Starting phenix.real_space_refine on Thu Sep 18 13:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ig9_9664/09_2025/6ig9_9664.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ig9_9664/09_2025/6ig9_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ig9_9664/09_2025/6ig9_9664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ig9_9664/09_2025/6ig9_9664.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ig9_9664/09_2025/6ig9_9664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ig9_9664/09_2025/6ig9_9664.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 215, 'GLN:plan1': 140, 'PHE:plan': 204, 'ARG:plan': 155, 'ASP:plan': 174, 'TYR:plan': 126, 'ASN:plan1': 206, 'HIS:plan': 72, 'TRP:plan': 39} Unresolved non-hydrogen planarities: 6152 Time building chain proxies: 4.53, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 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: 1.93 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.56 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: 4.87 Time building geometry restraints manager: 2.46 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: 0.00 - 2.14: 23014 2.14 - 4.29: 870 4.29 - 6.43: 145 6.43 - 8.57: 62 8.57 - 10.72: 12 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 3.120 nonbonded pdb=" O GLU T 705 " pdb=" N VAL T 709 " model vdw 2.376 3.120 nonbonded pdb=" O VAL T 51 " pdb=" N LEU T 55 " model vdw 2.392 3.120 nonbonded pdb=" O ARG T3202 " pdb=" N GLU T3206 " model vdw 2.393 3.120 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: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- 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= 0.459 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00715 (17220) covalent geometry : angle 1.07332 (24103) hydrogen bonds : bond 0.31780 ( 1639) hydrogen bonds : angle 9.22691 ( 4878) *********************** 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 to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.518 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.0675 time to fit residues: 11.5953 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.044125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.030474 restraints weight = 287789.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.030474 restraints weight = 276646.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.030475 restraints weight = 276615.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.030475 restraints weight = 276400.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.030475 restraints weight = 276400.130| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17220 Z= 0.205 Angle : 0.636 7.816 24103 Z= 0.368 Chirality : 0.038 0.154 3304 Planarity : 0.006 0.073 3481 Dihedral : 6.617 41.738 3347 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.13), residues: 3308 helix: -0.66 (0.09), residues: 2333 sheet: -1.89 (0.96), residues: 32 loop : -3.62 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00311 (17220) covalent geometry : angle 0.63565 (24103) hydrogen bonds : bond 0.05665 ( 1639) hydrogen bonds : angle 5.57159 ( 4878) *********************** 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 to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.665 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0740 time to fit residues: 12.3431 Evaluate side-chains 82 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 8 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 170 optimal weight: 0.0980 chunk 277 optimal weight: 20.0000 chunk 171 optimal weight: 0.4980 chunk 139 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 250 optimal weight: 0.0570 chunk 101 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.044923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.031034 restraints weight = 287538.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.031071 restraints weight = 277955.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.031122 restraints weight = 270681.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.031123 restraints weight = 263788.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.031128 restraints weight = 263608.453| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17220 Z= 0.117 Angle : 0.539 7.602 24103 Z= 0.291 Chirality : 0.037 0.145 3304 Planarity : 0.005 0.065 3481 Dihedral : 5.224 36.706 3347 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3308 helix: 1.04 (0.10), residues: 2391 sheet: -1.92 (0.87), residues: 42 loop : -3.63 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00208 (17220) covalent geometry : angle 0.53868 (24103) hydrogen bonds : bond 0.03879 ( 1639) hydrogen bonds : angle 4.32295 ( 4878) *********************** 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 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.613 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0726 time to fit residues: 12.3351 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 79 optimal weight: 0.0770 chunk 295 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 217 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.042916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029026 restraints weight = 284871.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029035 restraints weight = 279758.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029035 restraints weight = 276842.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029035 restraints weight = 276842.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029035 restraints weight = 276842.834| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17220 Z= 0.286 Angle : 0.650 7.229 24103 Z= 0.388 Chirality : 0.039 0.151 3304 Planarity : 0.005 0.064 3481 Dihedral : 5.809 38.067 3347 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.85 % Favored : 90.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 3308 helix: 0.64 (0.10), residues: 2379 sheet: -2.04 (0.98), residues: 34 loop : -3.43 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00424 (17220) covalent geometry : angle 0.65030 (24103) hydrogen bonds : bond 0.05029 ( 1639) hydrogen bonds : angle 4.99066 ( 4878) *********************** 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 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0756 time to fit residues: 12.8193 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 218 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 0.0030 chunk 307 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 overall best weight: 3.1594 ------------------------------------------------------------------------------- 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 = 0.3039 r_free = 0.3039 target = 0.043406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029955 restraints weight = 289684.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029955 restraints weight = 281136.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029955 restraints weight = 281136.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029955 restraints weight = 281136.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029955 restraints weight = 281136.954| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17220 Z= 0.194 Angle : 0.568 7.392 24103 Z= 0.323 Chirality : 0.038 0.150 3304 Planarity : 0.005 0.062 3481 Dihedral : 5.254 37.650 3347 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.15), residues: 3308 helix: 1.23 (0.11), residues: 2367 sheet: -1.39 (1.03), residues: 32 loop : -3.41 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00301 (17220) covalent geometry : angle 0.56840 (24103) hydrogen bonds : bond 0.04064 ( 1639) hydrogen bonds : angle 4.53550 ( 4878) *********************** 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 to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.672 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0721 time to fit residues: 12.2428 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 299 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 271 optimal weight: 50.0000 chunk 312 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3008 r_free = 0.3008 target = 0.042354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028465 restraints weight = 274649.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028465 restraints weight = 269741.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028465 restraints weight = 269741.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028465 restraints weight = 269741.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028465 restraints weight = 269741.323| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17220 Z= 0.288 Angle : 0.642 7.096 24103 Z= 0.383 Chirality : 0.039 0.145 3304 Planarity : 0.005 0.058 3481 Dihedral : 5.751 39.134 3347 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.40 % Favored : 89.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.15), residues: 3308 helix: 0.72 (0.11), residues: 2363 sheet: -1.48 (1.00), residues: 34 loop : -3.36 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00427 (17220) covalent geometry : angle 0.64201 (24103) hydrogen bonds : bond 0.04874 ( 1639) hydrogen bonds : angle 5.04888 ( 4878) *********************** 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 to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.634 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0789 time to fit residues: 13.2797 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 154 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 275 optimal weight: 40.0000 chunk 285 optimal weight: 20.0000 chunk 129 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 118 optimal weight: 0.0270 chunk 180 optimal weight: 0.2980 chunk 18 optimal weight: 30.0000 chunk 152 optimal weight: 0.5980 overall best weight: 3.3842 ------------------------------------------------------------------------------- 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 = 0.3025 r_free = 0.3025 target = 0.042762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.029515 restraints weight = 293260.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.029527 restraints weight = 282840.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.029574 restraints weight = 280397.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.029600 restraints weight = 272420.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029622 restraints weight = 267395.765| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17220 Z= 0.202 Angle : 0.569 7.196 24103 Z= 0.325 Chirality : 0.038 0.145 3304 Planarity : 0.005 0.061 3481 Dihedral : 5.271 38.089 3347 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3308 helix: 1.21 (0.11), residues: 2394 sheet: -1.51 (0.99), residues: 34 loop : -3.43 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00310 (17220) covalent geometry : angle 0.56855 (24103) hydrogen bonds : bond 0.04082 ( 1639) hydrogen bonds : angle 4.61609 ( 4878) *********************** 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 to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.685 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0743 time to fit residues: 12.5976 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 190 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 302 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 32 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 234 optimal weight: 0.0020 chunk 173 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 overall best weight: 3.6794 ------------------------------------------------------------------------------- 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 = 0.3009 r_free = 0.3009 target = 0.042222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.029137 restraints weight = 289205.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029178 restraints weight = 279080.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029178 restraints weight = 270933.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029178 restraints weight = 270766.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029178 restraints weight = 270763.677| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17220 Z= 0.222 Angle : 0.588 7.425 24103 Z= 0.340 Chirality : 0.038 0.138 3304 Planarity : 0.005 0.059 3481 Dihedral : 5.358 38.028 3347 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3308 helix: 1.19 (0.11), residues: 2392 sheet: -1.40 (0.98), residues: 34 loop : -3.38 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00338 (17220) covalent geometry : angle 0.58808 (24103) hydrogen bonds : bond 0.04201 ( 1639) hydrogen bonds : angle 4.70611 ( 4878) *********************** 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 to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.644 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0720 time to fit residues: 12.1443 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 223 optimal weight: 0.5980 chunk 125 optimal weight: 30.0000 chunk 177 optimal weight: 0.0470 chunk 336 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 335 optimal weight: 0.6980 chunk 152 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 186 optimal weight: 50.0000 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.3042 r_free = 0.3042 target = 0.043170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029401 restraints weight = 284997.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029401 restraints weight = 274841.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029401 restraints weight = 274841.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029401 restraints weight = 274841.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029401 restraints weight = 274841.955| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17220 Z= 0.111 Angle : 0.515 7.410 24103 Z= 0.275 Chirality : 0.037 0.136 3304 Planarity : 0.004 0.060 3481 Dihedral : 4.788 34.660 3347 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.16), residues: 3308 helix: 1.97 (0.11), residues: 2390 sheet: -1.22 (0.97), residues: 34 loop : -3.20 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00202 (17220) covalent geometry : angle 0.51454 (24103) hydrogen bonds : bond 0.03227 ( 1639) hydrogen bonds : angle 4.07632 ( 4878) *********************** 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 to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.715 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0727 time to fit residues: 12.2260 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 134 optimal weight: 30.0000 chunk 21 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 228 optimal weight: 0.4980 chunk 196 optimal weight: 40.0000 chunk 263 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 328 optimal weight: 0.6980 overall best weight: 3.7984 ------------------------------------------------------------------------------- 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 = 0.3011 r_free = 0.3011 target = 0.042251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.028227 restraints weight = 265259.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.028227 restraints weight = 261156.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 12)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.028227 restraints weight = 261156.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.028227 restraints weight = 261155.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.028227 restraints weight = 261154.934| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5023 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= 0.218 Angle : 0.571 6.910 24103 Z= 0.329 Chirality : 0.038 0.133 3304 Planarity : 0.005 0.058 3481 Dihedral : 5.028 35.225 3347 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.82 % Favored : 90.15 % 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 : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.16), residues: 3308 helix: 1.69 (0.11), residues: 2387 sheet: -1.37 (0.96), residues: 34 loop : -3.29 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00334 (17220) covalent geometry : angle 0.57100 (24103) hydrogen bonds : bond 0.03952 ( 1639) hydrogen bonds : angle 4.45652 ( 4878) ********************** 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 to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.686 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0762 time to fit residues: 12.3224 Evaluate side-chains 83 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 261 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 335 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 330 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.042429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.028047 restraints weight = 254246.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.028070 restraints weight = 247221.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.028119 restraints weight = 242771.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.028119 restraints weight = 233363.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.028119 restraints weight = 233363.409| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17220 Z= 0.210 Angle : 0.571 6.808 24103 Z= 0.328 Chirality : 0.038 0.138 3304 Planarity : 0.005 0.061 3481 Dihedral : 5.191 35.788 3347 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3308 helix: 1.45 (0.11), residues: 2392 sheet: -1.52 (0.95), residues: 34 loop : -3.27 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR T 25 PHE 0.000 0.000 PHE T 10 TRP 0.000 0.000 TRP T 619 Details of bonding type rmsd covalent geometry : bond 0.00322 (17220) covalent geometry : angle 0.57087 (24103) hydrogen bonds : bond 0.04020 ( 1639) hydrogen bonds : angle 4.60719 ( 4878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.57 seconds wall clock time: 49 minutes 38.30 seconds (2978.30 seconds total)