Starting phenix.real_space_refine on Sun Mar 17 08:27:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig9_9664/03_2024/6ig9_9664.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig9_9664/03_2024/6ig9_9664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig9_9664/03_2024/6ig9_9664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig9_9664/03_2024/6ig9_9664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig9_9664/03_2024/6ig9_9664.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig9_9664/03_2024/6ig9_9664.pdb" } resolution = 4.6 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= 0.003 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: 3 Type Number sf(0) Gaussians C 10350 2.51 5 N 3386 2.21 5 O 3386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17122 Number of models: 1 Model: "" Number of chains: 1 Chain: "T" Number of atoms: 17122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3386, 17122 Classifications: {'peptide': 3386} Incomplete info: {'truncation_to_alanine': 2983} Link IDs: {'PTRANS': 139, 'TRANS': 3246} Chain breaks: 38 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11085 Unresolved non-hydrogen angles: 14190 Unresolved non-hydrogen dihedrals: 9185 Unresolved non-hydrogen chiralities: 1088 Planarities with less than four sites: {'GLN:plan1': 140, 'HIS:plan': 72, 'TYR:plan': 126, 'ASN:plan1': 206, 'TRP:plan': 39, 'ASP:plan': 174, 'PHE:plan': 204, 'GLU:plan': 215, 'ARG:plan': 155} Unresolved non-hydrogen planarities: 6152 Time building chain proxies: 9.28, per 1000 atoms: 0.54 Number of scatterers: 17122 At special positions: 0 Unit cell: (134.496, 201.744, 142.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3386 8.00 N 3386 7.00 C 10350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.75 Conformation dependent library (CDL) restraints added in 4.5 seconds 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6608 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 3 sheets defined 75.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'T' and resid 3 through 13 Processing helix chain 'T' and resid 21 through 37 removed outlier: 3.828A pdb=" N LEU T 31 " --> pdb=" O THR T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 62 Proline residue: T 53 - end of helix Processing helix chain 'T' and resid 71 through 84 removed outlier: 3.856A pdb=" N ILE T 82 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 106 removed outlier: 4.075A pdb=" N TYR T 95 " --> pdb=" O THR T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 131 removed outlier: 3.657A pdb=" N LYS T 120 " --> pdb=" O ILE T 116 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER T 128 " --> pdb=" O THR T 124 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 156 removed outlier: 3.597A pdb=" N PHE T 140 " --> pdb=" O LYS T 136 " (cutoff:3.500A) Proline residue: T 152 - end of helix Processing helix chain 'T' and resid 217 through 222 Processing helix chain 'T' and resid 231 through 242 removed outlier: 3.710A pdb=" N SER T 237 " --> pdb=" O THR T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 248 through 258 removed outlier: 3.677A pdb=" N LEU T 252 " --> pdb=" O GLU T 248 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN T 258 " --> pdb=" O MET T 254 " (cutoff:3.500A) Processing helix chain 'T' and resid 292 through 310 removed outlier: 3.595A pdb=" N PHE T 304 " --> pdb=" O LYS T 300 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE T 309 " --> pdb=" O LEU T 305 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE T 310 " --> pdb=" O ALA T 306 " (cutoff:3.500A) Processing helix chain 'T' and resid 323 through 335 removed outlier: 4.106A pdb=" N ASP T 327 " --> pdb=" O ASN T 323 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 357 Processing helix chain 'T' and resid 358 through 368 Proline residue: T 365 - end of helix Processing helix chain 'T' and resid 369 through 373 Processing helix chain 'T' and resid 382 through 402 removed outlier: 3.949A pdb=" N THR T 386 " --> pdb=" O THR T 382 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU T 387 " --> pdb=" O MET T 383 " (cutoff:3.500A) Proline residue: T 389 - end of helix Processing helix chain 'T' and resid 407 through 424 Processing helix chain 'T' and resid 428 through 451 Processing helix chain 'T' and resid 456 through 503 removed outlier: 3.658A pdb=" N ASN T 473 " --> pdb=" O ASP T 469 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS T 487 " --> pdb=" O ASP T 483 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR T 488 " --> pdb=" O THR T 484 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY T 490 " --> pdb=" O MET T 486 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG T 491 " --> pdb=" O LYS T 487 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU T 498 " --> pdb=" O THR T 494 " (cutoff:3.500A) Processing helix chain 'T' and resid 512 through 520 removed outlier: 3.698A pdb=" N PHE T 517 " --> pdb=" O GLU T 513 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET T 518 " --> pdb=" O SER T 514 " (cutoff:3.500A) Processing helix chain 'T' and resid 560 through 566 removed outlier: 4.019A pdb=" N LYS T 564 " --> pdb=" O MET T 560 " (cutoff:3.500A) Processing helix chain 'T' and resid 578 through 600 Processing helix chain 'T' and resid 601 through 603 No H-bonds generated for 'chain 'T' and resid 601 through 603' Processing helix chain 'T' and resid 607 through 611 Processing helix chain 'T' and resid 627 through 645 removed outlier: 3.550A pdb=" N LEU T 637 " --> pdb=" O VAL T 633 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE T 638 " --> pdb=" O PHE T 634 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE T 643 " --> pdb=" O HIS T 639 " (cutoff:3.500A) Processing helix chain 'T' and resid 677 through 692 Processing helix chain 'T' and resid 694 through 714 Proline residue: T 707 - end of helix Processing helix chain 'T' and resid 717 through 729 removed outlier: 3.923A pdb=" N HIS T 721 " --> pdb=" O SER T 717 " (cutoff:3.500A) Processing helix chain 'T' and resid 732 through 748 removed outlier: 3.970A pdb=" N GLY T 738 " --> pdb=" O PRO T 734 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE T 739 " --> pdb=" O ASN T 735 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU T 740 " --> pdb=" O PHE T 736 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY T 746 " --> pdb=" O ARG T 742 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS T 747 " --> pdb=" O PHE T 743 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 752 removed outlier: 4.085A pdb=" N GLY T 752 " --> pdb=" O LYS T 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 749 through 752' Processing helix chain 'T' and resid 755 through 771 removed outlier: 3.502A pdb=" N MET T 771 " --> pdb=" O LYS T 767 " (cutoff:3.500A) Processing helix chain 'T' and resid 771 through 776 Processing helix chain 'T' and resid 784 through 802 removed outlier: 3.827A pdb=" N ASN T 789 " --> pdb=" O LEU T 785 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP T 790 " --> pdb=" O PRO T 786 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE T 792 " --> pdb=" O LEU T 788 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU T 793 " --> pdb=" O ASN T 789 " (cutoff:3.500A) Processing helix chain 'T' and resid 804 through 817 removed outlier: 4.203A pdb=" N TYR T 808 " --> pdb=" O GLU T 804 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE T 812 " --> pdb=" O TYR T 808 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG T 813 " --> pdb=" O PHE T 809 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR T 814 " --> pdb=" O TYR T 810 " (cutoff:3.500A) Processing helix chain 'T' and resid 824 through 846 removed outlier: 4.266A pdb=" N TYR T 828 " --> pdb=" O PHE T 824 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG T 829 " --> pdb=" O GLU T 825 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER T 830 " --> pdb=" O ASN T 826 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE T 831 " --> pdb=" O LEU T 827 " (cutoff:3.500A) Proline residue: T 833 - end of helix Processing helix chain 'T' and resid 852 through 861 removed outlier: 3.776A pdb=" N GLU T 856 " --> pdb=" O PRO T 852 " (cutoff:3.500A) Processing helix chain 'T' and resid 879 through 887 removed outlier: 3.913A pdb=" N LEU T 883 " --> pdb=" O LEU T 879 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL T 884 " --> pdb=" O MET T 880 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE T 885 " --> pdb=" O LYS T 881 " (cutoff:3.500A) Processing helix chain 'T' and resid 893 through 905 removed outlier: 3.645A pdb=" N GLY T 897 " --> pdb=" O LEU T 893 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU T 902 " --> pdb=" O LEU T 898 " (cutoff:3.500A) Processing helix chain 'T' and resid 920 through 932 removed outlier: 3.685A pdb=" N ASN T 930 " --> pdb=" O LYS T 926 " (cutoff:3.500A) Processing helix chain 'T' and resid 938 through 950 Processing helix chain 'T' and resid 996 through 1006 removed outlier: 3.667A pdb=" N LEU T1004 " --> pdb=" O ALA T1000 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN T1005 " --> pdb=" O LEU T1001 " (cutoff:3.500A) Processing helix chain 'T' and resid 1010 through 1031 removed outlier: 3.952A pdb=" N LEU T1026 " --> pdb=" O THR T1022 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR T1029 " --> pdb=" O LEU T1025 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER T1031 " --> pdb=" O LEU T1027 " (cutoff:3.500A) Processing helix chain 'T' and resid 1039 through 1052 Processing helix chain 'T' and resid 1068 through 1091 removed outlier: 3.591A pdb=" N TYR T1072 " --> pdb=" O ASN T1068 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL T1086 " --> pdb=" O LEU T1082 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE T1087 " --> pdb=" O LEU T1083 " (cutoff:3.500A) Processing helix chain 'T' and resid 1095 through 1124 removed outlier: 3.703A pdb=" N ALA T1099 " --> pdb=" O LEU T1095 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU T1112 " --> pdb=" O ASP T1108 " (cutoff:3.500A) Processing helix chain 'T' and resid 1142 through 1152 removed outlier: 4.071A pdb=" N ILE T1149 " --> pdb=" O ILE T1145 " (cutoff:3.500A) Proline residue: T1150 - end of helix Processing helix chain 'T' and resid 1157 through 1179 removed outlier: 3.625A pdb=" N ARG T1161 " --> pdb=" O ILE T1157 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR T1168 " --> pdb=" O GLY T1164 " (cutoff:3.500A) Processing helix chain 'T' and resid 1182 through 1189 Processing helix chain 'T' and resid 1189 through 1203 removed outlier: 3.872A pdb=" N LEU T1193 " --> pdb=" O PHE T1189 " (cutoff:3.500A) Processing helix chain 'T' and resid 1205 through 1224 removed outlier: 3.865A pdb=" N GLY T1211 " --> pdb=" O TYR T1207 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY T1212 " --> pdb=" O ASN T1208 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN T1222 " --> pdb=" O VAL T1218 " (cutoff:3.500A) Processing helix chain 'T' and resid 1227 through 1233 Processing helix chain 'T' and resid 1233 through 1248 removed outlier: 3.902A pdb=" N THR T1248 " --> pdb=" O VAL T1244 " (cutoff:3.500A) Processing helix chain 'T' and resid 1253 through 1272 removed outlier: 4.624A pdb=" N THR T1257 " --> pdb=" O PRO T1253 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU T1261 " --> pdb=" O THR T1257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU T1263 " --> pdb=" O SER T1259 " (cutoff:3.500A) Processing helix chain 'T' and resid 1283 through 1296 Processing helix chain 'T' and resid 1300 through 1317 removed outlier: 3.710A pdb=" N ALA T1306 " --> pdb=" O LYS T1302 " (cutoff:3.500A) Processing helix chain 'T' and resid 1321 through 1335 removed outlier: 3.543A pdb=" N HIS T1328 " --> pdb=" O LYS T1324 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER T1335 " --> pdb=" O GLN T1331 " (cutoff:3.500A) Processing helix chain 'T' and resid 1335 through 1340 removed outlier: 3.903A pdb=" N LYS T1340 " --> pdb=" O PRO T1336 " (cutoff:3.500A) Processing helix chain 'T' and resid 1346 through 1359 Processing helix chain 'T' and resid 1371 through 1384 removed outlier: 3.508A pdb=" N LEU T1378 " --> pdb=" O LEU T1374 " (cutoff:3.500A) Processing helix chain 'T' and resid 1403 through 1425 Processing helix chain 'T' and resid 1435 through 1451 removed outlier: 3.539A pdb=" N ARG T1439 " --> pdb=" O ASN T1435 " (cutoff:3.500A) Processing helix chain 'T' and resid 1452 through 1466 Processing helix chain 'T' and resid 1475 through 1491 removed outlier: 3.734A pdb=" N GLY T1481 " --> pdb=" O LEU T1477 " (cutoff:3.500A) Proline residue: T1484 - end of helix Processing helix chain 'T' and resid 1497 through 1510 Processing helix chain 'T' and resid 1516 through 1530 removed outlier: 3.870A pdb=" N ARG T1520 " --> pdb=" O VAL T1516 " (cutoff:3.500A) Processing helix chain 'T' and resid 1531 through 1538 removed outlier: 3.975A pdb=" N LEU T1535 " --> pdb=" O ARG T1531 " (cutoff:3.500A) Processing helix chain 'T' and resid 1546 through 1559 removed outlier: 3.596A pdb=" N PHE T1559 " --> pdb=" O ILE T1555 " (cutoff:3.500A) Processing helix chain 'T' and resid 1560 through 1562 No H-bonds generated for 'chain 'T' and resid 1560 through 1562' Processing helix chain 'T' and resid 1566 through 1585 removed outlier: 4.567A pdb=" N LEU T1574 " --> pdb=" O LEU T1570 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU T1575 " --> pdb=" O ASN T1571 " (cutoff:3.500A) Processing helix chain 'T' and resid 1593 through 1603 removed outlier: 3.594A pdb=" N ALA T1597 " --> pdb=" O ARG T1593 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN T1601 " --> pdb=" O ALA T1597 " (cutoff:3.500A) Processing helix chain 'T' and resid 1604 through 1614 Processing helix chain 'T' and resid 1617 through 1630 Processing helix chain 'T' and resid 1634 through 1654 removed outlier: 3.527A pdb=" N GLU T1638 " --> pdb=" O LYS T1634 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP T1645 " --> pdb=" O GLU T1641 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN T1646 " --> pdb=" O LYS T1642 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE T1652 " --> pdb=" O TYR T1648 " (cutoff:3.500A) Processing helix chain 'T' and resid 1660 through 1680 removed outlier: 3.558A pdb=" N MET T1669 " --> pdb=" O PHE T1665 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL T1670 " --> pdb=" O PHE T1666 " (cutoff:3.500A) Processing helix chain 'T' and resid 1689 through 1707 removed outlier: 3.764A pdb=" N LEU T1693 " --> pdb=" O GLY T1689 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET T1698 " --> pdb=" O LYS T1694 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN T1700 " --> pdb=" O LYS T1696 " (cutoff:3.500A) Processing helix chain 'T' and resid 1715 through 1736 removed outlier: 3.810A pdb=" N SER T1721 " --> pdb=" O GLN T1717 " (cutoff:3.500A) Processing helix chain 'T' and resid 1740 through 1753 removed outlier: 3.892A pdb=" N LEU T1744 " --> pdb=" O GLN T1740 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER T1753 " --> pdb=" O ASP T1749 " (cutoff:3.500A) Processing helix chain 'T' and resid 1758 through 1770 Processing helix chain 'T' and resid 1776 through 1790 Processing helix chain 'T' and resid 1797 through 1817 removed outlier: 3.508A pdb=" N VAL T1815 " --> pdb=" O LEU T1811 " (cutoff:3.500A) Processing helix chain 'T' and resid 1821 through 1826 Processing helix chain 'T' and resid 1831 through 1844 Processing helix chain 'T' and resid 1858 through 1874 Processing helix chain 'T' and resid 1880 through 1896 Processing helix chain 'T' and resid 1898 through 1916 Processing helix chain 'T' and resid 1919 through 1932 Processing helix chain 'T' and resid 1938 through 1960 Proline residue: T1951 - end of helix removed outlier: 4.026A pdb=" N HIS T1954 " --> pdb=" O THR T1950 " (cutoff:3.500A) Processing helix chain 'T' and resid 1965 through 1976 Processing helix chain 'T' and resid 1980 through 1998 removed outlier: 3.699A pdb=" N ILE T1984 " --> pdb=" O SER T1980 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS T1992 " --> pdb=" O PHE T1988 " (cutoff:3.500A) Proline residue: T1993 - end of helix Processing helix chain 'T' and resid 2000 through 2016 Processing helix chain 'T' and resid 2023 through 2041 Processing helix chain 'T' and resid 2090 through 2106 Processing helix chain 'T' and resid 2116 through 2129 Processing helix chain 'T' and resid 2158 through 2176 removed outlier: 4.145A pdb=" N THR T2176 " --> pdb=" O PHE T2172 " (cutoff:3.500A) Processing helix chain 'T' and resid 2182 through 2194 Processing helix chain 'T' and resid 2202 through 2218 Processing helix chain 'T' and resid 2231 through 2247 removed outlier: 4.392A pdb=" N LEU T2247 " --> pdb=" O ILE T2243 " (cutoff:3.500A) Processing helix chain 'T' and resid 2249 through 2267 Processing helix chain 'T' and resid 2274 through 2293 Processing helix chain 'T' and resid 2302 through 2322 removed outlier: 3.784A pdb=" N ILE T2306 " --> pdb=" O GLU T2302 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER T2319 " --> pdb=" O LEU T2315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU T2320 " --> pdb=" O TYR T2316 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS T2321 " --> pdb=" O ILE T2317 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL T2322 " --> pdb=" O LEU T2318 " (cutoff:3.500A) Processing helix chain 'T' and resid 2328 through 2342 removed outlier: 3.611A pdb=" N SER T2334 " --> pdb=" O ARG T2330 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR T2335 " --> pdb=" O PRO T2331 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL T2336 " --> pdb=" O PHE T2332 " (cutoff:3.500A) Processing helix chain 'T' and resid 2345 through 2361 removed outlier: 3.914A pdb=" N LEU T2349 " --> pdb=" O ASP T2345 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG T2350 " --> pdb=" O GLN T2346 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN T2354 " --> pdb=" O ARG T2350 " (cutoff:3.500A) Processing helix chain 'T' and resid 2369 through 2379 removed outlier: 3.509A pdb=" N LEU T2376 " --> pdb=" O LYS T2372 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS T2378 " --> pdb=" O ALA T2374 " (cutoff:3.500A) Processing helix chain 'T' and resid 2380 through 2383 Processing helix chain 'T' and resid 2388 through 2403 Processing helix chain 'T' and resid 2412 through 2425 removed outlier: 3.689A pdb=" N GLN T2418 " --> pdb=" O VAL T2414 " (cutoff:3.500A) Proline residue: T2419 - end of helix removed outlier: 3.683A pdb=" N VAL T2422 " --> pdb=" O GLN T2418 " (cutoff:3.500A) Processing helix chain 'T' and resid 2428 through 2442 Processing helix chain 'T' and resid 2446 through 2456 Processing helix chain 'T' and resid 2468 through 2479 removed outlier: 3.757A pdb=" N SER T2479 " --> pdb=" O LEU T2475 " (cutoff:3.500A) Processing helix chain 'T' and resid 2499 through 2503 removed outlier: 3.785A pdb=" N TYR T2503 " --> pdb=" O LEU T2500 " (cutoff:3.500A) Processing helix chain 'T' and resid 2516 through 2534 removed outlier: 3.560A pdb=" N PHE T2522 " --> pdb=" O GLU T2518 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE T2527 " --> pdb=" O VAL T2523 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS T2534 " --> pdb=" O MET T2530 " (cutoff:3.500A) Processing helix chain 'T' and resid 2537 through 2549 removed outlier: 3.775A pdb=" N PHE T2541 " --> pdb=" O ILE T2537 " (cutoff:3.500A) Processing helix chain 'T' and resid 2552 through 2568 removed outlier: 3.581A pdb=" N ILE T2556 " --> pdb=" O ASP T2552 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL T2561 " --> pdb=" O HIS T2557 " (cutoff:3.500A) Proline residue: T2565 - end of helix removed outlier: 3.886A pdb=" N TYR T2568 " --> pdb=" O PHE T2564 " (cutoff:3.500A) Processing helix chain 'T' and resid 2572 through 2589 Processing helix chain 'T' and resid 2602 through 2612 Processing helix chain 'T' and resid 2620 through 2628 Processing helix chain 'T' and resid 2633 through 2646 removed outlier: 3.530A pdb=" N ILE T2637 " --> pdb=" O TRP T2633 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN T2638 " --> pdb=" O TYR T2634 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE T2639 " --> pdb=" O GLN T2635 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE T2643 " --> pdb=" O ILE T2639 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN T2644 " --> pdb=" O LEU T2640 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER T2645 " --> pdb=" O GLU T2641 " (cutoff:3.500A) Processing helix chain 'T' and resid 2651 through 2669 removed outlier: 3.640A pdb=" N VAL T2667 " --> pdb=" O LEU T2663 " (cutoff:3.500A) Processing helix chain 'T' and resid 2671 through 2681 removed outlier: 4.003A pdb=" N PHE T2675 " --> pdb=" O GLU T2671 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG T2680 " --> pdb=" O TYR T2676 " (cutoff:3.500A) Processing helix chain 'T' and resid 2685 through 2697 removed outlier: 3.637A pdb=" N SER T2693 " --> pdb=" O ASN T2689 " (cutoff:3.500A) Processing helix chain 'T' and resid 2699 through 2715 removed outlier: 3.579A pdb=" N GLN T2705 " --> pdb=" O ASP T2701 " (cutoff:3.500A) Processing helix chain 'T' and resid 2722 through 2740 removed outlier: 3.912A pdb=" N TYR T2726 " --> pdb=" O SER T2722 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP T2729 " --> pdb=" O GLU T2725 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU T2740 " --> pdb=" O CYS T2736 " (cutoff:3.500A) Processing helix chain 'T' and resid 2742 through 2752 removed outlier: 4.640A pdb=" N HIS T2752 " --> pdb=" O GLU T2748 " (cutoff:3.500A) Processing helix chain 'T' and resid 2756 through 2764 Processing helix chain 'T' and resid 2768 through 2782 Processing helix chain 'T' and resid 2788 through 2806 removed outlier: 4.289A pdb=" N GLN T2792 " --> pdb=" O THR T2788 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA T2799 " --> pdb=" O LYS T2795 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU T2805 " --> pdb=" O GLN T2801 " (cutoff:3.500A) Processing helix chain 'T' and resid 2811 through 2817 Processing helix chain 'T' and resid 2818 through 2825 Processing helix chain 'T' and resid 2826 through 2830 removed outlier: 3.764A pdb=" N VAL T2829 " --> pdb=" O ILE T2826 " (cutoff:3.500A) Processing helix chain 'T' and resid 2837 through 2866 removed outlier: 4.011A pdb=" N HIS T2844 " --> pdb=" O LYS T2840 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET T2850 " --> pdb=" O PHE T2846 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN T2857 " --> pdb=" O LEU T2853 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE T2858 " --> pdb=" O GLU T2854 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU T2862 " --> pdb=" O ILE T2858 " (cutoff:3.500A) Processing helix chain 'T' and resid 2873 through 2887 removed outlier: 3.734A pdb=" N ILE T2880 " --> pdb=" O GLU T2876 " (cutoff:3.500A) Processing helix chain 'T' and resid 2894 through 2924 removed outlier: 3.593A pdb=" N ALA T2908 " --> pdb=" O TRP T2904 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL T2911 " --> pdb=" O HIS T2907 " (cutoff:3.500A) Proline residue: T2918 - end of helix Proline residue: T2921 - end of helix Processing helix chain 'T' and resid 2942 through 2958 removed outlier: 3.799A pdb=" N VAL T2946 " --> pdb=" O GLU T2942 " (cutoff:3.500A) Processing helix chain 'T' and resid 2960 through 2970 removed outlier: 3.674A pdb=" N ARG T2969 " --> pdb=" O SER T2965 " (cutoff:3.500A) Processing helix chain 'T' and resid 2977 through 2991 Processing helix chain 'T' and resid 2997 through 3009 removed outlier: 4.055A pdb=" N ASN T3008 " --> pdb=" O ASP T3004 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR T3009 " --> pdb=" O VAL T3005 " (cutoff:3.500A) Processing helix chain 'T' and resid 3015 through 3031 removed outlier: 3.881A pdb=" N LYS T3019 " --> pdb=" O GLY T3015 " (cutoff:3.500A) Processing helix chain 'T' and resid 3032 through 3034 No H-bonds generated for 'chain 'T' and resid 3032 through 3034' Processing helix chain 'T' and resid 3035 through 3051 removed outlier: 3.639A pdb=" N ALA T3039 " --> pdb=" O ALA T3035 " (cutoff:3.500A) Processing helix chain 'T' and resid 3055 through 3071 Processing helix chain 'T' and resid 3073 through 3091 removed outlier: 3.537A pdb=" N PHE T3077 " --> pdb=" O ASN T3073 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER T3079 " --> pdb=" O ILE T3075 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER T3083 " --> pdb=" O SER T3079 " (cutoff:3.500A) Processing helix chain 'T' and resid 3096 through 3110 removed outlier: 3.654A pdb=" N LEU T3100 " --> pdb=" O LYS T3096 " (cutoff:3.500A) Processing helix chain 'T' and resid 3116 through 3124 removed outlier: 3.558A pdb=" N ALA T3120 " --> pdb=" O MET T3116 " (cutoff:3.500A) Processing helix chain 'T' and resid 3129 through 3134 Processing helix chain 'T' and resid 3136 through 3147 removed outlier: 3.518A pdb=" N THR T3142 " --> pdb=" O PRO T3138 " (cutoff:3.500A) Processing helix chain 'T' and resid 3149 through 3163 removed outlier: 4.041A pdb=" N ARG T3158 " --> pdb=" O HIS T3154 " (cutoff:3.500A) Processing helix chain 'T' and resid 3165 through 3183 removed outlier: 3.961A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU T3176 " --> pdb=" O ARG T3172 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP T3177 " --> pdb=" O THR T3173 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL T3180 " --> pdb=" O GLU T3176 " (cutoff:3.500A) Processing helix chain 'T' and resid 3203 through 3218 Processing helix chain 'T' and resid 3219 through 3238 Processing helix chain 'T' and resid 3242 through 3263 removed outlier: 3.627A pdb=" N PHE T3246 " --> pdb=" O ASP T3242 " (cutoff:3.500A) Processing helix chain 'T' and resid 3274 through 3287 Processing helix chain 'T' and resid 3292 through 3302 removed outlier: 3.690A pdb=" N PHE T3296 " --> pdb=" O ILE T3292 " (cutoff:3.500A) Processing helix chain 'T' and resid 3306 through 3327 removed outlier: 3.767A pdb=" N ARG T3327 " --> pdb=" O ASN T3323 " (cutoff:3.500A) Processing helix chain 'T' and resid 3335 through 3338 Processing helix chain 'T' and resid 3339 through 3344 removed outlier: 3.828A pdb=" N ASN T3343 " --> pdb=" O PRO T3339 " (cutoff:3.500A) Processing helix chain 'T' and resid 3345 through 3348 Processing helix chain 'T' and resid 3411 through 3433 removed outlier: 3.526A pdb=" N ARG T3418 " --> pdb=" O ARG T3414 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG T3424 " --> pdb=" O PHE T3420 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN T3427 " --> pdb=" O TYR T3423 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS T3428 " --> pdb=" O ARG T3424 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER T3429 " --> pdb=" O LEU T3425 " (cutoff:3.500A) Processing helix chain 'T' and resid 3433 through 3439 removed outlier: 3.732A pdb=" N ARG T3437 " --> pdb=" O ASN T3433 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3478 removed outlier: 3.634A pdb=" N LYS T3478 " --> pdb=" O PHE T3474 " (cutoff:3.500A) Processing helix chain 'T' and resid 3481 through 3497 removed outlier: 3.692A pdb=" N LEU T3493 " --> pdb=" O MET T3489 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS T3497 " --> pdb=" O LEU T3493 " (cutoff:3.500A) Processing helix chain 'T' and resid 3504 through 3521 removed outlier: 3.727A pdb=" N LEU T3509 " --> pdb=" O ASP T3505 " (cutoff:3.500A) Processing helix chain 'T' and resid 3526 through 3535 removed outlier: 3.630A pdb=" N PHE T3531 " --> pdb=" O LEU T3527 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE T3535 " --> pdb=" O PHE T3531 " (cutoff:3.500A) Processing helix chain 'T' and resid 3537 through 3563 removed outlier: 3.804A pdb=" N SER T3550 " --> pdb=" O LYS T3546 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR T3552 " --> pdb=" O PHE T3548 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER T3554 " --> pdb=" O SER T3550 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL T3556 " --> pdb=" O TYR T3552 " (cutoff:3.500A) Processing helix chain 'T' and resid 3625 through 3633 removed outlier: 3.827A pdb=" N GLY T3633 " --> pdb=" O GLN T3629 " (cutoff:3.500A) Processing helix chain 'T' and resid 3633 through 3654 removed outlier: 3.887A pdb=" N GLU T3638 " --> pdb=" O ASP T3634 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA T3642 " --> pdb=" O GLU T3638 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL T3643 " --> pdb=" O GLY T3639 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU T3652 " --> pdb=" O ILE T3648 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE T3653 " --> pdb=" O SER T3649 " (cutoff:3.500A) Processing helix chain 'T' and resid 3657 through 3677 removed outlier: 3.707A pdb=" N TYR T3662 " --> pdb=" O GLU T3658 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG T3668 " --> pdb=" O ALA T3664 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE T3672 " --> pdb=" O ARG T3668 " (cutoff:3.500A) Processing helix chain 'T' and resid 3684 through 3704 removed outlier: 3.554A pdb=" N LEU T3688 " --> pdb=" O GLU T3684 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG T3689 " --> pdb=" O ASN T3685 " (cutoff:3.500A) Processing helix chain 'T' and resid 3717 through 3729 removed outlier: 3.701A pdb=" N CYS T3723 " --> pdb=" O PHE T3719 " (cutoff:3.500A) Processing helix chain 'T' and resid 3729 through 3736 removed outlier: 3.692A pdb=" N THR T3736 " --> pdb=" O ASN T3732 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 3331 through 3333 removed outlier: 3.573A pdb=" N GLU T3332 " --> pdb=" O VAL T3378 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL T3378 " --> pdb=" O GLU T3332 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 3373 through 3374 Processing sheet with id=AA3, first strand: chain 'T' and resid 3464 through 3466 1639 hydrogen bonds defined for protein. 4878 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: 9.38 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 3390 1.28 - 1.35: 3324 1.35 - 1.43: 23 1.43 - 1.50: 3760 1.50 - 1.57: 6723 Bond restraints: 17220 Sorted by residual: bond pdb=" C ASP T2465 " pdb=" N TYR T2466 " ideal model delta sigma weight residual 1.327 1.274 0.052 1.05e-02 9.07e+03 2.49e+01 bond pdb=" C LEU T1345 " pdb=" N PRO T1346 " ideal model delta sigma weight residual 1.330 1.390 -0.059 1.19e-02 7.06e+03 2.49e+01 bond pdb=" C LYS T3576 " pdb=" N THR T3577 " ideal model delta sigma weight residual 1.332 1.273 0.060 1.40e-02 5.10e+03 1.81e+01 bond pdb=" C ARG T 288 " pdb=" N PRO T 289 " ideal model delta sigma weight residual 1.326 1.377 -0.051 1.44e-02 4.82e+03 1.26e+01 bond pdb=" C ILE T1655 " pdb=" N PRO T1656 " ideal model delta sigma weight residual 1.331 1.357 -0.025 7.90e-03 1.60e+04 1.03e+01 ... (remaining 17215 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.08: 527 106.08 - 113.07: 9669 113.07 - 120.06: 5700 120.06 - 127.05: 8070 127.05 - 134.04: 137 Bond angle restraints: 24103 Sorted by residual: angle pdb=" N VAL T 920 " pdb=" CA VAL T 920 " pdb=" C VAL T 920 " ideal model delta sigma weight residual 111.88 101.33 10.55 1.06e+00 8.90e-01 9.91e+01 angle pdb=" N VAL T3526 " pdb=" CA VAL T3526 " pdb=" C VAL T3526 " ideal model delta sigma weight residual 111.58 102.97 8.61 1.06e+00 8.90e-01 6.59e+01 angle pdb=" N SER T3452 " pdb=" CA SER T3452 " pdb=" C SER T3452 " ideal model delta sigma weight residual 110.31 102.13 8.18 1.20e+00 6.94e-01 4.65e+01 angle pdb=" C PHE T3136 " pdb=" N ILE T3137 " pdb=" CA ILE T3137 " ideal model delta sigma weight residual 120.24 124.53 -4.29 6.30e-01 2.52e+00 4.63e+01 angle pdb=" C ILE T1190 " pdb=" CA ILE T1190 " pdb=" CB ILE T1190 " ideal model delta sigma weight residual 113.70 107.54 6.16 9.50e-01 1.11e+00 4.20e+01 ... (remaining 24098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.81: 9493 10.81 - 21.63: 773 21.63 - 32.44: 85 32.44 - 43.25: 12 43.25 - 54.06: 3 Dihedral angle restraints: 10366 sinusoidal: 411 harmonic: 9955 Sorted by residual: dihedral pdb=" CA ILE T2225 " pdb=" C ILE T2225 " pdb=" N ILE T2226 " pdb=" CA ILE T2226 " ideal model delta harmonic sigma weight residual -180.00 -125.94 -54.06 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA GLU T2411 " pdb=" C GLU T2411 " pdb=" N ILE T2412 " pdb=" CA ILE T2412 " ideal model delta harmonic sigma weight residual -180.00 -128.66 -51.34 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA THR T3009 " pdb=" C THR T3009 " pdb=" N ASN T3010 " pdb=" CA ASN T3010 " ideal model delta harmonic sigma weight residual -180.00 -136.56 -43.44 0 5.00e+00 4.00e-02 7.55e+01 ... (remaining 10363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2344 0.049 - 0.098: 776 0.098 - 0.148: 145 0.148 - 0.197: 35 0.197 - 0.246: 4 Chirality restraints: 3304 Sorted by residual: chirality pdb=" CA ALA T2300 " pdb=" N ALA T2300 " pdb=" C ALA T2300 " pdb=" CB ALA T2300 " both_signs ideal model delta sigma weight residual False 2.48 2.73 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA LEU T2301 " pdb=" N LEU T2301 " pdb=" C LEU T2301 " pdb=" CB LEU T2301 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LEU T2618 " pdb=" N LEU T2618 " pdb=" C LEU T2618 " pdb=" CB LEU T2618 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3301 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE T2564 " 0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO T2565 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO T2565 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO T2565 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO T3608 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO T3609 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO T3609 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO T3609 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET T 472 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C MET T 472 " 0.054 2.00e-02 2.50e+03 pdb=" O MET T 472 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN T 473 " -0.018 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6554 2.86 - 3.37: 20023 3.37 - 3.88: 25552 3.88 - 4.39: 29422 4.39 - 4.90: 38931 Nonbonded interactions: 120482 Sorted by model distance: nonbonded pdb=" O ASN T1488 " pdb=" N LYS T1494 " model vdw 2.349 2.520 nonbonded pdb=" O GLU T 705 " pdb=" N VAL T 709 " model vdw 2.376 2.520 nonbonded pdb=" O VAL T 51 " pdb=" N LEU T 55 " model vdw 2.392 2.520 nonbonded pdb=" O ARG T3202 " pdb=" N GLU T3206 " model vdw 2.393 2.520 nonbonded pdb=" N VAL T 920 " pdb=" N ILE T 921 " model vdw 2.404 2.560 ... (remaining 120477 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: 2.310 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: 0.020 Extract box with map and model: 9.920 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 53.600 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 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 : 0.007 0.094 17220 Z= 0.513 Angle : 1.073 10.717 24103 Z= 0.678 Chirality : 0.051 0.246 3304 Planarity : 0.009 0.084 3481 Dihedral : 9.508 54.064 3758 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.16 % Favored : 89.66 % Rotamer: Outliers : 0.73 % Allowed : 1.46 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.21 % Twisted General : 0.47 % 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: -3.99 (0.12), residues: 3308 helix: -2.37 (0.08), residues: 1940 sheet: -2.41 (0.83), residues: 32 loop : -2.93 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 2.148 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.1681 time to fit residues: 29.6167 Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 10.0000 chunk 256 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 87 optimal weight: 0.0010 chunk 172 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 264 optimal weight: 30.0000 chunk 102 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17220 Z= 0.188 Angle : 0.612 7.053 24103 Z= 0.349 Chirality : 0.038 0.146 3304 Planarity : 0.006 0.071 3481 Dihedral : 6.460 41.024 3347 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.11 (0.13), residues: 3308 helix: -0.48 (0.09), residues: 2323 sheet: -1.90 (0.98), residues: 32 loop : -3.60 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1764 time to fit residues: 29.9789 Evaluate side-chains 82 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 209 optimal weight: 0.3980 chunk 84 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 332 optimal weight: 6.9990 chunk 273 optimal weight: 30.0000 chunk 304 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 246 optimal weight: 0.2980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17220 Z= 0.272 Angle : 0.641 7.337 24103 Z= 0.379 Chirality : 0.038 0.144 3304 Planarity : 0.006 0.067 3481 Dihedral : 6.062 40.295 3347 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.64 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3308 helix: 0.24 (0.10), residues: 2364 sheet: -2.04 (0.98), residues: 34 loop : -3.53 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.861 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1536 time to fit residues: 26.5772 Evaluate side-chains 82 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 308 optimal weight: 20.0000 chunk 326 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17220 Z= 0.416 Angle : 0.762 8.734 24103 Z= 0.472 Chirality : 0.041 0.187 3304 Planarity : 0.006 0.068 3481 Dihedral : 7.005 42.221 3347 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.16 % 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 (0.14), residues: 3308 helix: -0.58 (0.10), residues: 2307 sheet: -2.54 (0.89), residues: 36 loop : -3.70 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1537 time to fit residues: 26.0821 Evaluate side-chains 82 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 278 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 166 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 82 optimal weight: 0.0040 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17220 Z= 0.284 Angle : 0.636 7.053 24103 Z= 0.375 Chirality : 0.038 0.146 3304 Planarity : 0.005 0.064 3481 Dihedral : 6.232 41.418 3347 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.63 (0.15), residues: 3308 helix: -0.04 (0.11), residues: 2339 sheet: -2.10 (0.95), residues: 36 loop : -3.70 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1603 time to fit residues: 28.1076 Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 271 optimal weight: 30.0000 chunk 151 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17220 Z= 0.223 Angle : 0.578 7.209 24103 Z= 0.331 Chirality : 0.038 0.150 3304 Planarity : 0.005 0.071 3481 Dihedral : 5.535 39.217 3347 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3308 helix: 0.78 (0.11), residues: 2370 sheet: -1.95 (0.94), residues: 36 loop : -3.55 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.834 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1581 time to fit residues: 27.6658 Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 186 optimal weight: 50.0000 chunk 238 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 325 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17220 Z= 0.320 Angle : 0.653 8.907 24103 Z= 0.392 Chirality : 0.039 0.161 3304 Planarity : 0.005 0.063 3481 Dihedral : 6.035 40.718 3347 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.13 (0.15), residues: 3308 helix: 0.35 (0.11), residues: 2340 sheet: -2.10 (0.90), residues: 36 loop : -3.57 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1495 time to fit residues: 26.3016 Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 30.0000 chunk 130 optimal weight: 0.0980 chunk 194 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 0.0170 chunk 207 optimal weight: 0.7980 chunk 221 optimal weight: 0.4980 chunk 161 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17220 Z= 0.154 Angle : 0.528 8.403 24103 Z= 0.283 Chirality : 0.037 0.138 3304 Planarity : 0.004 0.064 3481 Dihedral : 5.064 37.243 3347 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.46 (0.15), residues: 3308 helix: 1.61 (0.11), residues: 2375 sheet: -1.83 (0.92), residues: 36 loop : -3.40 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1559 time to fit residues: 27.4447 Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 5.9990 chunk 312 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 303 optimal weight: 0.6980 chunk 182 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 274 optimal weight: 50.0000 chunk 287 optimal weight: 7.9990 chunk 302 optimal weight: 6.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17220 Z= 0.341 Angle : 0.657 10.898 24103 Z= 0.398 Chirality : 0.039 0.153 3304 Planarity : 0.005 0.065 3481 Dihedral : 5.825 40.018 3347 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.55 % Favored : 87.39 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.66 (0.15), residues: 3308 helix: 0.72 (0.11), residues: 2340 sheet: -2.11 (0.91), residues: 36 loop : -3.47 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.906 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1678 time to fit residues: 29.1761 Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.0020 chunk 321 optimal weight: 7.9990 chunk 195 optimal weight: 0.0010 chunk 152 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 268 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17220 Z= 0.160 Angle : 0.536 9.999 24103 Z= 0.291 Chirality : 0.037 0.166 3304 Planarity : 0.005 0.089 3481 Dihedral : 5.113 37.753 3347 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.52 (0.16), residues: 3308 helix: 1.66 (0.11), residues: 2360 sheet: -2.01 (0.91), residues: 36 loop : -3.31 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.862 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1499 time to fit residues: 26.0419 Evaluate side-chains 83 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 7.9990 chunk 285 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 268 optimal weight: 50.0000 chunk 112 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.028803 restraints weight = 280501.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.028810 restraints weight = 275709.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.028810 restraints weight = 272427.551| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17220 Z= 0.173 Angle : 0.532 10.251 24103 Z= 0.291 Chirality : 0.037 0.138 3304 Planarity : 0.004 0.074 3481 Dihedral : 4.887 36.095 3347 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 3308 helix: 1.97 (0.11), residues: 2370 sheet: -1.89 (0.93), residues: 36 loop : -3.28 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 619 PHE 0.000 0.000 PHE T 10 TYR 0.000 0.000 TYR T 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.67 seconds wall clock time: 42 minutes 10.20 seconds (2530.20 seconds total)