Starting phenix.real_space_refine on Sat Dec 16 13:53:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/12_2023/6tax_10429_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/12_2023/6tax_10429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/12_2023/6tax_10429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/12_2023/6tax_10429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/12_2023/6tax_10429_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tax_10429/12_2023/6tax_10429_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 207 5.16 5 C 22436 2.51 5 N 6060 2.21 5 O 6526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 886": "NH1" <-> "NH2" Residue "A PHE 2371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2507": "NH1" <-> "NH2" Residue "A ARG 2523": "NH1" <-> "NH2" Residue "A TYR 2837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4926": "NH1" <-> "NH2" 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: 35235 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 35235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4420, 35235 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'peptide': 4416, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 181, 'TRANS': 4234, None: 4} Not linked: pdbres="GLY A5150 " pdbres="ATP A5201 " Not linked: pdbres="ATP A5201 " pdbres=" MG A5202 " Not linked: pdbres=" MG A5202 " pdbres=" ZN A5203 " Not linked: pdbres=" ZN A5203 " pdbres=" ZN A5204 " Chain breaks: 15 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'UNK:plan-1': 67, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26222 SG CYS A3962 90.097 130.185 218.776 1.00165.01 S ATOM 26386 SG CYS A3982 86.969 128.250 221.967 1.00171.20 S ATOM 26411 SG CYS A3985 90.556 128.936 222.124 1.00173.12 S ATOM 26112 SG CYS A3947 80.309 123.526 217.441 0.50141.40 S ATOM 26137 SG CYS A3950 77.879 120.194 215.933 1.00139.88 S ATOM 26265 SG CYS A3967 77.339 123.186 214.009 1.00159.05 S ATOM 26290 SG CYS A3970 75.799 123.843 217.598 1.00161.62 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS A3947 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS A3947 " occ=0.50 Time building chain proxies: 17.94, per 1000 atoms: 0.51 Number of scatterers: 35235 At special positions: 0 Unit cell: (128.96, 150.8, 242.32, 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 207 16.00 P 3 15.00 Mg 1 11.99 O 6526 8.00 N 6060 7.00 C 22436 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: 13.66 Conformation dependent library (CDL) restraints added in 6.4 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 A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " 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 A3970 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 9 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 13 sheets defined 53.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 21.44 Creating SS restraints... Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'A' and resid 497 through 511 Processing helix chain 'A' and resid 522 through 539 Processing helix chain 'A' and resid 593 through 604 removed outlier: 4.740A pdb=" N ALA A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 614 through 617 No H-bonds generated for 'chain 'A' and resid 614 through 617' 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 removed outlier: 3.563A pdb=" N CYS A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 657 " --> pdb=" O CYS A 653 " (cutoff:3.500A) 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 748 Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 760 through 774 Proline residue: A 773 - end of helix Processing helix chain 'A' and resid 781 through 800 Processing helix chain 'A' and resid 811 through 826 Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.905A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 888 removed outlier: 3.545A pdb=" N SER A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 917 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 1032 through 1043 removed outlier: 3.796A pdb=" N GLN A1036 " --> pdb=" O PRO A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1048 No H-bonds generated for 'chain 'A' and resid 1045 through 1048' 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 1101 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 1191 through 1202 Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1234 through 1240 removed outlier: 3.753A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1256 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 1277 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: 4.074A 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: 3.919A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1439 removed outlier: 4.644A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1463 removed outlier: 3.848A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1486 removed outlier: 4.114A pdb=" N ASN A1478 " --> pdb=" O ASP A1474 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A1479 " --> pdb=" O SER A1475 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU A1480 " --> pdb=" O ALA A1476 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP A1481 " --> pdb=" O ARG A1477 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 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: 3.637A 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 1690 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 removed outlier: 3.594A pdb=" N THR A1773 " --> pdb=" O ALA A1769 " (cutoff:3.500A) 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: 3.726A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (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: 3.644A 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: 3.990A pdb=" N ASP A2086 " --> pdb=" O PHE A2082 " (cutoff:3.500A) removed outlier: 4.328A 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: 4.080A 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 2317 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: 4.288A pdb=" N SER A2457 " --> pdb=" O GLU A2454 " (cutoff:3.500A) removed outlier: 3.682A 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 2629 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: 4.148A 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: 5.174A pdb=" N SER A2881 " --> pdb=" O GLY A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2884 through 2906 removed outlier: 5.893A pdb=" N GLY A2891 " --> pdb=" O ASP A2887 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A2892 " --> pdb=" O LYS A2888 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A2893 " --> pdb=" O ILE A2889 " (cutoff:3.500A) removed outlier: 4.850A 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: 3.916A pdb=" N CYS A3220 " --> pdb=" O ILE A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3223 through 3231 removed outlier: 4.671A pdb=" N SER A3230 " --> pdb=" O VAL A3226 " (cutoff:3.500A) removed outlier: 5.432A 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 3296 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: 3.821A 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: 4.979A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) removed outlier: 3.645A 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 3763 through 3783 removed outlier: 7.729A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3799 removed outlier: 5.790A pdb=" N ALA A3796 " --> pdb=" O SER A3793 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A3799 " --> pdb=" O ALA A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3808 through 3823 removed outlier: 3.671A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3838 Processing helix chain 'A' and resid 3840 through 3846 Processing helix chain 'A' and resid 3857 through 3889 removed outlier: 5.300A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3909 removed outlier: 4.072A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (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 4045 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: 3.646A 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 4245 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: 3.914A 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: 3.842A 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: 3.554A 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: 4.168A 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: 3.824A 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 4596 Processing helix chain 'A' and resid 4614 through 4634 removed outlier: 4.516A 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: 4.758A pdb=" N LEU A4723 " --> pdb=" O ALA A4719 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A4724 " --> pdb=" O GLU A4720 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS A4725 " --> pdb=" O LEU A4721 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) removed outlier: 4.085A 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: 3.837A 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: 5.283A pdb=" N ARG A5012 " --> pdb=" O LYS A5008 " (cutoff:3.500A) Processing helix chain 'A' and resid 5015 through 5035 removed outlier: 3.923A pdb=" N ILE A5018 " --> pdb=" O LEU A5015 " (cutoff:3.500A) removed outlier: 5.636A 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: 4.283A 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 5115 through 5120 Processing helix chain 'A' and resid 5132 through 5148 Processing sheet with id= A, first strand: chain 'A' and resid 1149 through 1151 Processing sheet with id= B, first strand: chain 'A' and resid 1625 through 1627 removed outlier: 3.673A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1792 through 1796 removed outlier: 7.151A pdb=" N LEU A1888 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A1795 " --> pdb=" O LEU A1888 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A1890 " --> pdb=" O ILE A1795 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 7.654A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLY A1949 " --> pdb=" O HIS A2055 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR A2057 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A1951 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A2059 " --> pdb=" O VAL A1951 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N SER A1953 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE A2061 " --> pdb=" O SER A1953 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A2014 " --> pdb=" O LEU A2056 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A2058 " --> pdb=" O VAL A2014 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A2016 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU A2060 " --> pdb=" O PHE A2016 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE A2018 " --> pdb=" O GLU A2060 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ILE A2020 " --> pdb=" O PRO A2062 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id= F, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id= G, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id= H, first strand: chain 'A' and resid 2377 through 2380 removed outlier: 4.388A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A2443 " --> pdb=" O HIS A2480 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A2482 " --> pdb=" O THR A2443 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A2445 " --> pdb=" O ILE A2482 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA A2484 " --> pdb=" O LEU A2445 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE A2447 " --> pdb=" O ALA A2484 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2859 through 2862 removed outlier: 6.216A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A2801 " --> pdb=" O GLN A2762 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS A2764 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A2803 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A2766 " --> pdb=" O VAL A2803 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 3130 through 3132 removed outlier: 6.148A pdb=" N LEU A3003 " --> pdb=" O HIS A3131 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.573A 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: 8.849A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 3080 through 3082 Processing sheet with id= L, first strand: chain 'A' and resid 3397 through 3399 removed outlier: 6.492A pdb=" N VAL A3371 " --> pdb=" O VAL A3273 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR A3275 " --> pdb=" O VAL A3371 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A3373 " --> pdb=" O THR A3275 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE A3277 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A3375 " --> pdb=" O ILE A3277 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR A3279 " --> pdb=" O PHE A3375 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A3377 " --> pdb=" O THR A3279 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A3304 " --> pdb=" O VAL A3335 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A3337 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A3306 " --> pdb=" O GLN A3337 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP A3339 " --> pdb=" O LEU A3306 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 4880 through 4883 1537 hydrogen bonds defined for protein. 4458 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: 20.59 Time building geometry restraints manager: 14.81 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: 10236 1.33 - 1.46: 7316 1.46 - 1.58: 18095 1.58 - 1.70: 5 1.70 - 1.82: 303 Bond restraints: 35955 Sorted by residual: bond pdb=" C4 ATP A5201 " pdb=" C5 ATP A5201 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C5 ATP A5201 " pdb=" C6 ATP A5201 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.28e+01 bond pdb=" C5 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 1.374 1.322 0.052 1.00e-02 1.00e+04 2.68e+01 bond pdb=" C8 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.310 1.350 -0.040 1.00e-02 1.00e+04 1.61e+01 ... (remaining 35950 not shown) Histogram of bond angle deviations from ideal: 96.41 - 104.37: 542 104.37 - 112.34: 17860 112.34 - 120.31: 16897 120.31 - 128.27: 13017 128.27 - 136.24: 347 Bond angle restraints: 48663 Sorted by residual: angle pdb=" PB ATP A5201 " pdb=" O3B ATP A5201 " pdb=" PG ATP A5201 " ideal model delta sigma weight residual 139.87 121.13 18.74 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PA ATP A5201 " pdb=" O3A ATP A5201 " pdb=" PB ATP A5201 " ideal model delta sigma weight residual 136.83 121.91 14.92 1.00e+00 1.00e+00 2.23e+02 angle pdb=" C5 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N3 ATP A5201 " ideal model delta sigma weight residual 126.80 118.94 7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" N3 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 127.04 134.61 -7.57 1.15e+00 7.59e-01 4.35e+01 angle pdb=" N GLU A4279 " pdb=" CA GLU A4279 " pdb=" C GLU A4279 " ideal model delta sigma weight residual 114.56 107.03 7.53 1.27e+00 6.20e-01 3.52e+01 ... (remaining 48658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 20577 16.70 - 33.40: 1088 33.40 - 50.10: 197 50.10 - 66.79: 16 66.79 - 83.49: 34 Dihedral angle restraints: 21912 sinusoidal: 8926 harmonic: 12986 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 180.00 119.33 60.67 0 5.00e+00 4.00e-02 1.47e+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 180.00 132.87 47.13 0 5.00e+00 4.00e-02 8.88e+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 -136.64 -43.36 0 5.00e+00 4.00e-02 7.52e+01 ... (remaining 21909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4550 0.080 - 0.159: 860 0.159 - 0.239: 88 0.239 - 0.318: 7 0.318 - 0.398: 6 Chirality restraints: 5511 Sorted by residual: chirality pdb=" CB ILE A1373 " pdb=" CA ILE A1373 " pdb=" CG1 ILE A1373 " pdb=" CG2 ILE A1373 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB ILE A 896 " pdb=" CA ILE A 896 " pdb=" CG1 ILE A 896 " pdb=" CG2 ILE A 896 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL A4048 " pdb=" CA VAL A4048 " pdb=" CG1 VAL A4048 " pdb=" CG2 VAL A4048 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5508 not shown) Planarity restraints: 6228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A3122 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A3123 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A3123 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A3123 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 687 " -0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO A 688 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A5023 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLN A5023 " 0.063 2.00e-02 2.50e+03 pdb=" O GLN A5023 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A5024 " -0.021 2.00e-02 2.50e+03 ... (remaining 6225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 393 2.63 - 3.20: 31500 3.20 - 3.77: 55974 3.77 - 4.33: 76296 4.33 - 4.90: 123574 Nonbonded interactions: 287737 Sorted by model distance: nonbonded pdb=" OG SER A1961 " pdb="MG MG A5202 " model vdw 2.065 2.170 nonbonded pdb=" OG1 THR A1820 " pdb=" OD1 ASP A1822 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A1666 " pdb=" O MET A1690 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR A3664 " pdb=" OG1 THR A3692 " model vdw 2.273 2.440 nonbonded pdb=" O LEU A2945 " pdb=" OG SER A2949 " model vdw 2.274 2.440 ... (remaining 287732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.870 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: 11.370 Check model and map are aligned: 0.600 Set scattering table: 0.390 Process input model: 104.990 Find NCS groups from input model: 0.940 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.009 0.108 35955 Z= 0.595 Angle : 1.127 19.136 48663 Z= 0.606 Chirality : 0.063 0.398 5511 Planarity : 0.008 0.114 6228 Dihedral : 11.276 83.492 13448 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.49 % Favored : 90.32 % Rotamer: Outliers : 0.46 % Allowed : 2.82 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.81 % Twisted General : 0.14 % 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: -4.10 (0.10), residues: 4319 helix: -2.34 (0.08), residues: 2479 sheet: -1.45 (0.31), residues: 232 loop : -3.35 (0.13), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A5135 HIS 0.023 0.003 HIS A2688 PHE 0.058 0.004 PHE A2960 TYR 0.048 0.004 TYR A2057 ARG 0.018 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 473 time to evaluate : 4.145 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 outliers start: 18 outliers final: 5 residues processed: 489 average time/residue: 0.6376 time to fit residues: 469.6548 Evaluate side-chains 297 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 3.970 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3218 time to fit residues: 8.8980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 0.9980 chunk 335 optimal weight: 0.9980 chunk 185 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 401 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 GLN A 822 HIS A 827 ASN A 831 ASN A1089 HIS A1186 HIS ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN A1429 HIS A1453 ASN A1579 ASN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 HIS A1770 HIS A1791 GLN A1816 GLN A1920 ASN A1930 GLN A2139 GLN A2161 HIS A2273 HIS A2480 HIS A2677 ASN A2790 GLN A2942 HIS A2981 GLN A3013 GLN ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 HIS A3252 HIS A3337 GLN A3542 GLN A3575 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3705 GLN A3914 ASN A4008 HIS A4176 GLN A4196 GLN A4242 GLN A4249 HIS ** A4252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4382 ASN A4420 ASN A4543 HIS A4560 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4587 HIS ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4674 GLN A4697 HIS A4757 HIS A4834 HIS ** A4842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN A4879 ASN A4886 GLN A4892 GLN ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4932 HIS A4957 GLN A5017 HIS A5028 HIS A5056 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35955 Z= 0.207 Angle : 0.663 12.427 48663 Z= 0.337 Chirality : 0.042 0.272 5511 Planarity : 0.005 0.089 6228 Dihedral : 6.369 88.710 4796 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.38 % Favored : 91.53 % Rotamer: Outliers : 1.08 % Allowed : 7.23 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -2.28 (0.12), residues: 4319 helix: -0.60 (0.10), residues: 2455 sheet: -1.15 (0.32), residues: 238 loop : -2.98 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A3659 HIS 0.009 0.001 HIS A4587 PHE 0.035 0.002 PHE A2371 TYR 0.029 0.002 TYR A3901 ARG 0.007 0.001 ARG A4155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 305 time to evaluate : 4.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 334 average time/residue: 0.5708 time to fit residues: 300.9872 Evaluate side-chains 289 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 270 time to evaluate : 4.559 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3584 time to fit residues: 19.9697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 chunk 273 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 402 optimal weight: 7.9990 chunk 434 optimal weight: 0.8980 chunk 358 optimal weight: 0.0570 chunk 398 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 322 optimal weight: 2.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A 683 ASN A1378 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1757 HIS A2273 HIS ** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3037 GLN A3600 GLN A3705 GLN A3799 HIS ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4176 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4623 HIS A4757 HIS ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35955 Z= 0.191 Angle : 0.622 11.534 48663 Z= 0.313 Chirality : 0.041 0.191 5511 Planarity : 0.005 0.092 6228 Dihedral : 5.895 87.840 4796 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.80 % Favored : 91.16 % Rotamer: Outliers : 1.10 % Allowed : 8.41 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4319 helix: 0.17 (0.10), residues: 2463 sheet: -1.06 (0.32), residues: 239 loop : -2.75 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4555 HIS 0.006 0.001 HIS A 796 PHE 0.030 0.001 PHE A2371 TYR 0.023 0.001 TYR A2146 ARG 0.009 0.000 ARG A3662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 295 time to evaluate : 4.553 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 outliers start: 43 outliers final: 12 residues processed: 325 average time/residue: 0.6058 time to fit residues: 307.7262 Evaluate side-chains 272 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 260 time to evaluate : 4.220 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3440 time to fit residues: 13.7359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 403 optimal weight: 3.9990 chunk 427 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 382 optimal weight: 0.0670 chunk 115 optimal weight: 7.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A 683 ASN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3017 GLN ** A3871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN A4757 HIS A5014 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35955 Z= 0.173 Angle : 0.602 10.542 48663 Z= 0.301 Chirality : 0.041 0.231 5511 Planarity : 0.004 0.093 6228 Dihedral : 5.665 87.854 4796 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.45 % Favored : 91.50 % Rotamer: Outliers : 1.18 % Allowed : 9.00 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4319 helix: 0.55 (0.11), residues: 2456 sheet: -0.97 (0.32), residues: 248 loop : -2.58 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2541 HIS 0.005 0.001 HIS A 796 PHE 0.027 0.001 PHE A2371 TYR 0.021 0.001 TYR A2146 ARG 0.006 0.000 ARG A3662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 277 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 310 average time/residue: 0.5794 time to fit residues: 285.0305 Evaluate side-chains 280 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 260 time to evaluate : 4.186 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3419 time to fit residues: 18.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 8.9990 chunk 242 optimal weight: 0.9990 chunk 6 optimal weight: 0.0040 chunk 318 optimal weight: 0.0060 chunk 176 optimal weight: 0.7980 chunk 364 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A 683 ASN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 GLN A3538 GLN A3600 GLN ** A3871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN ** A4634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4679 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35955 Z= 0.160 Angle : 0.589 10.154 48663 Z= 0.294 Chirality : 0.040 0.192 5511 Planarity : 0.004 0.092 6228 Dihedral : 5.511 88.101 4796 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.52 % Favored : 91.46 % Rotamer: Outliers : 0.74 % Allowed : 9.85 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -0.74 (0.13), residues: 4319 helix: 0.77 (0.11), residues: 2458 sheet: -0.81 (0.32), residues: 246 loop : -2.49 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A4555 HIS 0.005 0.001 HIS A1454 PHE 0.024 0.001 PHE A2371 TYR 0.033 0.001 TYR A 648 ARG 0.007 0.000 ARG A1327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 269 time to evaluate : 3.169 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 outliers start: 29 outliers final: 15 residues processed: 290 average time/residue: 0.4286 time to fit residues: 198.7419 Evaluate side-chains 270 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 3.189 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2804 time to fit residues: 12.3487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.0980 chunk 384 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 250 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 427 optimal weight: 0.8980 chunk 355 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: