Starting phenix.real_space_refine on Sat Dec 16 21:48:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oik_12931/12_2023/7oik_12931_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oik_12931/12_2023/7oik_12931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oik_12931/12_2023/7oik_12931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oik_12931/12_2023/7oik_12931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oik_12931/12_2023/7oik_12931_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oik_12931/12_2023/7oik_12931_updated.pdb" } resolution = 3.5 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 3 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 23443 2.51 5 N 6312 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1523": "OD1" <-> "OD2" Residue "A ASP 2019": "OD1" <-> "OD2" Residue "A PHE 2371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2403": "OE1" <-> "OE2" Residue "A GLU 3553": "OE1" <-> "OE2" Residue "A ASP 3716": "OD1" <-> "OD2" Residue "A PHE 3757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 28": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36779 Number of models: 1 Model: "" Number of chains: 3 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: "B" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 138} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26526 SG CYS A3962 89.136 133.575 219.167 1.00485.84 S ATOM 26690 SG CYS A3982 86.914 131.918 222.010 1.00504.02 S ATOM 26715 SG CYS A3985 90.759 132.082 222.071 1.00513.48 S ATOM 26416 SG CYS A3947 79.101 126.941 217.704 1.00394.59 S ATOM 26441 SG CYS A3950 76.880 123.812 216.785 1.00385.02 S ATOM 26569 SG CYS A3967 76.748 126.402 214.552 1.00428.91 S ATOM 26594 SG CYS A3970 75.336 127.264 217.955 1.00452.42 S Time building chain proxies: 18.93, per 1000 atoms: 0.51 Number of scatterers: 36779 At special positions: 0 Unit cell: (131.856, 154.368, 244.416, 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 214 16.00 P 3 15.00 Mg 1 11.99 O 6804 8.00 N 6312 7.00 C 23443 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=2.04 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: 13.58 Conformation dependent library (CDL) restraints added in 6.5 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 A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3970 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 9 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 207 helices and 13 sheets defined 52.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 23.80 Creating SS restraints... Processing helix chain 'A' and resid 493 through 512 Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 555 through 575 removed outlier: 3.716A pdb=" N TRP A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Proline residue: A 572 - end of helix removed outlier: 3.719A pdb=" N GLU A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 629 through 639 Proline residue: A 637 - end of helix Processing helix chain 'A' and resid 644 through 657 Processing helix chain 'A' and resid 663 through 666 Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.655A pdb=" N SER A 750 " --> pdb=" O TYR A 746 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 774 Proline residue: A 773 - end of helix Processing helix chain 'A' and resid 781 through 799 Processing helix chain 'A' and resid 811 through 826 Processing helix chain 'A' and resid 835 through 849 removed outlier: 3.934A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 888 Processing helix chain 'A' and resid 909 through 916 Processing helix chain 'A' and resid 930 through 938 Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 963 through 981 Processing helix chain 'A' and resid 995 through 1009 Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1033 through 1043 Processing helix chain 'A' and resid 1054 through 1071 Processing helix chain 'A' and resid 1080 through 1088 Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1114 through 1142 Processing helix chain 'A' and resid 1155 through 1158 No H-bonds generated for 'chain 'A' and resid 1155 through 1158' Processing helix chain 'A' and resid 1167 through 1170 Processing helix chain 'A' and resid 1192 through 1203 Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1234 through 1240 removed outlier: 3.811A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1258 Processing helix chain 'A' and resid 1263 through 1269 Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1278 through 1288 Processing helix chain 'A' and resid 1299 through 1328 Processing helix chain 'A' and resid 1339 through 1345 Processing helix chain 'A' and resid 1362 through 1367 removed outlier: 4.432A pdb=" N ALA A1366 " --> pdb=" O GLN A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1386 Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1404 through 1414 removed outlier: 4.139A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1439 removed outlier: 4.488A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1463 removed outlier: 3.814A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1486 removed outlier: 4.142A pdb=" N ASN A1478 " --> pdb=" O ASP A1474 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A1479 " --> pdb=" O SER A1475 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU A1480 " --> pdb=" O ALA A1476 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP A1481 " --> pdb=" O ARG A1477 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1506 Processing helix chain 'A' and resid 1522 through 1525 No H-bonds generated for 'chain 'A' and resid 1522 through 1525' Processing helix chain 'A' and resid 1545 through 1556 Processing helix chain 'A' and resid 1564 through 1593 Processing helix chain 'A' and resid 1631 through 1659 removed outlier: 3.652A pdb=" N GLU A1659 " --> pdb=" O GLN A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1665 Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1685 through 1693 removed outlier: 4.240A pdb=" N SER A1692 " --> pdb=" O LEU A1688 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A1693 " --> pdb=" O MET A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1700 through 1708 Processing helix chain 'A' and resid 1714 through 1725 Processing helix chain 'A' and resid 1727 through 1730 No H-bonds generated for 'chain 'A' and resid 1727 through 1730' Processing helix chain 'A' and resid 1736 through 1749 Processing helix chain 'A' and resid 1761 through 1774 Processing helix chain 'A' and resid 1799 through 1801 No H-bonds generated for 'chain 'A' and resid 1799 through 1801' Processing helix chain 'A' and resid 1803 through 1811 removed outlier: 3.745A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A1811 " --> pdb=" O LEU A1807 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1843 Processing helix chain 'A' and resid 1859 through 1861 No H-bonds generated for 'chain 'A' and resid 1859 through 1861' Processing helix chain 'A' and resid 1864 through 1880 Processing helix chain 'A' and resid 1901 through 1904 No H-bonds generated for 'chain 'A' and resid 1901 through 1904' Processing helix chain 'A' and resid 1906 through 1908 No H-bonds generated for 'chain 'A' and resid 1906 through 1908' Processing helix chain 'A' and resid 1918 through 1929 Processing helix chain 'A' and resid 1938 through 1941 removed outlier: 3.709A pdb=" N VAL A1941 " --> pdb=" O ALA A1938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1938 through 1941' Processing helix chain 'A' and resid 1960 through 1973 Processing helix chain 'A' and resid 1994 through 2002 Processing helix chain 'A' and resid 2028 through 2036 Processing helix chain 'A' and resid 2081 through 2087 removed outlier: 4.067A pdb=" N ASP A2086 " --> pdb=" O PHE A2082 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A2087 " --> pdb=" O LYS A2083 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2120 No H-bonds generated for 'chain 'A' and resid 2117 through 2120' Processing helix chain 'A' and resid 2123 through 2136 Proline residue: A2128 - end of helix removed outlier: 4.090A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2165 Processing helix chain 'A' and resid 2173 through 2192 Processing helix chain 'A' and resid 2195 through 2202 Processing helix chain 'A' and resid 2208 through 2223 Processing helix chain 'A' and resid 2309 through 2318 Processing helix chain 'A' and resid 2331 through 2341 Processing helix chain 'A' and resid 2358 through 2373 Processing helix chain 'A' and resid 2388 through 2399 Processing helix chain 'A' and resid 2418 through 2439 Processing helix chain 'A' and resid 2454 through 2463 removed outlier: 4.404A pdb=" N SER A2457 " --> pdb=" O GLU A2454 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A2463 " --> pdb=" O LYS A2460 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2500 Processing helix chain 'A' and resid 2522 through 2524 No H-bonds generated for 'chain 'A' and resid 2522 through 2524' Processing helix chain 'A' and resid 2551 through 2563 Processing helix chain 'A' and resid 2572 through 2588 Processing helix chain 'A' and resid 2601 through 2614 Processing helix chain 'A' and resid 2618 through 2630 Processing helix chain 'A' and resid 2643 through 2653 Processing helix chain 'A' and resid 2661 through 2668 Processing helix chain 'A' and resid 2674 through 2676 No H-bonds generated for 'chain 'A' and resid 2674 through 2676' Processing helix chain 'A' and resid 2679 through 2696 Processing helix chain 'A' and resid 2707 through 2721 Processing helix chain 'A' and resid 2738 through 2746 Processing helix chain 'A' and resid 2776 through 2790 Processing helix chain 'A' and resid 2818 through 2824 removed outlier: 4.059A pdb=" N HIS A2822 " --> pdb=" O LYS A2819 " (cutoff:3.500A) Proline residue: A2823 - end of helix Processing helix chain 'A' and resid 2852 through 2855 No H-bonds generated for 'chain 'A' and resid 2852 through 2855' Processing helix chain 'A' and resid 2868 through 2881 removed outlier: 5.145A pdb=" N SER A2881 " --> pdb=" O GLY A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2884 through 2906 removed outlier: 5.964A pdb=" N GLY A2891 " --> pdb=" O ASP A2887 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR A2892 " --> pdb=" O LYS A2888 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A2893 " --> pdb=" O ILE A2889 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA A2894 " --> pdb=" O ARG A2890 " (cutoff:3.500A) Proline residue: A2895 - end of helix Processing helix chain 'A' and resid 2914 through 2931 Processing helix chain 'A' and resid 2937 through 2947 Processing helix chain 'A' and resid 2956 through 2962 Processing helix chain 'A' and resid 2975 through 2983 Processing helix chain 'A' and resid 3011 through 3017 Processing helix chain 'A' and resid 3038 through 3055 Processing helix chain 'A' and resid 3072 through 3076 Processing helix chain 'A' and resid 3113 through 3119 Processing helix chain 'A' and resid 3125 through 3127 No H-bonds generated for 'chain 'A' and resid 3125 through 3127' Processing helix chain 'A' and resid 3141 through 3158 Processing helix chain 'A' and resid 3173 through 3176 No H-bonds generated for 'chain 'A' and resid 3173 through 3176' Processing helix chain 'A' and resid 3184 through 3196 Processing helix chain 'A' and resid 3205 through 3220 removed outlier: 3.822A pdb=" N CYS A3220 " --> pdb=" O ILE A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3223 through 3231 removed outlier: 4.525A pdb=" N SER A3230 " --> pdb=" O VAL A3226 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY A3231 " --> pdb=" O VAL A3227 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3248 Processing helix chain 'A' and resid 3255 through 3262 Processing helix chain 'A' and resid 3288 through 3295 Processing helix chain 'A' and resid 3308 through 3310 No H-bonds generated for 'chain 'A' and resid 3308 through 3310' Processing helix chain 'A' and resid 3314 through 3325 Processing helix chain 'A' and resid 3349 through 3364 Processing helix chain 'A' and resid 3414 through 3419 Processing helix chain 'A' and resid 3422 through 3426 removed outlier: 3.845A pdb=" N PHE A3426 " --> pdb=" O ILE A3422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3422 through 3426' Processing helix chain 'A' and resid 3477 through 3491 removed outlier: 4.830A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3511 Processing helix chain 'A' and resid 3518 through 3539 Processing helix chain 'A' and resid 3549 through 3554 Processing helix chain 'A' and resid 3557 through 3563 Processing helix chain 'A' and resid 3566 through 3589 Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3596 through 3599 No H-bonds generated for 'chain 'A' and resid 3596 through 3599' Processing helix chain 'A' and resid 3605 through 3614 Processing helix chain 'A' and resid 3658 through 3675 Processing helix chain 'A' and resid 3681 through 3690 Processing helix chain 'A' and resid 3693 through 3698 Processing helix chain 'A' and resid 3703 through 3721 Processing helix chain 'A' and resid 3728 through 3745 Processing helix chain 'A' and resid 3762 through 3770 Processing helix chain 'A' and resid 3772 through 3783 removed outlier: 4.022A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3799 removed outlier: 5.794A pdb=" N ALA A3796 " --> pdb=" O SER A3793 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A3799 " --> pdb=" O ALA A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3808 through 3823 removed outlier: 3.945A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3846 removed outlier: 4.781A pdb=" N THR A3841 " --> pdb=" O LYS A3837 " (cutoff:3.500A) Proline residue: A3842 - end of helix Processing helix chain 'A' and resid 3857 through 3889 removed outlier: 5.313A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3911 removed outlier: 3.924A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU A3911 " --> pdb=" O LYS A3907 " (cutoff:3.500A) Processing helix chain 'A' and resid 3918 through 3940 Processing helix chain 'A' and resid 3968 through 3974 Processing helix chain 'A' and resid 4000 through 4025 Processing helix chain 'A' and resid 4036 through 4044 Processing helix chain 'A' and resid 4083 through 4088 Processing helix chain 'A' and resid 4093 through 4095 No H-bonds generated for 'chain 'A' and resid 4093 through 4095' Processing helix chain 'A' and resid 4097 through 4110 Processing helix chain 'A' and resid 4117 through 4137 Processing helix chain 'A' and resid 4143 through 4155 Processing helix chain 'A' and resid 4172 through 4197 removed outlier: 3.634A pdb=" N GLU A4197 " --> pdb=" O SER A4193 " (cutoff:3.500A) Processing helix chain 'A' and resid 4205 through 4218 Processing helix chain 'A' and resid 4223 through 4235 Processing helix chain 'A' and resid 4238 through 4244 Processing helix chain 'A' and resid 4252 through 4254 No H-bonds generated for 'chain 'A' and resid 4252 through 4254' Processing helix chain 'A' and resid 4257 through 4261 removed outlier: 3.870A pdb=" N ALA A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4257 through 4261' Processing helix chain 'A' and resid 4272 through 4275 removed outlier: 3.819A pdb=" N VAL A4275 " --> pdb=" O ARG A4272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4272 through 4275' Processing helix chain 'A' and resid 4280 through 4292 Processing helix chain 'A' and resid 4297 through 4303 Processing helix chain 'A' and resid 4310 through 4330 Processing helix chain 'A' and resid 4343 through 4352 Processing helix chain 'A' and resid 4359 through 4369 removed outlier: 3.560A pdb=" N SER A4367 " --> pdb=" O CYS A4363 " (cutoff:3.500A) Processing helix chain 'A' and resid 4385 through 4402 Processing helix chain 'A' and resid 4406 through 4416 Proline residue: A4410 - end of helix removed outlier: 4.141A pdb=" N PHE A4416 " --> pdb=" O ASN A4413 " (cutoff:3.500A) Processing helix chain 'A' and resid 4418 through 4420 No H-bonds generated for 'chain 'A' and resid 4418 through 4420' Processing helix chain 'A' and resid 4523 through 4543 removed outlier: 3.912A pdb=" N HIS A4543 " --> pdb=" O VAL A4539 " (cutoff:3.500A) Processing helix chain 'A' and resid 4545 through 4551 Processing helix chain 'A' and resid 4560 through 4577 Processing helix chain 'A' and resid 4582 through 4595 Processing helix chain 'A' and resid 4614 through 4634 removed outlier: 4.670A pdb=" N HIS A4634 " --> pdb=" O ARG A4630 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4648 Processing helix chain 'A' and resid 4656 through 4659 No H-bonds generated for 'chain 'A' and resid 4656 through 4659' Processing helix chain 'A' and resid 4666 through 4668 No H-bonds generated for 'chain 'A' and resid 4666 through 4668' Processing helix chain 'A' and resid 4692 through 4701 Processing helix chain 'A' and resid 4709 through 4716 Processing helix chain 'A' and resid 4718 through 4740 removed outlier: 4.704A pdb=" N LEU A4723 " --> pdb=" O ALA A4719 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A4724 " --> pdb=" O GLU A4720 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS A4725 " --> pdb=" O LEU A4721 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N PHE A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A4727 " --> pdb=" O LEU A4723 " (cutoff:3.500A) Proline residue: A4728 - end of helix Processing helix chain 'A' and resid 4752 through 4756 Processing helix chain 'A' and resid 4762 through 4782 Processing helix chain 'A' and resid 4786 through 4789 No H-bonds generated for 'chain 'A' and resid 4786 through 4789' Processing helix chain 'A' and resid 4821 through 4844 Processing helix chain 'A' and resid 4860 through 4862 No H-bonds generated for 'chain 'A' and resid 4860 through 4862' Processing helix chain 'A' and resid 4868 through 4871 No H-bonds generated for 'chain 'A' and resid 4868 through 4871' Processing helix chain 'A' and resid 4873 through 4877 Processing helix chain 'A' and resid 4896 through 4904 Processing helix chain 'A' and resid 4931 through 4940 Processing helix chain 'A' and resid 4948 through 4956 removed outlier: 3.929A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4961 through 4979 Processing helix chain 'A' and resid 4989 through 4993 Processing helix chain 'A' and resid 5004 through 5012 removed outlier: 5.303A pdb=" N ARG A5012 " --> pdb=" O LYS A5008 " (cutoff:3.500A) Processing helix chain 'A' and resid 5015 through 5035 removed outlier: 3.875A pdb=" N ILE A5018 " --> pdb=" O LEU A5015 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A5019 " --> pdb=" O ARG A5016 " (cutoff:3.500A) Processing helix chain 'A' and resid 5046 through 5048 No H-bonds generated for 'chain 'A' and resid 5046 through 5048' Processing helix chain 'A' and resid 5054 through 5065 Processing helix chain 'A' and resid 5069 through 5083 removed outlier: 4.339A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5099 through 5108 Processing helix chain 'A' and resid 5116 through 5120 Processing helix chain 'A' and resid 5132 through 5148 Processing helix chain 'B' and resid 1 through 17 removed outlier: 3.583A pdb=" N ARG B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 133 through 147 Processing sheet with id= A, first strand: chain 'A' and resid 1625 through 1627 removed outlier: 3.669A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1792 through 1796 removed outlier: 7.237A pdb=" N LEU A1888 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE A1795 " --> pdb=" O LEU A1888 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A1890 " --> pdb=" O ILE A1795 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2090 through 2093 removed outlier: 7.873A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N CYS A2093 " --> pdb=" O ILE A1950 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A1952 " --> pdb=" O CYS A2093 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR A2057 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A1951 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A2059 " --> pdb=" O VAL A1951 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER A1953 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE A2061 " --> pdb=" O SER A1953 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id= E, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id= F, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id= G, first strand: chain 'A' and resid 2377 through 2380 removed outlier: 4.145A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A2443 " --> pdb=" O HIS A2480 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A2482 " --> pdb=" O THR A2443 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A2445 " --> pdb=" O ILE A2482 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA A2484 " --> pdb=" O LEU A2445 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE A2447 " --> pdb=" O ALA A2484 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2859 through 2862 removed outlier: 6.196A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A2801 " --> pdb=" O GLN A2762 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS A2764 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL A2803 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A2766 " --> pdb=" O VAL A2803 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 3130 through 3132 removed outlier: 6.355A pdb=" N LEU A3003 " --> pdb=" O HIS A3131 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE A3110 " --> pdb=" O VAL A3059 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A3061 " --> pdb=" O ILE A3110 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 3080 through 3082 removed outlier: 4.507A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 3397 through 3399 removed outlier: 6.379A pdb=" N VAL A3371 " --> pdb=" O VAL A3273 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR A3275 " --> pdb=" O VAL A3371 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A3373 " --> pdb=" O THR A3275 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A3277 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N PHE A3375 " --> pdb=" O ILE A3277 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR A3279 " --> pdb=" O PHE A3375 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A3377 " --> pdb=" O THR A3279 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A3304 " --> pdb=" O VAL A3335 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN A3337 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A3306 " --> pdb=" O GLN A3337 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ASP A3339 " --> pdb=" O LEU A3306 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 4880 through 4883 Processing sheet with id= M, first strand: chain 'B' and resid 34 through 40 1603 hydrogen bonds defined for protein. 4653 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: 23.01 Time building geometry restraints manager: 14.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9615 1.33 - 1.46: 9502 1.46 - 1.59: 18110 1.59 - 1.71: 3 1.71 - 1.84: 316 Bond restraints: 37546 Sorted by residual: bond pdb=" C LYS A4310 " pdb=" N PRO A4311 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" CB MET A1811 " pdb=" CG MET A1811 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.87e+00 bond pdb=" CG ARG A2316 " pdb=" CD ARG A2316 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.90e+00 bond pdb=" C LYS A3826 " pdb=" N PRO A3827 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.79e+00 bond pdb=" CB ASN A1014 " pdb=" CG ASN A1014 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.85e+00 ... (remaining 37541 not shown) Histogram of bond angle deviations from ideal: 94.18 - 103.28: 341 103.28 - 112.39: 18122 112.39 - 121.49: 23393 121.49 - 130.59: 8700 130.59 - 139.69: 241 Bond angle restraints: 50797 Sorted by residual: angle pdb=" CA MET A 721 " pdb=" CB MET A 721 " pdb=" CG MET A 721 " ideal model delta sigma weight residual 114.10 131.68 -17.58 2.00e+00 2.50e-01 7.72e+01 angle pdb=" N GLU A1135 " pdb=" CA GLU A1135 " pdb=" CB GLU A1135 " ideal model delta sigma weight residual 110.28 122.67 -12.39 1.55e+00 4.16e-01 6.39e+01 angle pdb=" CA MET A2012 " pdb=" CB MET A2012 " pdb=" CG MET A2012 " ideal model delta sigma weight residual 114.10 129.74 -15.64 2.00e+00 2.50e-01 6.11e+01 angle pdb=" CA GLN A5121 " pdb=" CB GLN A5121 " pdb=" CG GLN A5121 " ideal model delta sigma weight residual 114.10 129.19 -15.09 2.00e+00 2.50e-01 5.69e+01 angle pdb=" C ARG A3000 " pdb=" N TYR A3001 " pdb=" CA TYR A3001 " ideal model delta sigma weight residual 121.54 134.92 -13.38 1.91e+00 2.74e-01 4.91e+01 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 21399 17.96 - 35.93: 1255 35.93 - 53.89: 175 53.89 - 71.86: 48 71.86 - 89.82: 21 Dihedral angle restraints: 22898 sinusoidal: 9433 harmonic: 13465 Sorted by residual: dihedral pdb=" CA VAL A3122 " pdb=" C VAL A3122 " pdb=" N PRO A3123 " pdb=" CA PRO A3123 " ideal model delta harmonic sigma weight residual 180.00 120.90 59.10 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU A1170 " pdb=" C GLU A1170 " pdb=" N ALA A1171 " pdb=" CA ALA A1171 " ideal model delta harmonic sigma weight residual 180.00 133.77 46.23 0 5.00e+00 4.00e-02 8.55e+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 -137.10 -42.90 0 5.00e+00 4.00e-02 7.36e+01 ... (remaining 22895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5039 0.104 - 0.208: 591 0.208 - 0.312: 62 0.312 - 0.416: 21 0.416 - 0.520: 6 Chirality restraints: 5719 Sorted by residual: chirality pdb=" CA GLN A5121 " pdb=" N GLN A5121 " pdb=" C GLN A5121 " pdb=" CB GLN A5121 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" CB ILE A2830 " pdb=" CA ILE A2830 " pdb=" CG1 ILE A2830 " pdb=" CG2 ILE A2830 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA LYS A3826 " pdb=" N LYS A3826 " pdb=" C LYS A3826 " pdb=" CB LYS A3826 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 5716 not shown) Planarity restraints: 6499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 615 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ASP A 615 " -0.082 2.00e-02 2.50e+03 pdb=" O ASP A 615 " 0.031 2.00e-02 2.50e+03 pdb=" N SER A 616 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A3122 " -0.069 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A3123 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A3123 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A3123 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2312 " -0.044 2.00e-02 2.50e+03 3.14e-02 1.72e+01 pdb=" CG PHE A2312 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A2312 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A2312 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A2312 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A2312 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A2312 " -0.019 2.00e-02 2.50e+03 ... (remaining 6496 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 980 2.70 - 3.25: 35510 3.25 - 3.80: 58379 3.80 - 4.35: 75599 4.35 - 4.90: 121950 Nonbonded interactions: 292418 Sorted by model distance: nonbonded pdb=" O2B ATP A5201 " pdb="MG MG A5202 " model vdw 2.148 2.170 nonbonded pdb=" OE2 GLU A2060 " pdb="MG MG A5202 " model vdw 2.174 2.170 nonbonded pdb=" OG1 THR A1820 " pdb=" OD1 ASP A1822 " model vdw 2.238 2.440 nonbonded pdb=" O SER A3790 " pdb=" OG SER A3793 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR A2513 " pdb=" OD2 ASP A2812 " model vdw 2.280 2.440 ... (remaining 292413 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: 0.010 Normalize map: mean=0, sd=1: 3.620 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: 11.130 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 106.060 Find NCS groups from input model: 1.120 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 0.097 37546 Z= 0.357 Angle : 1.313 21.707 50797 Z= 0.668 Chirality : 0.072 0.520 5719 Planarity : 0.008 0.106 6499 Dihedral : 12.170 89.824 14124 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.91 % Favored : 90.94 % Rotamer: Outliers : 0.02 % Allowed : 1.34 % Favored : 98.64 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -3.74 (0.10), residues: 4545 helix: -2.12 (0.08), residues: 2558 sheet: -1.22 (0.29), residues: 263 loop : -3.11 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A3832 HIS 0.020 0.002 HIS A4587 PHE 0.067 0.003 PHE A2312 TYR 0.061 0.003 TYR A1277 ARG 0.020 0.001 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 4.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 311 average time/residue: 0.4997 time to fit residues: 260.8342 Evaluate side-chains 212 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 4.525 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3816 time to fit residues: 6.4517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 0.0670 chunk 346 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 415 optimal weight: 8.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A 827 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 HIS ** A1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN A2186 GLN ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2947 ASN ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS ** A4276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37546 Z= 0.213 Angle : 0.695 13.339 50797 Z= 0.350 Chirality : 0.043 0.222 5719 Planarity : 0.005 0.083 6499 Dihedral : 6.152 64.495 4975 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 0.58 % Allowed : 6.67 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -1.95 (0.12), residues: 4545 helix: -0.37 (0.10), residues: 2583 sheet: -0.90 (0.30), residues: 272 loop : -2.80 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A3832 HIS 0.006 0.001 HIS A4587 PHE 0.036 0.002 PHE A2312 TYR 0.034 0.002 TYR A1133 ARG 0.007 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 4.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 241 average time/residue: 0.4683 time to fit residues: 196.0077 Evaluate side-chains 207 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 4.379 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3584 time to fit residues: 15.3240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 0.4980 chunk 128 optimal weight: 9.9990 chunk 345 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 415 optimal weight: 6.9990 chunk 449 optimal weight: 30.0000 chunk 370 optimal weight: 0.7980 chunk 412 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 333 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN A1478 ASN A1746 GLN A2126 GLN A2136 HIS ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 HIS A3337 GLN A4134 GLN A4263 GLN A4276 HIS ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4643 ASN A4674 GLN A4836 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37546 Z= 0.228 Angle : 0.673 12.891 50797 Z= 0.337 Chirality : 0.042 0.197 5719 Planarity : 0.004 0.079 6499 Dihedral : 5.769 71.025 4975 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.49 % Favored : 91.49 % Rotamer: Outliers : 0.90 % Allowed : 9.06 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -1.15 (0.12), residues: 4545 helix: 0.35 (0.10), residues: 2588 sheet: -0.68 (0.29), residues: 299 loop : -2.60 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1031 HIS 0.008 0.001 HIS A 803 PHE 0.034 0.002 PHE A2371 TYR 0.023 0.001 TYR A3652 ARG 0.011 0.000 ARG A1121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 223 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 248 average time/residue: 0.4635 time to fit residues: 201.1599 Evaluate side-chains 206 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 4.556 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3411 time to fit residues: 15.0772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 417 optimal weight: 1.9990 chunk 441 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 395 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS A1453 ASN A2273 HIS ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2712 ASN A2790 GLN ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3119 GLN A4347 ASN ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37546 Z= 0.231 Angle : 0.671 15.971 50797 Z= 0.333 Chirality : 0.042 0.235 5719 Planarity : 0.004 0.071 6499 Dihedral : 5.623 73.484 4975 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.45 % Favored : 91.53 % Rotamer: Outliers : 1.24 % Allowed : 10.40 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.78 (0.13), residues: 4545 helix: 0.66 (0.10), residues: 2597 sheet: -0.55 (0.29), residues: 303 loop : -2.47 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1031 HIS 0.008 0.001 HIS A 803 PHE 0.031 0.002 PHE A2371 TYR 0.020 0.001 TYR A1133 ARG 0.009 0.000 ARG A1121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 22 residues processed: 245 average time/residue: 0.4700 time to fit residues: 201.4987 Evaluate side-chains 215 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 4.722 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3540 time to fit residues: 20.9903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 367 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 6 optimal weight: 40.0000 chunk 328 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 225 optimal weight: 0.0970 chunk 396 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN ** A1641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2712 ASN ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37546 Z= 0.178 Angle : 0.651 14.691 50797 Z= 0.318 Chirality : 0.041 0.214 5719 Planarity : 0.004 0.075 6499 Dihedral : 5.457 70.678 4975 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.01 % Favored : 91.97 % Rotamer: Outliers : 0.78 % Allowed : 11.67 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.57 (0.13), residues: 4545 helix: 0.84 (0.11), residues: 2604 sheet: -0.48 (0.30), residues: 304 loop : -2.42 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1031 HIS 0.007 0.001 HIS A 803 PHE 0.029 0.001 PHE A2371 TYR 0.019 0.001 TYR A1309 ARG 0.006 0.000 ARG A1121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 11 residues processed: 246 average time/residue: 0.4874 time to fit residues: 208.7217 Evaluate side-chains 205 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 4.350 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4271 time to fit residues: 14.3155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 148 optimal weight: 6.9990 chunk 397 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 442 optimal weight: 20.0000 chunk 367 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 ASN ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN A1518 GLN A1641 GLN ** A1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1928 HIS ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3502 ASN A3642 GLN ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37546 Z= 0.187 Angle : 0.660 13.905 50797 Z= 0.322 Chirality : 0.042 0.273 5719 Planarity : 0.004 0.068 6499 Dihedral : 5.385 67.118 4975 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.36 % Favored : 91.62 % Rotamer: Outliers : 0.97 % Allowed : 12.08 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.46 (0.13), residues: 4545 helix: 0.92 (0.11), residues: 2608 sheet: -0.42 (0.30), residues: 304 loop : -2.37 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A3832 HIS 0.007 0.001 HIS A 803 PHE 0.032 0.001 PHE A2371 TYR 0.017 0.001 TYR A3652 ARG 0.005 0.000 ARG A1121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 15 residues processed: 240 average time/residue: 0.4689 time to fit residues: 197.2821 Evaluate side-chains 213 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 4.350 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4187 time to fit residues: 17.0390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 372 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 440 optimal weight: 0.9980 chunk 275 optimal weight: 0.9980 chunk 268 optimal weight: 0.2980 chunk 203 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN ** A1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3642 GLN ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4590 HIS ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37546 Z= 0.147 Angle : 0.656 14.201 50797 Z= 0.316 Chirality : 0.042 0.267 5719 Planarity : 0.004 0.072 6499 Dihedral : 5.261 64.583 4975 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 0.49 % Allowed : 12.94 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4545 helix: 1.01 (0.11), residues: 2597 sheet: -0.31 (0.30), residues: 303 loop : -2.29 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A3832 HIS 0.007 0.001 HIS A2273 PHE 0.033 0.001 PHE A2371 TYR 0.020 0.001 TYR A1309 ARG 0.005 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 238 average time/residue: 0.4677 time to fit residues: 197.3299 Evaluate side-chains 202 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 4.270 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3569 time to fit residues: 9.3567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 272 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 chunk 300 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN A1791 GLN ** A1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2712 ASN ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3126 ASN A3642 GLN A3838 ASN A4252 GLN A4382 ASN A4789 ASN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37546 Z= 0.271 Angle : 0.714 14.019 50797 Z= 0.354 Chirality : 0.043 0.316 5719 Planarity : 0.004 0.067 6499 Dihedral : 5.399 69.037 4975 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.65 % Favored : 91.33 % Rotamer: Outliers : 0.58 % Allowed : 13.47 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.43 (0.13), residues: 4545 helix: 0.91 (0.11), residues: 2596 sheet: -0.34 (0.30), residues: 302 loop : -2.26 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A3832 HIS 0.008 0.001 HIS A2273 PHE 0.033 0.002 PHE A2371 TYR 0.039 0.002 TYR A4322 ARG 0.008 0.001 ARG A 937 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 4.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 233 average time/residue: 0.4723 time to fit residues: 193.0637 Evaluate side-chains 208 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 4.314 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3495 time to fit residues: 10.6112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 400 optimal weight: 0.0970 chunk 421 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 410 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 322 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 370 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 409 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN ** A1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2712 ASN ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37546 Z= 0.162 Angle : 0.681 17.878 50797 Z= 0.326 Chirality : 0.042 0.291 5719 Planarity : 0.004 0.072 6499 Dihedral : 5.300 76.247 4975 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.63 % Favored : 92.34 % Rotamer: Outliers : 0.19 % Allowed : 14.15 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.22 (0.13), residues: 4545 helix: 1.07 (0.11), residues: 2584 sheet: -0.26 (0.30), residues: 301 loop : -2.16 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A3832 HIS 0.006 0.001 HIS A2273 PHE 0.033 0.001 PHE A2371 TYR 0.046 0.001 TYR A4322 ARG 0.009 0.000 ARG A1121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 215 average time/residue: 0.4612 time to fit residues: 174.5956 Evaluate side-chains 199 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 4.144 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3435 time to fit residues: 7.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 269 optimal weight: 2.9990 chunk 434 optimal weight: 0.2980 chunk 264 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 455 optimal weight: 30.0000 chunk 419 optimal weight: 0.3980 chunk 362 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 280 optimal weight: 0.2980 chunk 222 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 37546 Z= 0.149 Angle : 0.688 17.322 50797 Z= 0.326 Chirality : 0.042 0.275 5719 Planarity : 0.004 0.068 6499 Dihedral : 5.194 75.419 4975 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 0.22 % Allowed : 14.28 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.17 (0.13), residues: 4545 helix: 1.11 (0.11), residues: 2580 sheet: -0.19 (0.30), residues: 302 loop : -2.11 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A3832 HIS 0.005 0.001 HIS A2273 PHE 0.032 0.001 PHE A2371 TYR 0.042 0.001 TYR A4322 ARG 0.008 0.000 ARG A1121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 207 time to evaluate : 4.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 214 average time/residue: 0.5172 time to fit residues: 194.0518 Evaluate side-chains 205 residues out of total 4117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 4.452 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3660 time to fit residues: 10.2779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 287 optimal weight: 7.9990 chunk 386 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 334 optimal weight: 50.0000 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 363 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 372 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4879 ASN ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.063137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048377 restraints weight = 276050.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.049671 restraints weight = 147661.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.050515 restraints weight = 97560.800| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37546 Z= 0.153 Angle : 0.691 18.422 50797 Z= 0.328 Chirality : 0.042 0.258 5719 Planarity : 0.004 0.071 6499 Dihedral : 5.138 74.703 4975 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 0.19 % Allowed : 14.30 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.11 (0.13), residues: 4545 helix: 1.14 (0.11), residues: 2579 sheet: -0.14 (0.30), residues: 302 loop : -2.07 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1031 HIS 0.005 0.001 HIS A 803 PHE 0.029 0.001 PHE A2371 TYR 0.043 0.001 TYR A4322 ARG 0.011 0.000 ARG A1121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6356.79 seconds wall clock time: 119 minutes 4.09 seconds (7144.09 seconds total)