 3.698A pdb=" N ASP A2887 " --> pdb=" O ARG A2883 " (cutoff:3.500A) Processing helix chain 'A' and resid 2892 through 2907 Processing helix chain 'A' and resid 2913 through 2932 removed outlier: 3.915A pdb=" N TYR A2917 " --> pdb=" O GLY A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2948 removed outlier: 3.689A pdb=" N ILE A2940 " --> pdb=" O SER A2936 " (cutoff:3.500A) Processing helix chain 'A' and resid 2955 through 2963 removed outlier: 3.634A pdb=" N SER A2963 " --> pdb=" O ILE A2959 " (cutoff:3.500A) Processing helix chain 'A' and resid 2974 through 2984 removed outlier: 3.851A pdb=" N LEU A2978 " --> pdb=" O SER A2974 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3018 removed outlier: 3.660A pdb=" N ILE A3014 " --> pdb=" O VAL A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3037 through 3056 Processing helix chain 'A' and resid 3073 through 3077 removed outlier: 3.523A pdb=" N ASN A3076 " --> pdb=" O ASP A3073 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A3077 " --> pdb=" O ALA A3074 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3073 through 3077' Processing helix chain 'A' and resid 3113 through 3119 Processing helix chain 'A' and resid 3122 through 3128 removed outlier: 3.644A pdb=" N ASN A3126 " --> pdb=" O VAL A3122 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A3127 " --> pdb=" O PRO A3123 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A3128 " --> pdb=" O LEU A3124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3122 through 3128' Processing helix chain 'A' and resid 3140 through 3159 Processing helix chain 'A' and resid 3172 through 3177 Processing helix chain 'A' and resid 3183 through 3197 removed outlier: 3.860A pdb=" N SER A3187 " --> pdb=" O ASP A3183 " (cutoff:3.500A) Processing helix chain 'A' and resid 3203 through 3219 removed outlier: 4.022A pdb=" N ARG A3207 " --> pdb=" O GLU A3203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A3208 " --> pdb=" O GLU A3204 " (cutoff:3.500A) Processing helix chain 'A' and resid 3222 through 3229 Processing helix chain 'A' and resid 3230 through 3232 No H-bonds generated for 'chain 'A' and resid 3230 through 3232' Processing helix chain 'A' and resid 3236 through 3249 Processing helix chain 'A' and resid 3254 through 3264 removed outlier: 4.088A pdb=" N ARG A3264 " --> pdb=" O GLN A3260 " (cutoff:3.500A) Processing helix chain 'A' and resid 3287 through 3295 Processing helix chain 'A' and resid 3313 through 3326 removed outlier: 3.950A pdb=" N PHE A3317 " --> pdb=" O THR A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3348 through 3365 removed outlier: 4.503A pdb=" N SER A3352 " --> pdb=" O GLN A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3413 through 3420 removed outlier: 3.826A pdb=" N LEU A3417 " --> pdb=" O ASP A3413 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A3420 " --> pdb=" O LYS A3416 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3427 removed outlier: 3.688A pdb=" N LYS A3427 " --> pdb=" O GLN A3424 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3490 removed outlier: 5.012A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) Processing helix chain 'A' and resid 3501 through 3512 Processing helix chain 'A' and resid 3517 through 3539 Processing helix chain 'A' and resid 3548 through 3555 Processing helix chain 'A' and resid 3556 through 3564 Processing helix chain 'A' and resid 3565 through 3590 Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3595 through 3600 Processing helix chain 'A' and resid 3604 through 3615 removed outlier: 3.936A pdb=" N GLN A3608 " --> pdb=" O PRO A3604 " (cutoff:3.500A) Processing helix chain 'A' and resid 3657 through 3676 removed outlier: 4.061A pdb=" N ILE A3661 " --> pdb=" O PHE A3657 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3691 Processing helix chain 'A' and resid 3692 through 3699 Processing helix chain 'A' and resid 3702 through 3722 Processing helix chain 'A' and resid 3727 through 3746 Processing helix chain 'A' and resid 3762 through 3784 removed outlier: 7.657A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3800 removed outlier: 3.737A pdb=" N SER A3791 " --> pdb=" O GLN A3787 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A3794 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A3796 " --> pdb=" O LEU A3792 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU A3797 " --> pdb=" O SER A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3807 through 3824 removed outlier: 3.884A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A3824 " --> pdb=" O LEU A3820 " (cutoff:3.500A) Processing helix chain 'A' and resid 3828 through 3839 Processing helix chain 'A' and resid 3839 through 3847 removed outlier: 3.646A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3856 through 3890 removed outlier: 5.225A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3894 through 3910 removed outlier: 4.077A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A3910 " --> pdb=" O ASP A3906 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3941 removed outlier: 4.165A pdb=" N PHE A3921 " --> pdb=" O THR A3917 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A3941 " --> pdb=" O LYS A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3975 Processing helix chain 'A' and resid 4000 through 4026 Processing helix chain 'A' and resid 4035 through 4045 removed outlier: 3.697A pdb=" N ILE A4039 " --> pdb=" O GLU A4035 " (cutoff:3.500A) Processing helix chain 'A' and resid 4082 through 4089 Processing helix chain 'A' and resid 4092 through 4095 removed outlier: 3.575A pdb=" N GLU A4095 " --> pdb=" O SER A4092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4092 through 4095' Processing helix chain 'A' and resid 4096 through 4111 removed outlier: 3.760A pdb=" N ILE A4100 " --> pdb=" O VAL A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4116 through 4138 removed outlier: 4.312A pdb=" N LEU A4120 " --> pdb=" O ASP A4116 " (cutoff:3.500A) Processing helix chain 'A' and resid 4142 through 4156 removed outlier: 3.824A pdb=" N VAL A4146 " --> pdb=" O ASN A4142 " (cutoff:3.500A) Processing helix chain 'A' and resid 4171 through 4198 removed outlier: 3.643A pdb=" N GLU A4197 " --> pdb=" O SER A4193 " (cutoff:3.500A) Processing helix chain 'A' and resid 4204 through 4219 Processing helix chain 'A' and resid 4222 through 4236 Processing helix chain 'A' and resid 4237 through 4245 removed outlier: 3.814A pdb=" N VAL A4241 " --> pdb=" O GLY A4237 " (cutoff:3.500A) Processing helix chain 'A' and resid 4251 through 4255 removed outlier: 3.516A pdb=" N VAL A4254 " --> pdb=" O CYS A4251 " (cutoff:3.500A) Processing helix chain 'A' and resid 4256 through 4262 removed outlier: 4.013A pdb=" N ILE A4260 " --> pdb=" O PRO A4256 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A4262 " --> pdb=" O LYS A4258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4256 through 4262' Processing helix chain 'A' and resid 4271 through 4276 removed outlier: 3.664A pdb=" N LEU A4274 " --> pdb=" O ASP A4271 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A4275 " --> pdb=" O ARG A4272 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A4276 " --> pdb=" O TYR A4273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4271 through 4276' Processing helix chain 'A' and resid 4279 through 4293 removed outlier: 3.867A pdb=" N VAL A4283 " --> pdb=" O GLU A4279 " (cutoff:3.500A) Processing helix chain 'A' and resid 4296 through 4305 removed outlier: 4.192A pdb=" N GLY A4300 " --> pdb=" O THR A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4309 through 4331 removed outlier: 3.759A pdb=" N GLN A4313 " --> pdb=" O PRO A4309 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) Processing helix chain 'A' and resid 4342 through 4353 Processing helix chain 'A' and resid 4358 through 4370 removed outlier: 3.743A pdb=" N SER A4367 " --> pdb=" O CYS A4363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A4370 " --> pdb=" O ARG A4366 " (cutoff:3.500A) Processing helix chain 'A' and resid 4384 through 4403 removed outlier: 3.952A pdb=" N THR A4388 " --> pdb=" O ILE A4384 " (cutoff:3.500A) Processing helix chain 'A' and resid 4405 through 4407 No H-bonds generated for 'chain 'A' and resid 4405 through 4407' Processing helix chain 'A' and resid 4408 through 4417 removed outlier: 3.676A pdb=" N ASN A4413 " --> pdb=" O LYS A4409 " (cutoff:3.500A) Processing helix chain 'A' and resid 4418 through 4421 Processing helix chain 'A' and resid 4522 through 4542 Processing helix chain 'A' and resid 4544 through 4552 removed outlier: 3.680A pdb=" N LEU A4548 " --> pdb=" O ASN A4544 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4578 Processing helix chain 'A' and resid 4581 through 4596 Processing helix chain 'A' and resid 4613 through 4633 Processing helix chain 'A' and resid 4638 through 4648 Processing helix chain 'A' and resid 4655 through 4660 removed outlier: 4.063A pdb=" N LYS A4659 " --> pdb=" O ASN A4655 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A4660 " --> pdb=" O PRO A4656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4655 through 4660' Processing helix chain 'A' and resid 4665 through 4669 removed outlier: 4.201A pdb=" N PHE A4668 " --> pdb=" O PRO A4665 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A4669 " --> pdb=" O ALA A4666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4665 through 4669' Processing helix chain 'A' and resid 4691 through 4702 removed outlier: 3.503A pdb=" N LEU A4695 " --> pdb=" O THR A4691 " (cutoff:3.500A) Processing helix chain 'A' and resid 4708 through 4717 removed outlier: 3.661A pdb=" N TRP A4712 " --> pdb=" O VAL A4708 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A4717 " --> pdb=" O HIS A4713 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4722 Processing helix chain 'A' and resid 4723 through 4725 No H-bonds generated for 'chain 'A' and resid 4723 through 4725' Processing helix chain 'A' and resid 4726 through 4741 Processing helix chain 'A' and resid 4751 through 4757 Processing helix chain 'A' and resid 4761 through 4783 Processing helix chain 'A' and resid 4785 through 4790 Processing helix chain 'A' and resid 4820 through 4845 removed outlier: 4.035A pdb=" N THR A4824 " --> pdb=" O GLY A4820 " (cutoff:3.500A) Processing helix chain 'A' and resid 4859 through 4863 removed outlier: 3.755A pdb=" N HIS A4862 " --> pdb=" O ALA A4859 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A4863 " --> pdb=" O ASP A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4859 through 4863' Processing helix chain 'A' and resid 4872 through 4878 Processing helix chain 'A' and resid 4895 through 4905 removed outlier: 3.592A pdb=" N ILE A4899 " --> pdb=" O ASP A4895 " (cutoff:3.500A) Processing helix chain 'A' and resid 4930 through 4941 Processing helix chain 'A' and resid 4947 through 4957 removed outlier: 3.930A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4960 through 4980 removed outlier: 3.575A pdb=" N ALA A4964 " --> pdb=" O SER A4960 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A4980 " --> pdb=" O GLY A4976 " (cutoff:3.500A) Processing helix chain 'A' and resid 4989 through 4994 Processing helix chain 'A' and resid 5003 through 5011 removed outlier: 3.891A pdb=" N LEU A5007 " --> pdb=" O THR A5003 " (cutoff:3.500A) Processing helix chain 'A' and resid 5017 through 5036 Processing helix chain 'A' and resid 5045 through 5049 removed outlier: 3.760A pdb=" N TYR A5048 " --> pdb=" O ASP A5045 " (cutoff:3.500A) Processing helix chain 'A' and resid 5053 through 5066 removed outlier: 4.180A pdb=" N GLU A5066 " --> pdb=" O THR A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5068 through 5084 removed outlier: 4.739A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5098 through 5107 removed outlier: 3.582A pdb=" N THR A5102 " --> pdb=" O SER A5098 " (cutoff:3.500A) Processing helix chain 'A' and resid 5115 through 5121 Processing helix chain 'A' and resid 5131 through 5149 removed outlier: 3.701A pdb=" N TRP A5135 " --> pdb=" O CYS A5131 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A5149 " --> pdb=" O ARG A5145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 6.456A pdb=" N GLN A1149 " --> pdb=" O VAL A1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1541 through 1543 removed outlier: 3.615A pdb=" N LEU A1625 " --> pdb=" O MET A1615 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1793 through 1796 removed outlier: 6.316A pdb=" N TYR A1854 " --> pdb=" O VAL A1889 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A1891 " --> pdb=" O TYR A1854 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A1856 " --> pdb=" O LEU A1891 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1982 through 1987 removed outlier: 3.617A pdb=" N ILE A1985 " --> pdb=" O HIS A2017 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A2020 " --> pdb=" O GLU A2060 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A1951 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A1953 " --> pdb=" O ILE A2061 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id=AA6, first strand: chain 'A' and resid 2266 through 2269 removed outlier: 4.000A pdb=" N PHE A2268 " --> pdb=" O THR A2277 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A2277 " --> pdb=" O PHE A2268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id=AA8, first strand: chain 'A' and resid 2407 through 2411 removed outlier: 6.779A pdb=" N VAL A2377 " --> pdb=" O ALA A2483 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS A2485 " --> pdb=" O VAL A2377 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A2379 " --> pdb=" O CYS A2485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP A2541 " --> pdb=" O ILE A2378 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A2380 " --> pdb=" O TRP A2541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2467 through 2468 Processing sheet with id=AB1, first strand: chain 'A' and resid 2763 through 2767 Processing sheet with id=AB2, first strand: chain 'A' and resid 3026 through 3028 removed outlier: 6.746A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A3110 " --> pdb=" O VAL A3059 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A3061 " --> pdb=" O ILE A3110 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A3111 " --> pdb=" O VAL A3004 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A3006 " --> pdb=" O GLU A3111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3086 through 3091 removed outlier: 4.248A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3304 through 3307 removed outlier: 5.813A pdb=" N VAL A3304 " --> pdb=" O VAL A3335 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLN A3337 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU A3306 " --> pdb=" O GLN A3337 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP A3339 " --> pdb=" O LEU A3306 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL A3399 " --> pdb=" O PHE A3274 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A3276 " --> pdb=" O VAL A3399 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3958 through 3959 Processing sheet with id=AB6, first strand: chain 'A' and resid 4880 through 4883 1746 hydrogen bonds defined for protein. 5136 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: 20.60 Time building geometry restraints manager: 15.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10804 1.34 - 1.49: 9902 1.49 - 1.64: 15321 1.64 - 1.80: 135 1.80 - 1.95: 175 Bond restraints: 36337 Sorted by residual: bond pdb=" C ALA A3411 " pdb=" N SER A3412 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.13e-02 7.83e+03 1.17e+01 bond pdb=" C THR A3415 " pdb=" N LYS A3416 " ideal model delta sigma weight residual 1.335 1.294 0.041 1.30e-02 5.92e+03 9.89e+00 bond pdb=" C LYS A2731 " pdb=" N PRO A2732 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.12e-02 7.97e+03 8.33e+00 bond pdb=" CA ILE A1901 " pdb=" CB ILE A1901 " ideal model delta sigma weight residual 1.534 1.553 -0.018 6.80e-03 2.16e+04 7.28e+00 bond pdb=" N GLN A4701 " pdb=" CA GLN A4701 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.23e-02 6.61e+03 5.74e+00 ... (remaining 36332 not shown) Histogram of bond angle deviations from ideal: 95.48 - 104.34: 573 104.34 - 113.20: 19141 113.20 - 122.07: 22850 122.07 - 130.93: 6378 130.93 - 139.80: 233 Bond angle restraints: 49175 Sorted by residual: angle pdb=" O LEU A1494 " pdb=" C LEU A1494 " pdb=" N SER A1495 " ideal model delta sigma weight residual 122.59 137.07 -14.48 1.33e+00 5.65e-01 1.18e+02 angle pdb=" CA GLN A4701 " pdb=" CB GLN A4701 " pdb=" CG GLN A4701 " ideal model delta sigma weight residual 114.10 132.05 -17.95 2.00e+00 2.50e-01 8.05e+01 angle pdb=" CA LEU A1494 " pdb=" C LEU A1494 " pdb=" N SER A1495 " ideal model delta sigma weight residual 116.84 103.37 13.47 1.71e+00 3.42e-01 6.20e+01 angle pdb=" C PRO A3121 " pdb=" N VAL A3122 " pdb=" CA VAL A3122 " ideal model delta sigma weight residual 122.13 136.42 -14.29 1.85e+00 2.92e-01 5.97e+01 angle pdb=" N GLN A4701 " pdb=" CA GLN A4701 " pdb=" CB GLN A4701 " ideal model delta sigma weight residual 110.16 121.11 -10.95 1.48e+00 4.57e-01 5.47e+01 ... (remaining 49170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.22: 21209 27.22 - 54.43: 817 54.43 - 81.65: 91 81.65 - 108.86: 13 108.86 - 136.08: 3 Dihedral angle restraints: 22133 sinusoidal: 9121 harmonic: 13012 Sorted by residual: dihedral pdb=" CA GLU A1170 " pdb=" C GLU A1170 " pdb=" N ALA A1171 " pdb=" CA ALA A1171 " ideal model delta harmonic sigma weight residual 180.00 133.29 46.71 0 5.00e+00 4.00e-02 8.73e+01 dihedral pdb=" CA GLU A4165 " pdb=" C GLU A4165 " pdb=" N PRO A4166 " pdb=" CA PRO A4166 " ideal model delta harmonic sigma weight residual -180.00 -136.97 -43.03 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CA GLU A1016 " pdb=" C GLU A1016 " pdb=" N PRO A1017 " pdb=" CA PRO A1017 " ideal model delta harmonic sigma weight residual 180.00 144.32 35.68 0 5.00e+00 4.00e-02 5.09e+01 ... (remaining 22130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4885 0.106 - 0.211: 583 0.211 - 0.317: 62 0.317 - 0.422: 14 0.422 - 0.528: 4 Chirality restraints: 5548 Sorted by residual: chirality pdb=" CB ILE A4792 " pdb=" CA ILE A4792 " pdb=" CG1 ILE A4792 " pdb=" CG2 ILE A4792 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA GLU A4700 " pdb=" N GLU A4700 " pdb=" C GLU A4700 " pdb=" CB GLU A4700 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CB VAL A3543 " pdb=" CA VAL A3543 " pdb=" CG1 VAL A3543 " pdb=" CG2 VAL A3543 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 5545 not shown) Planarity restraints: 6274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1031 " 0.039 2.00e-02 2.50e+03 3.97e-02 3.94e+01 pdb=" CG TRP A1031 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TRP A1031 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1031 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1031 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP A1031 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A5104 " -0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C VAL A5104 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A5104 " -0.033 2.00e-02 2.50e+03 pdb=" N SER A5105 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A4322 " 0.042 2.00e-02 2.50e+03 3.45e-02 2.38e+01 pdb=" CG TYR A4322 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TYR A4322 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A4322 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A4322 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A4322 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A4322 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A4322 " -0.003 2.00e-02 2.50e+03 ... (remaining 6271 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 365 2.64 - 3.20: 30336 3.20 - 3.77: 55364 3.77 - 4.33: 71365 4.33 - 4.90: 116526 Nonbonded interactions: 273956 Sorted by model distance: nonbonded pdb=" OE1 GLU A1417 " pdb=" OG SER A1496 " model vdw 2.069 2.440 nonbonded pdb=" O GLY A 936 " pdb=" OG1 THR A3238 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLU A3562 " pdb=" OH TYR A4961 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR A1988 " pdb=" OG SER A2457 " model vdw 2.277 2.440 nonbonded pdb=" O THR A2406 " pdb=" OG1 THR A2443 " model vdw 2.278 2.440 ... (remaining 273951 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.030 Extract box with map and model: 1.400 Check model and map are aligned: 0.250 Set scattering table: 0.360 Process input model: 103.470 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 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 : 0.006 0.078 36337 Z= 0.361 Angle : 1.319 20.633 49175 Z= 0.680 Chirality : 0.071 0.528 5548 Planarity : 0.008 0.109 6274 Dihedral : 14.126 136.076 13655 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.15 % Favored : 91.67 % Rotamer: Outliers : 0.05 % Allowed : 1.23 % Favored : 98.72 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.09 % 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: -3.63 (0.10), residues: 4394 helix: -2.04 (0.08), residues: 2432 sheet: -1.36 (0.32), residues: 237 loop : -2.96 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.003 TRP A1031 HIS 0.013 0.001 HIS A4590 PHE 0.067 0.003 PHE A 607 TYR 0.084 0.002 TYR A4322 ARG 0.027 0.001 ARG A4002 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4592 ILE cc_start: 0.7811 (mm) cc_final: 0.7575 (tp) REVERT: A 4696 GLN cc_start: 0.8392 (tt0) cc_final: 0.8131 (tp-100) outliers start: 2 outliers final: 1 residues processed: 392 average time/residue: 0.4918 time to fit residues: 315.5397 Evaluate side-chains 233 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4842 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 185 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 210 optimal weight: 0.7980 chunk 257 optimal weight: 0.0670 chunk 401 optimal weight: 9.9990 overall best weight: 2.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN A 827 ASN A1849 GLN A1928 HIS A1991 HIS A2138 GLN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 ASN A2360 ASN A2438 GLN ** A2790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2797 GLN A3085 GLN A3400 HIS ** A3646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4010 GLN A4196 GLN A4263 GLN A4312 GLN A4413 ASN A4500 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN A4713 HIS ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4990 ASN A5077 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36337 Z= 0.241 Angle : 0.738 14.448 49175 Z= 0.373 Chirality : 0.044 0.224 5548 Planarity : 0.005 0.060 6274 Dihedral : 7.399 135.935 4844 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.03 % Rotamer: Outliers : 1.06 % Allowed : 8.87 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.05 % 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: -1.81 (0.12), residues: 4394 helix: -0.27 (0.10), residues: 2462 sheet: -1.26 (0.32), residues: 250 loop : -2.59 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1031 HIS 0.008 0.001 HIS A3785 PHE 0.035 0.002 PHE A3921 TYR 0.033 0.002 TYR A4316 ARG 0.005 0.000 ARG A1377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6334 (ppp) cc_final: 0.5887 (ppp) REVERT: A 1689 MET cc_start: 0.7255 (tmm) cc_final: 0.6800 (tmm) REVERT: A 4842 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6955 (tp-100) outliers start: 42 outliers final: 21 residues processed: 267 average time/residue: 0.4389 time to fit residues: 203.6998 Evaluate side-chains 229 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1643 GLU Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2650 ILE Chi-restraints excluded: chain A residue 2652 VAL Chi-restraints excluded: chain A residue 3292 LEU Chi-restraints excluded: chain A residue 3379 LEU Chi-restraints excluded: chain A residue 3402 ASP Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3595 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3865 GLU Chi-restraints excluded: chain A residue 4085 LEU Chi-restraints excluded: chain A residue 4637 LYS Chi-restraints excluded: chain A residue 4701 GLN Chi-restraints excluded: chain A residue 4786 LEU Chi-restraints excluded: chain A residue 4842 GLN Chi-restraints excluded: chain A residue 4875 LEU Chi-restraints excluded: chain A residue 5021 LEU Chi-restraints excluded: chain A residue 5070 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 402 optimal weight: 0.0870 chunk 434 optimal weight: 5.9990 chunk 358 optimal weight: 7.9990 chunk 398 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 322 optimal weight: 1.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS A1478 ASN A2039 GLN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2438 GLN A2785 GLN ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3359 ASN ** A3646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4152 HIS A4342 GLN A4347 ASN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN A4696 GLN A4836 ASN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4939 ASN ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5005 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36337 Z= 0.292 Angle : 0.732 12.475 49175 Z= 0.371 Chirality : 0.044 0.206 5548 Planarity : 0.005 0.093 6274 Dihedral : 7.023 134.876 4844 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.58 % Favored : 91.37 % Rotamer: Outliers : 1.84 % Allowed : 11.36 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.02 % 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: -1.20 (0.13), residues: 4394 helix: 0.29 (0.10), residues: 2471 sheet: -1.27 (0.32), residues: 258 loop : -2.39 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 884 HIS 0.011 0.001 HIS A2491 PHE 0.037 0.002 PHE A3921 TYR 0.027 0.002 TYR A4316 ARG 0.005 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 209 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1037 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8927 (tp) REVERT: A 1689 MET cc_start: 0.7549 (tmm) cc_final: 0.7283 (tmm) REVERT: A 3265 MET cc_start: 0.7098 (ppp) cc_final: 0.6689 (ppp) REVERT: A 4636 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.6975 (t0) REVERT: A 4842 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7138 (tp-100) outliers start: 73 outliers final: 41 residues processed: 264 average time/residue: 0.4409 time to fit residues: 200.8259 Evaluate side-chains 236 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 192 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1204 LYS Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1643 GLU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2650 ILE Chi-restraints excluded: chain A residue 2652 VAL Chi-restraints excluded: chain A residue 3009 TYR Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3138 VAL Chi-restraints excluded: chain A residue 3200 ASP Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3227 VAL Chi-restraints excluded: chain A residue 3278 THR Chi-restraints excluded: chain A residue 3305 VAL Chi-restraints excluded: chain A residue 3379 LEU Chi-restraints excluded: chain A residue 3402 ASP Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3595 LEU Chi-restraints excluded: chain A residue 3618 ILE Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3864 GLN Chi-restraints excluded: chain A residue 4085 LEU Chi-restraints excluded: chain A residue 4346 VAL Chi-restraints excluded: chain A residue 4417 TYR Chi-restraints excluded: chain A residue 4423 ASN Chi-restraints excluded: chain A residue 4513 VAL Chi-restraints excluded: chain A residue 4636 ASP Chi-restraints excluded: chain A residue 4637 LYS Chi-restraints excluded: chain A residue 4692 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4786 LEU Chi-restraints excluded: chain A residue 4842 GLN Chi-restraints excluded: chain A residue 5070 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 8.9990 chunk 302 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 191 optimal weight: 0.0010 chunk 270 optimal weight: 7.9990 chunk 403 optimal weight: 9.9990 chunk 427 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1090 GLN A2039 GLN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2556 GLN A2790 GLN ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3016 GLN ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3644 HIS A3646 ASN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36337 Z= 0.194 Angle : 0.662 14.422 49175 Z= 0.328 Chirality : 0.042 0.229 5548 Planarity : 0.004 0.083 6274 Dihedral : 6.734 134.448 4844 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.76 % Favored : 92.19 % Rotamer: Outliers : 1.79 % Allowed : 12.64 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.82 (0.13), residues: 4394 helix: 0.63 (0.11), residues: 2478 sheet: -1.02 (0.32), residues: 256 loop : -2.32 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 884 HIS 0.007 0.001 HIS A1928 PHE 0.025 0.001 PHE A3921 TYR 0.023 0.001 TYR A4316 ARG 0.004 0.000 ARG A3195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 210 time to evaluate : 4.042 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: A 1037 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8907 (tp) REVERT: A 1689 MET cc_start: 0.7549 (tmm) cc_final: 0.7278 (tmm) REVERT: A 2585 MET cc_start: 0.7668 (mmm) cc_final: 0.7041 (mmt) REVERT: A 4842 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7202 (tp-100) outliers start: 71 outliers final: 42 residues processed: 266 average time/residue: 0.4313 time to fit residues: 200.9834 Evaluate side-chains 240 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2650 ILE Chi-restraints excluded: chain A residue 2742 ILE Chi-restraints excluded: chain A residue 2994 LEU Chi-restraints excluded: chain A residue 3009 TYR Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3138 VAL Chi-restraints excluded: chain A residue 3200 ASP Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3295 GLU Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3379 LEU Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3402 ASP Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3592 ASP Chi-restraints excluded: chain A residue 3595 LEU Chi-restraints excluded: chain A residue 3618 ILE Chi-restraints excluded: chain A residue 3624 SER Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3864 GLN Chi-restraints excluded: chain A residue 3865 GLU Chi-restraints excluded: chain A residue 4085 LEU Chi-restraints excluded: chain A residue 4637 LYS Chi-restraints excluded: chain A residue 4710 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4786 LEU Chi-restraints excluded: chain A residue 4842 GLN Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4884 VAL Chi-restraints excluded: chain A residue 4916 LEU Chi-restraints excluded: chain A residue 5070 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 364 optimal weight: 30.0000 chunk 295 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 218 optimal weight: 2.9990 chunk 383 optimal weight: 9.9990 chunk 107 optimal weight: 0.1980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 GLN A1793 ASN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2790 GLN ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36337 Z= 0.187 Angle : 0.657 14.153 49175 Z= 0.322 Chirality : 0.042 0.227 5548 Planarity : 0.004 0.076 6274 Dihedral : 6.628 135.713 4844 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.94 % Favored : 92.01 % Rotamer: Outliers : 2.22 % Allowed : 13.80 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.58 (0.13), residues: 4394 helix: 0.84 (0.11), residues: 2470 sheet: -0.78 (0.33), residues: 244 loop : -2.23 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 884 HIS 0.007 0.001 HIS A1928 PHE 0.022 0.001 PHE A2727 TYR 0.021 0.001 TYR A4316 ARG 0.004 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 202 time to evaluate : 3.984 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: A 1665 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.5851 (m-10) REVERT: A 1689 MET cc_start: 0.7611 (tmm) cc_final: 0.7304 (tmm) REVERT: A 2585 MET cc_start: 0.7706 (mmm) cc_final: 0.7501 (mmm) REVERT: A 3265 MET cc_start: 0.7263 (ppp) cc_final: 0.6754 (ppp) REVERT: A 4842 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7278 (tp-100) outliers start: 88 outliers final: 51 residues processed: 273 average time/residue: 0.4282 time to fit residues: 205.1198 Evaluate side-chains 246 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 193 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1980 VAL Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2312 PHE Chi-restraints excluded: chain A residue 2513 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2650 ILE Chi-restraints excluded: chain A residue 2742 ILE Chi-restraints excluded: chain A residue 2973 VAL Chi-restraints excluded: chain A residue 2994 LEU Chi-restraints excluded: chain A residue 3009 TYR Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3200 ASP Chi-restraints excluded: chain A residue 3217 LEU Chi-restraints excluded: chain A residue 3260 GLN Chi-restraints excluded: chain A residue 3278 THR Chi-restraints excluded: chain A residue 3295 GLU Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3379 LEU Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3402 ASP Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3592 ASP Chi-restraints excluded: chain A residue 3618 ILE Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3864 GLN Chi-restraints excluded: chain A residue 3865 GLU Chi-restraints excluded: chain A residue 3880 VAL Chi-restraints excluded: chain A residue 4085 LEU Chi-restraints excluded: chain A residue 4417 TYR Chi-restraints excluded: chain A residue 4637 LYS Chi-restraints excluded: chain A residue 4710 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4786 LEU Chi-restraints excluded: chain A residue 4842 GLN Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4884 VAL Chi-restraints excluded: chain A residue 4916 LEU Chi-restraints excluded: chain A residue 5070 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 427 optimal weight: 0.8980 chunk 355 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1553 ASN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4696 GLN ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4957 GLN A5017 HIS A5146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36337 Z= 0.234 Angle : 0.685 15.807 49175 Z= 0.338 Chirality : 0.042 0.277 5548 Planarity : 0.004 0.074 6274 Dihedral : 6.525 137.370 4844 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.31 % Favored : 91.65 % Rotamer: Outliers : 2.54 % Allowed : 14.31 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4394 helix: 0.87 (0.11), residues: 2482 sheet: -0.79 (0.34), residues: 241 loop : -2.28 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 884 HIS 0.007 0.001 HIS A1928 PHE 0.022 0.002 PHE A2727 TYR 0.020 0.001 TYR A4322 ARG 0.005 0.000 ARG A2528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 196 time to evaluate : 4.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.2586 (OUTLIER) cc_final: 0.2272 (m-10) REVERT: A 1665 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6014 (m-10) REVERT: A 1689 MET cc_start: 0.7664 (tmm) cc_final: 0.7321 (tmm) REVERT: A 2219 MET cc_start: 0.7248 (mmp) cc_final: 0.6812 (mmt) REVERT: A 4577 MET cc_start: 0.8573 (ppp) cc_final: 0.7889 (ppp) REVERT: A 4875 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7923 (pp) outliers start: 101 outliers final: 66 residues processed: 274 average time/residue: 0.4358 time to fit residues: 209.2500 Evaluate side-chains 254 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 185 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 TRP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1615 MET Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1980 VAL Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2223 PHE Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2312 PHE Chi-restraints excluded: chain A residue 2513 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2650 ILE Chi-restraints excluded: chain A residue 2652 VAL Chi-restraints excluded: chain A residue 2742 ILE Chi-restraints excluded: chain A residue 2939 ASP Chi-restraints excluded: chain A residue 2994 LEU Chi-restraints excluded: chain A residue 3009 TYR Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3150 LEU Chi-restraints excluded: chain A residue 3200 ASP Chi-restraints excluded: chain A residue 3217 LEU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3260 GLN Chi-restraints excluded: chain A residue 3278 THR Chi-restraints excluded: chain A residue 3295 GLU Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3379 LEU Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3402 ASP Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3592 ASP Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3864 GLN Chi-restraints excluded: chain A residue 3865 GLU Chi-restraints excluded: chain A residue 3880 VAL Chi-restraints excluded: chain A residue 4014 MET Chi-restraints excluded: chain A residue 4085 LEU Chi-restraints excluded: chain A residue 4346 VAL Chi-restraints excluded: chain A residue 4417 TYR Chi-restraints excluded: chain A residue 4423 ASN Chi-restraints excluded: chain A residue 4636 ASP Chi-restraints excluded: chain A residue 4637 LYS Chi-restraints excluded: chain A residue 4710 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4786 LEU Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4875 LEU Chi-restraints excluded: chain A residue 4916 LEU Chi-restraints excluded: chain A residue 5070 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 359 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 426 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4211 HIS ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4789 ASN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5096 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36337 Z= 0.268 Angle : 0.724 18.402 49175 Z= 0.356 Chirality : 0.043 0.304 5548 Planarity : 0.004 0.073 6274 Dihedral : 6.447 139.206 4841 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.51 % Favored : 91.44 % Rotamer: Outliers : 2.62 % Allowed : 15.09 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.61 (0.13), residues: 4394 helix: 0.84 (0.11), residues: 2477 sheet: -0.86 (0.34), residues: 238 loop : -2.28 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 884 HIS 0.010 0.001 HIS A1928 PHE 0.024 0.002 PHE A2727 TYR 0.019 0.002 TYR A4322 ARG 0.005 0.000 ARG A1720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 192 time to evaluate : 4.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.2887 (OUTLIER) cc_final: 0.2589 (m-10) REVERT: A 747 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 1665 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5982 (m-10) REVERT: A 1689 MET cc_start: 0.7652 (tmm) cc_final: 0.7284 (tmm) REVERT: A 1811 MET cc_start: 0.7328 (ptp) cc_final: 0.7082 (ptp) REVERT: A 1978 GLU cc_start: 0.5834 (OUTLIER) cc_final: 0.5206 (pm20) REVERT: A 2274 MET cc_start: 0.7709 (mmm) cc_final: 0.7097 (mmm) REVERT: A 2585 MET cc_start: 0.7557 (mmm) cc_final: 0.6862 (mmt) REVERT: A 4270 MET cc_start: 0.7351 (tpt) cc_final: 0.7014 (tpt) REVERT: A 4429 MET cc_start: 0.6155 (tpp) cc_final: 0.5765 (tpp) REVERT: A 5103 LEU cc_start: 0.8627 (mt) cc_final: 0.8350 (mt) outliers start: 104 outliers final: 73 residues processed: 276 average time/residue: 0.4502 time to fit residues: 216.2639 Evaluate side-chains 259 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 182 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 TRP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1615 MET Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1978 GLU Chi-restraints excluded: chain A residue 1980 VAL Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2273 HIS Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2312 PHE Chi-restraints excluded: chain A residue 2324 ILE Chi-restraints excluded: chain A residue 2513 THR Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2650 ILE Chi-restraints excluded: chain A residue 2652 VAL Chi-restraints excluded: chain A residue 2742 ILE Chi-restraints excluded: chain A residue 2939 ASP Chi-restraints excluded: chain A residue 2994 LEU Chi-restraints excluded: chain A residue 3009 TYR Chi-restraints excluded: chain A residue 3016 GLN Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3138 VAL Chi-restraints excluded: chain A residue 3150 LEU Chi-restraints excluded: chain A residue 3200 ASP Chi-restraints excluded: chain A residue 3217 LEU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3260 GLN Chi-restraints excluded: chain A residue 3278 THR Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3305 VAL Chi-restraints excluded: chain A residue 3341 ASP Chi-restraints excluded: chain A residue 3379 LEU Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3402 ASP Chi-restraints excluded: chain A residue 3529 MET Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3578 VAL Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3773 THR Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3864 GLN Chi-restraints excluded: chain A residue 3865 GLU Chi-restraints excluded: chain A residue 3880 VAL Chi-restraints excluded: chain A residue 3881 GLU Chi-restraints excluded: chain A residue 4002 ARG Chi-restraints excluded: chain A residue 4014 MET Chi-restraints excluded: chain A residue 4085 LEU Chi-restraints excluded: chain A residue 4346 VAL Chi-restraints excluded: chain A residue 4417 TYR Chi-restraints excluded: chain A residue 4636 ASP Chi-restraints excluded: chain A residue 4637 LYS Chi-restraints excluded: chain A residue 4710 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4884 VAL Chi-restraints excluded: chain A residue 5070 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 290 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 chunk 39 optimal weight: 0.0000 chunk 334 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 ASN ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS A1553 ASN A2161 HIS ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4263 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4939 ASN ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 36337 Z= 0.160 Angle : 0.694 18.084 49175 Z= 0.330 Chirality : 0.042 0.288 5548 Planarity : 0.004 0.076 6274 Dihedral : 6.221 139.181 4841 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 1.86 % Allowed : 16.02 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.37 (0.13), residues: 4394 helix: 1.02 (0.11), residues: 2486 sheet: -0.66 (0.34), residues: 242 loop : -2.20 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 912 HIS 0.005 0.001 HIS A1928 PHE 0.019 0.001 PHE A2727 TYR 0.020 0.001 TYR A4322 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 207 time to evaluate : 3.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6296 (ppp) cc_final: 0.5951 (ppp) REVERT: A 721 MET cc_start: 0.7800 (mmm) cc_final: 0.7549 (tpp) REVERT: A 747 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 1665 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.5768 (m-10) REVERT: A 1689 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7278 (tmm) REVERT: A 2274 MET cc_start: 0.7768 (mmm) cc_final: 0.7107 (mmm) REVERT: A 2585 MET cc_start: 0.7655 (mmm) cc_final: 0.6971 (mmt) REVERT: A 3265 MET cc_start: 0.7202 (ppp) cc_final: 0.6864 (ppp) REVERT: A 4429 MET cc_start: 0.6000 (tpp) cc_final: 0.5714 (tpp) outliers start: 74 outliers final: 56 residues processed: 265 average time/residue: 0.4205 time to fit residues: 195.1931 Evaluate side-chains 251 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 192 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 TRP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1665 PHE Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1980 VAL Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2273 HIS Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2312 PHE Chi-restraints excluded: chain A residue 2513 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2650 ILE Chi-restraints excluded: chain A residue 2742 ILE Chi-restraints excluded: chain A residue 3009 TYR Chi-restraints excluded: chain A residue 3016 GLN Chi-restraints excluded: chain A residue 3018 THR Chi-restraints excluded: chain A residue 3150 LEU Chi-restraints excluded: chain A residue 3217 LEU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3260 GLN Chi-restraints excluded: chain A residue 3304 VAL Chi-restraints excluded: chain A residue 3341 ASP Chi-restraints excluded: chain A residue 3379 LEU Chi-restraints excluded: chain A residue 3395 LEU Chi-restraints excluded: chain A residue 3402 ASP Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3624 SER Chi-restraints excluded: chain A residue 3773 THR Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3864 GLN Chi-restraints excluded: chain A residue 3865 GLU Chi-restraints excluded: chain A residue 3880 VAL Chi-restraints excluded: chain A residue 4002 ARG Chi-restraints excluded: chain A residue 4014 MET Chi-restraints excluded: chain A residue 4085 LEU Chi-restraints excluded: chain A residue 4417 TYR Chi-restraints excluded: chain A residue 4532 LEU Chi-restraints excluded: chain A residue 4637 LYS Chi-restraints excluded: chain A residue 4710 VAL Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4762 ASP Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4884 VAL Chi-restraints excluded: chain A residue 5070 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7682 > 50: distance: 57 - 66: 35.441 distance: 67 - 70: 55.503 distance: 68 - 69: 39.026 distance: 70 - 72: 41.472 distance: 73 - 74: 56.034 distance: 74 - 75: 40.366 distance: 75 - 76: 56.785 distance: 75 - 80: 39.954 distance: 77 - 78: 56.594 distance: 81 - 82: 22.107 distance: 82 - 83: 20.633 distance: 82 - 91: 60.352 distance: 86 - 88: 57.068 distance: 88 - 90: 39.140 distance: 89 - 90: 41.161 distance: 92 - 93: 31.313 distance: 92 - 95: 40.019 distance: 93 - 94: 10.667 distance: 93 - 99: 30.513 distance: 96 - 97: 42.492 distance: 99 - 100: 36.636 distance: 100 - 101: 13.254 distance: 100 - 103: 48.316 distance: 101 - 107: 39.325 distance: 103 - 105: 41.199 distance: 104 - 106: 39.173 distance: 107 - 108: 39.828 distance: 109 - 115: 40.450 distance: 111 - 112: 56.391 distance: 112 - 113: 35.609 distance: 115 - 116: 55.413 distance: 116 - 119: 39.393 distance: 117 - 126: 21.967 distance: 119 - 120: 39.951 distance: 120 - 121: 40.323 distance: 120 - 122: 40.663 distance: 121 - 123: 39.886 distance: 122 - 124: 39.866 distance: 124 - 125: 56.291 distance: 126 - 127: 18.270 distance: 127 - 128: 40.380 distance: 127 - 130: 59.047 distance: 128 - 129: 56.733 distance: 130 - 131: 49.700 distance: 131 - 133: 40.748 distance: 135 - 136: 57.341 distance: 135 - 138: 39.724 distance: 136 - 142: 39.490 distance: 138 - 139: 39.323 distance: 139 - 140: 56.791 distance: 139 - 141: 39.593 distance: 142 - 143: 40.721 distance: 143 - 144: 14.252 distance: 143 - 146: 39.283 distance: 144 - 145: 15.640 distance: 144 - 150: 28.477 distance: 146 - 147: 41.384 distance: 147 - 149: 38.952