Starting phenix.real_space_refine on Fri May 30 07:01:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qgu_18391/05_2025/8qgu_18391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qgu_18391/05_2025/8qgu_18391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qgu_18391/05_2025/8qgu_18391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qgu_18391/05_2025/8qgu_18391.map" model { file = "/net/cci-nas-00/data/ceres_data/8qgu_18391/05_2025/8qgu_18391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qgu_18391/05_2025/8qgu_18391.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 21138 2.51 5 N 5532 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.84s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32838 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2032, 16419 Classifications: {'peptide': 2032} Link IDs: {'PTRANS': 71, 'TRANS': 1960} Chain breaks: 6 Restraints were copied for chains: B Time building chain proxies: 62.84, per 1000 atoms: 1.91 Number of scatterers: 32838 At special positions: 0 Unit cell: (192.131, 165.283, 128.367, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 5994 8.00 N 5532 7.00 C 21138 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: 7.34 Conformation dependent library (CDL) restraints added in 3.8 seconds 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7760 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 38 sheets defined 57.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 20 through 48 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.714A pdb=" N ILE A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 116 through 146 removed outlier: 5.115A pdb=" N ALA A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 176 through 197 removed outlier: 3.578A pdb=" N VAL A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.740A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 282 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.882A pdb=" N ARG A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.309A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.938A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 4.747A pdb=" N LYS A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 635 removed outlier: 3.867A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.636A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 675 removed outlier: 3.647A pdb=" N VAL A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 4.001A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 733 Processing helix chain 'A' and resid 734 through 760 Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.586A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.809A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.557A pdb=" N SER A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 824 " --> pdb=" O TYR A 821 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR A 825 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 826 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 827 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 930 through 948 removed outlier: 4.273A pdb=" N ALA A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 991 removed outlier: 4.312A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1013 removed outlier: 3.814A pdb=" N ASN A1003 " --> pdb=" O ASN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.690A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1114 through 1126 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 5.878A pdb=" N HIS A1130 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP A1131 " --> pdb=" O HIS A1128 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1127 through 1132' Processing helix chain 'A' and resid 1138 through 1153 removed outlier: 3.535A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 4.032A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER A1194 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP A1195 " --> pdb=" O GLY A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1297 Processing helix chain 'A' and resid 1302 through 1319 Processing helix chain 'A' and resid 1322 through 1326 Processing helix chain 'A' and resid 1349 through 1353 removed outlier: 3.636A pdb=" N MET A1352 " --> pdb=" O PHE A1349 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A1353 " --> pdb=" O ALA A1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1349 through 1353' Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 4.026A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 4.404A pdb=" N PHE A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.728A pdb=" N ASN A1439 " --> pdb=" O SER A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1455 Processing helix chain 'A' and resid 1463 through 1470 Processing helix chain 'A' and resid 1502 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1546 Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing helix chain 'A' and resid 1616 through 1642 Processing helix chain 'A' and resid 1645 through 1651 Processing helix chain 'A' and resid 1660 through 1671 Processing helix chain 'A' and resid 1675 through 1677 No H-bonds generated for 'chain 'A' and resid 1675 through 1677' Processing helix chain 'A' and resid 1678 through 1690 Processing helix chain 'A' and resid 1693 through 1704 removed outlier: 3.595A pdb=" N GLN A1697 " --> pdb=" O TYR A1693 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1778 removed outlier: 3.501A pdb=" N LEU A1763 " --> pdb=" O GLN A1759 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1823 Processing helix chain 'A' and resid 1867 through 1871 Processing helix chain 'A' and resid 1888 through 1894 Processing helix chain 'A' and resid 1896 through 1903 Processing helix chain 'A' and resid 1909 through 1918 Processing helix chain 'A' and resid 1923 through 1937 Processing helix chain 'A' and resid 2034 through 2041 Processing helix chain 'A' and resid 2054 through 2069 removed outlier: 3.685A pdb=" N ILE A2059 " --> pdb=" O PRO A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2092 removed outlier: 3.517A pdb=" N GLU A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 removed outlier: 3.766A pdb=" N VAL A2098 " --> pdb=" O TRP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2116 removed outlier: 3.614A pdb=" N ASN A2115 " --> pdb=" O ASN A2111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A2116 " --> pdb=" O MET A2112 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2142 Processing helix chain 'A' and resid 2146 through 2151 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 20 through 48 Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.715A pdb=" N ILE B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 116 through 146 removed outlier: 5.115A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 176 through 197 removed outlier: 3.578A pdb=" N VAL B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 239 through 252 removed outlier: 3.740A pdb=" N LEU B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.881A pdb=" N ARG B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 343 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 379 through 391 Processing helix chain 'B' and resid 409 through 429 Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 463 through 469 removed outlier: 4.309A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 490 removed outlier: 3.936A pdb=" N HIS B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.747A pdb=" N LYS B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 572 through 593 Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 616 through 635 removed outlier: 3.866A pdb=" N TYR B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Proline residue: B 631 - end of helix Processing helix chain 'B' and resid 639 through 649 removed outlier: 3.636A pdb=" N LEU B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 675 removed outlier: 3.647A pdb=" N VAL B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 726 removed outlier: 4.000A pdb=" N LEU B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 734 through 760 Processing helix chain 'B' and resid 760 through 767 removed outlier: 3.586A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 777 Processing helix chain 'B' and resid 786 through 802 removed outlier: 3.809A pdb=" N VAL B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 814 Processing helix chain 'B' and resid 820 through 828 removed outlier: 3.557A pdb=" N SER B 823 " --> pdb=" O PRO B 820 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 824 " --> pdb=" O TYR B 821 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N THR B 825 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG B 826 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 827 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 859 Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'B' and resid 898 through 917 Processing helix chain 'B' and resid 918 through 920 No H-bonds generated for 'chain 'B' and resid 918 through 920' Processing helix chain 'B' and resid 930 through 948 removed outlier: 4.273A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 948 " --> pdb=" O ARG B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 991 removed outlier: 4.312A pdb=" N ARG B 987 " --> pdb=" O ALA B 983 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 988 " --> pdb=" O LYS B 984 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET B 991 " --> pdb=" O ARG B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1013 removed outlier: 3.814A pdb=" N ASN B1003 " --> pdb=" O ASN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1029 Processing helix chain 'B' and resid 1034 through 1044 removed outlier: 3.690A pdb=" N PHE B1044 " --> pdb=" O PHE B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1084 Processing helix chain 'B' and resid 1114 through 1126 Processing helix chain 'B' and resid 1127 through 1132 removed outlier: 5.878A pdb=" N HIS B1130 " --> pdb=" O GLY B1127 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP B1131 " --> pdb=" O HIS B1128 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B1132 " --> pdb=" O LEU B1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1127 through 1132' Processing helix chain 'B' and resid 1138 through 1153 removed outlier: 3.536A pdb=" N GLY B1153 " --> pdb=" O ILE B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1168 through 1181 Processing helix chain 'B' and resid 1184 through 1195 removed outlier: 4.031A pdb=" N ILE B1188 " --> pdb=" O PRO B1184 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B1193 " --> pdb=" O LEU B1189 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B1194 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP B1195 " --> pdb=" O GLY B1191 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1219 Processing helix chain 'B' and resid 1221 through 1241 Processing helix chain 'B' and resid 1249 through 1253 Processing helix chain 'B' and resid 1272 through 1279 Processing helix chain 'B' and resid 1282 through 1297 Processing helix chain 'B' and resid 1302 through 1319 Processing helix chain 'B' and resid 1322 through 1326 Processing helix chain 'B' and resid 1349 through 1353 removed outlier: 3.636A pdb=" N MET B1352 " --> pdb=" O PHE B1349 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR B1353 " --> pdb=" O ALA B1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1349 through 1353' Processing helix chain 'B' and resid 1354 through 1365 Processing helix chain 'B' and resid 1366 through 1370 Processing helix chain 'B' and resid 1375 through 1388 removed outlier: 4.027A pdb=" N ILE B1381 " --> pdb=" O ASP B1377 " (cutoff:3.500A) Processing helix chain 'B' and resid 1389 through 1397 Processing helix chain 'B' and resid 1402 through 1412 removed outlier: 4.403A pdb=" N PHE B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B1407 " --> pdb=" O GLN B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1425 through 1439 removed outlier: 3.728A pdb=" N ASN B1439 " --> pdb=" O SER B1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1455 Processing helix chain 'B' and resid 1463 through 1470 Processing helix chain 'B' and resid 1502 through 1512 Processing helix chain 'B' and resid 1514 through 1525 Processing helix chain 'B' and resid 1527 through 1529 No H-bonds generated for 'chain 'B' and resid 1527 through 1529' Processing helix chain 'B' and resid 1530 through 1546 Processing helix chain 'B' and resid 1552 through 1564 Proline residue: B1561 - end of helix Processing helix chain 'B' and resid 1581 through 1592 Processing helix chain 'B' and resid 1616 through 1642 Processing helix chain 'B' and resid 1645 through 1651 Processing helix chain 'B' and resid 1660 through 1671 Processing helix chain 'B' and resid 1675 through 1677 No H-bonds generated for 'chain 'B' and resid 1675 through 1677' Processing helix chain 'B' and resid 1678 through 1690 Processing helix chain 'B' and resid 1693 through 1704 removed outlier: 3.595A pdb=" N GLN B1697 " --> pdb=" O TYR B1693 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B1704 " --> pdb=" O ALA B1700 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1778 removed outlier: 3.501A pdb=" N LEU B1763 " --> pdb=" O GLN B1759 " (cutoff:3.500A) Processing helix chain 'B' and resid 1820 through 1823 Processing helix chain 'B' and resid 1867 through 1871 Processing helix chain 'B' and resid 1888 through 1894 Processing helix chain 'B' and resid 1896 through 1903 Processing helix chain 'B' and resid 1909 through 1918 Processing helix chain 'B' and resid 1923 through 1937 Processing helix chain 'B' and resid 2034 through 2041 Processing helix chain 'B' and resid 2054 through 2069 removed outlier: 3.685A pdb=" N ILE B2059 " --> pdb=" O PRO B2055 " (cutoff:3.500A) Processing helix chain 'B' and resid 2080 through 2092 removed outlier: 3.517A pdb=" N GLU B2086 " --> pdb=" O TYR B2082 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2099 removed outlier: 3.767A pdb=" N VAL B2098 " --> pdb=" O TRP B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2102 through 2116 removed outlier: 3.614A pdb=" N ASN B2115 " --> pdb=" O ASN B2111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B2116 " --> pdb=" O MET B2112 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2142 Processing helix chain 'B' and resid 2146 through 2151 Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 102 removed outlier: 3.983A pdb=" N ASN A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 109 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 159 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 112 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.608A pdb=" N PHE A1090 " --> pdb=" O GLY A1105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.710A pdb=" N SER A 950 " --> pdb=" O MET A 962 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.657A pdb=" N PHE A 527 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 683 through 685 Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA9, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.158A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 895 through 897 removed outlier: 4.874A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1417 through 1419 removed outlier: 3.734A pdb=" N GLU A1422 " --> pdb=" O LEU A1419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1473 through 1476 removed outlier: 4.207A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1486 through 1490 removed outlier: 3.613A pdb=" N ARG A1570 " --> pdb=" O PHE A1490 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1658 through 1659 Processing sheet with id=AB6, first strand: chain 'A' and resid 1706 through 1710 removed outlier: 4.854A pdb=" N GLY A1707 " --> pdb=" O ASN A1734 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN A1734 " --> pdb=" O GLY A1707 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A1729 " --> pdb=" O ILE A1744 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A1738 " --> pdb=" O PHE A1735 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL A1817 " --> pdb=" O TYR A1751 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A1753 " --> pdb=" O VAL A1817 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1717 through 1719 Processing sheet with id=AB8, first strand: chain 'A' and resid 1783 through 1786 removed outlier: 3.552A pdb=" N VAL A1786 " --> pdb=" O CYS A1810 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A1811 " --> pdb=" O LYS A1796 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A1794 " --> pdb=" O TYR A1813 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A1804 " --> pdb=" O VAL A1793 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1833 through 1837 removed outlier: 3.632A pdb=" N MET A1833 " --> pdb=" O GLN A1846 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A1846 " --> pdb=" O MET A1833 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA A1845 " --> pdb=" O LEU A1855 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU A1855 " --> pdb=" O ALA A1845 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AC2, first strand: chain 'B' and resid 98 through 102 removed outlier: 3.982A pdb=" N ASN B 98 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 109 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 159 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 112 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 260 through 261 removed outlier: 3.609A pdb=" N PHE B1090 " --> pdb=" O GLY B1105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 260 through 261 removed outlier: 3.710A pdb=" N SER B 950 " --> pdb=" O MET B 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AC7, first strand: chain 'B' and resid 499 through 503 removed outlier: 3.657A pdb=" N PHE B 527 " --> pdb=" O MET B 560 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 Processing sheet with id=AD1, first strand: chain 'B' and resid 832 through 837 removed outlier: 5.158A pdb=" N SER B 844 " --> pdb=" O GLY B 835 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 895 through 897 removed outlier: 4.874A pdb=" N ILE B 881 " --> pdb=" O PHE B1018 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1417 through 1419 removed outlier: 3.734A pdb=" N GLU B1422 " --> pdb=" O LEU B1419 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1473 through 1476 removed outlier: 4.207A pdb=" N THR B1598 " --> pdb=" O ILE B1476 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1486 through 1490 removed outlier: 3.613A pdb=" N ARG B1570 " --> pdb=" O PHE B1490 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1658 through 1659 Processing sheet with id=AD7, first strand: chain 'B' and resid 1706 through 1710 removed outlier: 4.855A pdb=" N GLY B1707 " --> pdb=" O ASN B1734 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B1734 " --> pdb=" O GLY B1707 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B1729 " --> pdb=" O ILE B1744 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B1738 " --> pdb=" O PHE B1735 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL B1817 " --> pdb=" O TYR B1751 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B1753 " --> pdb=" O VAL B1817 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1717 through 1719 Processing sheet with id=AD9, first strand: chain 'B' and resid 1783 through 1786 removed outlier: 3.551A pdb=" N VAL B1786 " --> pdb=" O CYS B1810 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B1811 " --> pdb=" O LYS B1796 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU B1794 " --> pdb=" O TYR B1813 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B1804 " --> pdb=" O VAL B1793 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1833 through 1837 removed outlier: 3.632A pdb=" N MET B1833 " --> pdb=" O GLN B1846 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B1846 " --> pdb=" O MET B1833 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA B1845 " --> pdb=" O LEU B1855 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B1855 " --> pdb=" O ALA B1845 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1878 through 1881 1797 hydrogen bonds defined for protein. 5145 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: 16.14 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10476 1.34 - 1.46: 7770 1.46 - 1.58: 15038 1.58 - 1.70: 0 1.70 - 1.81: 286 Bond restraints: 33570 Sorted by residual: bond pdb=" CG ARG B1238 " pdb=" CD ARG B1238 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.72e-01 bond pdb=" CG ARG A1238 " pdb=" CD ARG A1238 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CB ARG A1211 " pdb=" CG ARG A1211 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.65e-01 bond pdb=" C TYR A1705 " pdb=" N SER A1706 " ideal model delta sigma weight residual 1.325 1.336 -0.011 1.14e-02 7.69e+03 9.32e-01 bond pdb=" CB ARG B1211 " pdb=" CG ARG B1211 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.24e-01 ... (remaining 33565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 44797 1.97 - 3.93: 509 3.93 - 5.90: 60 5.90 - 7.87: 2 7.87 - 9.83: 2 Bond angle restraints: 45370 Sorted by residual: angle pdb=" C SER B1706 " pdb=" CA SER B1706 " pdb=" CB SER B1706 " ideal model delta sigma weight residual 115.79 110.25 5.54 1.19e+00 7.06e-01 2.17e+01 angle pdb=" C SER A1706 " pdb=" CA SER A1706 " pdb=" CB SER A1706 " ideal model delta sigma weight residual 115.79 110.26 5.53 1.19e+00 7.06e-01 2.16e+01 angle pdb=" N VAL A 800 " pdb=" CA VAL A 800 " pdb=" C VAL A 800 " ideal model delta sigma weight residual 111.81 109.14 2.67 8.60e-01 1.35e+00 9.62e+00 angle pdb=" N ILE A 919 " pdb=" CA ILE A 919 " pdb=" C ILE A 919 " ideal model delta sigma weight residual 112.29 109.42 2.87 9.40e-01 1.13e+00 9.30e+00 angle pdb=" N VAL B 800 " pdb=" CA VAL B 800 " pdb=" C VAL B 800 " ideal model delta sigma weight residual 111.81 109.19 2.62 8.60e-01 1.35e+00 9.27e+00 ... (remaining 45365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18256 18.00 - 36.00: 1644 36.00 - 54.00: 256 54.00 - 71.99: 52 71.99 - 89.99: 22 Dihedral angle restraints: 20230 sinusoidal: 8254 harmonic: 11976 Sorted by residual: dihedral pdb=" CA ASP A1034 " pdb=" C ASP A1034 " pdb=" N PRO A1035 " pdb=" CA PRO A1035 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ASP B1034 " pdb=" C ASP B1034 " pdb=" N PRO B1035 " pdb=" CA PRO B1035 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA MET A1246 " pdb=" C MET A1246 " pdb=" N VAL A1247 " pdb=" CA VAL A1247 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 20227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3873 0.042 - 0.084: 899 0.084 - 0.127: 271 0.127 - 0.169: 7 0.169 - 0.211: 2 Chirality restraints: 5052 Sorted by residual: chirality pdb=" CG LEU B1684 " pdb=" CB LEU B1684 " pdb=" CD1 LEU B1684 " pdb=" CD2 LEU B1684 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU A1684 " pdb=" CB LEU A1684 " pdb=" CD1 LEU A1684 " pdb=" CD2 LEU A1684 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PHE B 640 " pdb=" N PHE B 640 " pdb=" C PHE B 640 " pdb=" CB PHE B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 5049 not shown) Planarity restraints: 5722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 630 " -0.057 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO B 631 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 630 " 0.057 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO A 631 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 631 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 631 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 354 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 355 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.036 5.00e-02 4.00e+02 ... (remaining 5719 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 355 2.66 - 3.22: 30983 3.22 - 3.78: 51543 3.78 - 4.34: 67977 4.34 - 4.90: 113694 Nonbonded interactions: 264552 Sorted by model distance: nonbonded pdb=" O SER B1133 " pdb=" OG SER B1141 " model vdw 2.105 3.040 nonbonded pdb=" O SER A1133 " pdb=" OG SER A1141 " model vdw 2.105 3.040 nonbonded pdb=" ND2 ASN A 351 " pdb=" O LYS A 360 " model vdw 2.138 3.120 nonbonded pdb=" ND2 ASN B 351 " pdb=" O LYS B 360 " model vdw 2.138 3.120 nonbonded pdb=" OH TYR B 341 " pdb=" OH TYR B 353 " model vdw 2.188 3.040 ... (remaining 264547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 116.380 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.002 0.032 33570 Z= 0.113 Angle : 0.503 9.832 45370 Z= 0.265 Chirality : 0.039 0.211 5052 Planarity : 0.004 0.104 5722 Dihedral : 13.812 89.992 12470 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.13), residues: 4036 helix: 1.92 (0.11), residues: 2106 sheet: 0.63 (0.28), residues: 368 loop : -0.74 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1423 HIS 0.004 0.000 HIS B 742 PHE 0.022 0.001 PHE B 371 TYR 0.022 0.001 TYR B 32 ARG 0.010 0.000 ARG B 289 Details of bonding type rmsd hydrogen bonds : bond 0.15013 ( 1761) hydrogen bonds : angle 5.90974 ( 5145) covalent geometry : bond 0.00249 (33570) covalent geometry : angle 0.50349 (45370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 754 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8401 (mt) cc_final: 0.8094 (tp) REVERT: A 184 MET cc_start: 0.7002 (ptm) cc_final: 0.6619 (ptm) REVERT: A 1355 SER cc_start: 0.7757 (t) cc_final: 0.7485 (p) REVERT: A 1564 TYR cc_start: 0.7264 (t80) cc_final: 0.6968 (t80) REVERT: A 1629 LEU cc_start: 0.8704 (tp) cc_final: 0.8489 (tp) REVERT: A 1679 ILE cc_start: 0.7510 (mm) cc_final: 0.7123 (mt) REVERT: A 1702 ARG cc_start: 0.8481 (ptm-80) cc_final: 0.8263 (ptm-80) REVERT: A 1742 LEU cc_start: 0.9009 (tp) cc_final: 0.8766 (tp) REVERT: A 1764 LYS cc_start: 0.9805 (tttt) cc_final: 0.9582 (tptt) REVERT: A 1768 ASP cc_start: 0.9404 (m-30) cc_final: 0.8930 (m-30) REVERT: A 1779 MET cc_start: 0.6030 (pmm) cc_final: 0.5208 (tmm) REVERT: A 2111 ASN cc_start: 0.7735 (t0) cc_final: 0.7053 (t0) REVERT: B 63 PHE cc_start: 0.9238 (m-80) cc_final: 0.8991 (m-80) REVERT: B 88 LEU cc_start: 0.8457 (mt) cc_final: 0.8131 (tp) REVERT: B 184 MET cc_start: 0.7177 (ptm) cc_final: 0.6797 (ptm) REVERT: B 349 MET cc_start: 0.6211 (ttt) cc_final: 0.6010 (ttt) REVERT: B 735 MET cc_start: 0.7440 (tpp) cc_final: 0.7089 (tpp) REVERT: B 833 MET cc_start: 0.8665 (ttm) cc_final: 0.8317 (ttm) REVERT: B 1026 TYR cc_start: 0.8607 (t80) cc_final: 0.8397 (t80) REVERT: B 1138 MET cc_start: 0.6328 (ptt) cc_final: 0.6039 (ptt) REVERT: B 1355 SER cc_start: 0.7731 (t) cc_final: 0.7451 (p) REVERT: B 1564 TYR cc_start: 0.7276 (t80) cc_final: 0.6970 (t80) REVERT: B 1629 LEU cc_start: 0.8656 (tp) cc_final: 0.8449 (tp) REVERT: B 1679 ILE cc_start: 0.7570 (mm) cc_final: 0.7176 (mt) REVERT: B 1742 LEU cc_start: 0.9068 (tp) cc_final: 0.8818 (tp) REVERT: B 1779 MET cc_start: 0.5856 (pmm) cc_final: 0.5257 (ptt) REVERT: B 2111 ASN cc_start: 0.7800 (t0) cc_final: 0.7103 (t0) outliers start: 0 outliers final: 0 residues processed: 754 average time/residue: 0.4994 time to fit residues: 587.8129 Evaluate side-chains 456 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 105 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 318 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 193 optimal weight: 0.0470 chunk 236 optimal weight: 0.0030 chunk 368 optimal weight: 0.0050 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 363 GLN A 406 ASN A 457 ASN A 827 ASN A1287 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN A1881 HIS A2070 ASN A2133 HIS ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 140 HIS B 363 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN B1287 ASN ** B1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1575 GLN B1881 HIS B2133 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.177017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.139798 restraints weight = 54112.495| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.81 r_work: 0.3727 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33570 Z= 0.114 Angle : 0.559 12.087 45370 Z= 0.284 Chirality : 0.040 0.192 5052 Planarity : 0.004 0.053 5722 Dihedral : 3.652 21.536 4412 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.10 % Allowed : 9.14 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.13), residues: 4036 helix: 2.00 (0.11), residues: 2096 sheet: 0.84 (0.28), residues: 376 loop : -0.73 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1423 HIS 0.009 0.001 HIS B 82 PHE 0.024 0.001 PHE B1667 TYR 0.017 0.001 TYR B 32 ARG 0.007 0.001 ARG B1703 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1761) hydrogen bonds : angle 4.61426 ( 5145) covalent geometry : bond 0.00242 (33570) covalent geometry : angle 0.55859 (45370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 470 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7098 (ptm) cc_final: 0.6535 (ptm) REVERT: A 406 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8578 (t0) REVERT: A 679 PHE cc_start: 0.7950 (p90) cc_final: 0.7703 (p90) REVERT: A 884 LYS cc_start: 0.7176 (mtmm) cc_final: 0.6704 (mttm) REVERT: A 1322 PHE cc_start: 0.6917 (m-10) cc_final: 0.6619 (m-80) REVERT: A 1355 SER cc_start: 0.8134 (t) cc_final: 0.7848 (p) REVERT: A 1387 LEU cc_start: 0.8534 (tt) cc_final: 0.8212 (tp) REVERT: A 1536 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7928 (mmtm) REVERT: A 1562 MET cc_start: 0.7783 (ptp) cc_final: 0.7423 (ptp) REVERT: A 1605 LYS cc_start: 0.7983 (mppt) cc_final: 0.7576 (mtmm) REVERT: A 1654 TRP cc_start: 0.7906 (t-100) cc_final: 0.7572 (t-100) REVERT: A 1768 ASP cc_start: 0.9319 (m-30) cc_final: 0.9036 (t70) REVERT: A 1779 MET cc_start: 0.5898 (pmm) cc_final: 0.5253 (ptt) REVERT: A 2108 GLU cc_start: 0.7647 (tt0) cc_final: 0.7345 (tt0) REVERT: A 2111 ASN cc_start: 0.8492 (t0) cc_final: 0.7939 (t0) REVERT: A 2135 MET cc_start: 0.8297 (mmt) cc_final: 0.7768 (mmt) REVERT: B 184 MET cc_start: 0.7360 (ptm) cc_final: 0.6782 (ptm) REVERT: B 884 LYS cc_start: 0.7052 (mtmm) cc_final: 0.6584 (mttm) REVERT: B 1026 TYR cc_start: 0.8867 (t80) cc_final: 0.8586 (t80) REVERT: B 1322 PHE cc_start: 0.7017 (m-80) cc_final: 0.6755 (m-80) REVERT: B 1355 SER cc_start: 0.8116 (t) cc_final: 0.7834 (p) REVERT: B 1387 LEU cc_start: 0.8495 (tt) cc_final: 0.8174 (tp) REVERT: B 1536 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7946 (mmtm) REVERT: B 1562 MET cc_start: 0.7833 (ptp) cc_final: 0.7473 (ptp) REVERT: B 1605 LYS cc_start: 0.7993 (mppt) cc_final: 0.7589 (mtmm) REVERT: B 1654 TRP cc_start: 0.7924 (t-100) cc_final: 0.7594 (t-100) REVERT: B 1679 ILE cc_start: 0.7431 (mm) cc_final: 0.7213 (mt) REVERT: B 1768 ASP cc_start: 0.9333 (m-30) cc_final: 0.9043 (t70) REVERT: B 1779 MET cc_start: 0.5757 (pmm) cc_final: 0.5131 (ptt) REVERT: B 2108 GLU cc_start: 0.7620 (tt0) cc_final: 0.7344 (tt0) REVERT: B 2111 ASN cc_start: 0.8458 (t0) cc_final: 0.7875 (t0) outliers start: 40 outliers final: 22 residues processed: 496 average time/residue: 0.4776 time to fit residues: 382.2974 Evaluate side-chains 422 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 399 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 909 GLU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 909 GLU Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 SER Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 1 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 382 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 314 optimal weight: 0.9980 chunk 169 optimal weight: 40.0000 chunk 11 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 363 GLN A 413 GLN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1298 HIS A1365 HIS B 8 HIS ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 363 GLN B 406 ASN B 413 GLN B1365 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.173654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.132985 restraints weight = 54086.847| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.50 r_work: 0.3702 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33570 Z= 0.127 Angle : 0.541 9.588 45370 Z= 0.275 Chirality : 0.040 0.244 5052 Planarity : 0.004 0.050 5722 Dihedral : 3.677 21.973 4412 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.71 % Allowed : 11.29 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.13), residues: 4036 helix: 1.91 (0.11), residues: 2128 sheet: 0.66 (0.28), residues: 378 loop : -0.75 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1139 HIS 0.007 0.001 HIS A1298 PHE 0.020 0.002 PHE A1093 TYR 0.017 0.001 TYR A 339 ARG 0.007 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1761) hydrogen bonds : angle 4.46062 ( 5145) covalent geometry : bond 0.00296 (33570) covalent geometry : angle 0.54087 (45370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 421 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9221 (mm) cc_final: 0.8935 (mt) REVERT: A 140 HIS cc_start: 0.8616 (t70) cc_final: 0.8388 (t70) REVERT: A 184 MET cc_start: 0.7164 (ptm) cc_final: 0.6700 (ptm) REVERT: A 884 LYS cc_start: 0.7109 (mtmm) cc_final: 0.6593 (mttm) REVERT: A 1322 PHE cc_start: 0.6867 (m-80) cc_final: 0.6600 (m-80) REVERT: A 1355 SER cc_start: 0.8154 (t) cc_final: 0.7806 (p) REVERT: A 1387 LEU cc_start: 0.8600 (tt) cc_final: 0.8283 (tp) REVERT: A 1536 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7876 (mmtm) REVERT: A 1562 MET cc_start: 0.7892 (ptp) cc_final: 0.7525 (ptp) REVERT: A 1654 TRP cc_start: 0.7924 (t-100) cc_final: 0.7640 (t-100) REVERT: A 1768 ASP cc_start: 0.9072 (m-30) cc_final: 0.8841 (m-30) REVERT: A 1779 MET cc_start: 0.5741 (pmm) cc_final: 0.4793 (ppp) REVERT: A 2111 ASN cc_start: 0.8526 (t0) cc_final: 0.7948 (t0) REVERT: A 2135 MET cc_start: 0.8323 (mmt) cc_final: 0.7839 (mmt) REVERT: B 184 MET cc_start: 0.7391 (ptm) cc_final: 0.7109 (ptm) REVERT: B 337 MET cc_start: 0.6104 (ttm) cc_final: 0.5795 (ttm) REVERT: B 884 LYS cc_start: 0.7136 (mtmm) cc_final: 0.6611 (mttm) REVERT: B 1355 SER cc_start: 0.8165 (t) cc_final: 0.7828 (p) REVERT: B 1469 ASN cc_start: 0.7545 (m110) cc_final: 0.7290 (m110) REVERT: B 1536 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7868 (mmtm) REVERT: B 1562 MET cc_start: 0.7866 (ptp) cc_final: 0.7475 (ptp) REVERT: B 1654 TRP cc_start: 0.7951 (t-100) cc_final: 0.7668 (t-100) REVERT: B 1679 ILE cc_start: 0.7452 (mm) cc_final: 0.7171 (mt) REVERT: B 1768 ASP cc_start: 0.9083 (m-30) cc_final: 0.8865 (m-30) REVERT: B 1779 MET cc_start: 0.5593 (pmm) cc_final: 0.4879 (ptt) REVERT: B 2135 MET cc_start: 0.8312 (mmt) cc_final: 0.7803 (mmt) outliers start: 62 outliers final: 38 residues processed: 460 average time/residue: 0.4528 time to fit residues: 335.4973 Evaluate side-chains 423 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 385 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 294 optimal weight: 6.9990 chunk 363 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 387 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 GLN A1125 GLN ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1469 ASN A1497 GLN A2070 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 824 GLN B 838 GLN B1298 HIS B1497 GLN ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.169991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.132211 restraints weight = 53921.284| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.41 r_work: 0.3623 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33570 Z= 0.205 Angle : 0.593 11.022 45370 Z= 0.303 Chirality : 0.043 0.257 5052 Planarity : 0.004 0.051 5722 Dihedral : 3.945 24.880 4412 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.21 % Allowed : 11.84 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.13), residues: 4036 helix: 1.60 (0.11), residues: 2134 sheet: 0.67 (0.28), residues: 364 loop : -0.81 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1116 HIS 0.022 0.001 HIS B 140 PHE 0.032 0.002 PHE B1655 TYR 0.018 0.002 TYR A 662 ARG 0.006 0.001 ARG B1238 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1761) hydrogen bonds : angle 4.57223 ( 5145) covalent geometry : bond 0.00500 (33570) covalent geometry : angle 0.59346 (45370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 402 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9236 (mm) cc_final: 0.8946 (mt) REVERT: A 140 HIS cc_start: 0.8652 (t70) cc_final: 0.8393 (t70) REVERT: A 184 MET cc_start: 0.7049 (ptm) cc_final: 0.6595 (ptm) REVERT: A 650 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7427 (ttm110) REVERT: A 1322 PHE cc_start: 0.6877 (m-80) cc_final: 0.6591 (m-80) REVERT: A 1414 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7613 (mtp) REVERT: A 1536 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7864 (mmtm) REVERT: A 1562 MET cc_start: 0.7916 (ptp) cc_final: 0.7508 (ptp) REVERT: A 1564 TYR cc_start: 0.7454 (t80) cc_final: 0.7213 (t80) REVERT: A 1605 LYS cc_start: 0.8042 (mppt) cc_final: 0.7669 (mtmm) REVERT: A 1646 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.4992 (m-80) REVERT: A 1768 ASP cc_start: 0.9072 (m-30) cc_final: 0.8866 (m-30) REVERT: A 1779 MET cc_start: 0.5597 (pmm) cc_final: 0.4647 (ppp) REVERT: A 2111 ASN cc_start: 0.8657 (t0) cc_final: 0.8271 (t0) REVERT: A 2135 MET cc_start: 0.8389 (mmt) cc_final: 0.7873 (mmt) REVERT: B 926 TYR cc_start: 0.6987 (m-80) cc_final: 0.6759 (m-10) REVERT: B 1414 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: B 1469 ASN cc_start: 0.7460 (m110) cc_final: 0.7127 (m-40) REVERT: B 1536 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7884 (mmtm) REVERT: B 1562 MET cc_start: 0.7892 (ptp) cc_final: 0.7492 (ptp) REVERT: B 1564 TYR cc_start: 0.7501 (t80) cc_final: 0.7239 (t80) REVERT: B 1590 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 1605 LYS cc_start: 0.8038 (mppt) cc_final: 0.7663 (mtmm) REVERT: B 1646 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.4996 (m-80) REVERT: B 1679 ILE cc_start: 0.7513 (mm) cc_final: 0.7235 (mt) REVERT: B 1779 MET cc_start: 0.5387 (pmm) cc_final: 0.4661 (ptt) REVERT: B 2135 MET cc_start: 0.8379 (mmt) cc_final: 0.7905 (mmt) outliers start: 80 outliers final: 50 residues processed: 445 average time/residue: 0.4486 time to fit residues: 325.9237 Evaluate side-chains 427 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 371 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 970 SER Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 SER Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 322 optimal weight: 0.9980 chunk 368 optimal weight: 6.9990 chunk 397 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 364 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 328 optimal weight: 0.3980 chunk 212 optimal weight: 0.8980 chunk 378 optimal weight: 10.0000 chunk 182 optimal weight: 0.4980 chunk 336 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN B 82 HIS ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.171926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.134899 restraints weight = 53858.854| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.35 r_work: 0.3664 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33570 Z= 0.114 Angle : 0.529 10.500 45370 Z= 0.268 Chirality : 0.039 0.236 5052 Planarity : 0.004 0.047 5722 Dihedral : 3.788 23.707 4412 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.93 % Allowed : 13.00 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4036 helix: 1.79 (0.11), residues: 2134 sheet: 0.71 (0.28), residues: 360 loop : -0.75 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1116 HIS 0.004 0.001 HIS A 742 PHE 0.027 0.001 PHE B1655 TYR 0.021 0.001 TYR B 339 ARG 0.008 0.000 ARG B1702 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 1761) hydrogen bonds : angle 4.34873 ( 5145) covalent geometry : bond 0.00264 (33570) covalent geometry : angle 0.52941 (45370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 395 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9206 (mm) cc_final: 0.8953 (mt) REVERT: A 140 HIS cc_start: 0.8655 (t70) cc_final: 0.8416 (t70) REVERT: A 184 MET cc_start: 0.6976 (ptm) cc_final: 0.6529 (ptm) REVERT: A 1322 PHE cc_start: 0.6856 (m-80) cc_final: 0.6568 (m-80) REVERT: A 1536 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7880 (mmtm) REVERT: A 1557 LYS cc_start: 0.8142 (tptt) cc_final: 0.7876 (tttt) REVERT: A 1562 MET cc_start: 0.7857 (ptp) cc_final: 0.7485 (ptp) REVERT: A 1564 TYR cc_start: 0.7392 (t80) cc_final: 0.7175 (t80) REVERT: A 1646 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.4914 (m-80) REVERT: A 1679 ILE cc_start: 0.7593 (mt) cc_final: 0.7118 (mm) REVERT: A 1767 MET cc_start: 0.9475 (ptp) cc_final: 0.9148 (ptp) REVERT: A 1768 ASP cc_start: 0.9152 (m-30) cc_final: 0.8916 (m-30) REVERT: A 1779 MET cc_start: 0.5609 (pmm) cc_final: 0.4635 (ppp) REVERT: A 2111 ASN cc_start: 0.8647 (t0) cc_final: 0.7934 (t0) REVERT: A 2135 MET cc_start: 0.8379 (mmt) cc_final: 0.7904 (mmt) REVERT: B 650 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7422 (ttm110) REVERT: B 1387 LEU cc_start: 0.8678 (tt) cc_final: 0.8384 (tp) REVERT: B 1469 ASN cc_start: 0.7485 (m110) cc_final: 0.7142 (m-40) REVERT: B 1536 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7870 (mmtm) REVERT: B 1557 LYS cc_start: 0.8156 (tptt) cc_final: 0.7870 (tttt) REVERT: B 1562 MET cc_start: 0.7839 (ptp) cc_final: 0.7468 (ptp) REVERT: B 1564 TYR cc_start: 0.7397 (t80) cc_final: 0.7177 (t80) REVERT: B 1590 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8499 (mp) REVERT: B 1646 TYR cc_start: 0.6192 (OUTLIER) cc_final: 0.4896 (m-80) REVERT: B 1679 ILE cc_start: 0.7608 (mm) cc_final: 0.7292 (mt) REVERT: B 1767 MET cc_start: 0.9475 (ptp) cc_final: 0.8692 (ptp) REVERT: B 1779 MET cc_start: 0.5517 (pmm) cc_final: 0.4796 (ptt) outliers start: 70 outliers final: 43 residues processed: 427 average time/residue: 0.4461 time to fit residues: 308.5184 Evaluate side-chains 416 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 369 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 399 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 271 optimal weight: 0.6980 chunk 301 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 177 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129235 restraints weight = 54293.161| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.47 r_work: 0.3649 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33570 Z= 0.137 Angle : 0.535 11.049 45370 Z= 0.270 Chirality : 0.040 0.141 5052 Planarity : 0.004 0.048 5722 Dihedral : 3.794 24.426 4412 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.43 % Allowed : 12.95 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4036 helix: 1.83 (0.11), residues: 2128 sheet: 0.68 (0.28), residues: 360 loop : -0.78 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1116 HIS 0.004 0.001 HIS A 8 PHE 0.024 0.001 PHE B1655 TYR 0.015 0.001 TYR A 713 ARG 0.012 0.000 ARG A 316 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1761) hydrogen bonds : angle 4.28544 ( 5145) covalent geometry : bond 0.00328 (33570) covalent geometry : angle 0.53467 (45370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 376 time to evaluate : 4.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 HIS cc_start: 0.8596 (t70) cc_final: 0.8365 (t70) REVERT: A 184 MET cc_start: 0.7025 (ptm) cc_final: 0.6572 (ptm) REVERT: A 645 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 735 MET cc_start: 0.7320 (tpp) cc_final: 0.7034 (tpp) REVERT: A 1322 PHE cc_start: 0.6900 (m-80) cc_final: 0.6600 (m-80) REVERT: A 1536 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7848 (mmtm) REVERT: A 1562 MET cc_start: 0.7823 (ptp) cc_final: 0.7456 (ptp) REVERT: A 1564 TYR cc_start: 0.7421 (t80) cc_final: 0.7219 (t80) REVERT: A 1646 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.4854 (m-80) REVERT: A 1768 ASP cc_start: 0.9209 (m-30) cc_final: 0.8954 (m-30) REVERT: A 1779 MET cc_start: 0.5770 (pmm) cc_final: 0.4783 (ppp) REVERT: B 650 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7390 (ttm110) REVERT: B 735 MET cc_start: 0.7305 (tpp) cc_final: 0.6996 (tpp) REVERT: B 1469 ASN cc_start: 0.7540 (m110) cc_final: 0.7206 (m110) REVERT: B 1536 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7870 (mmtm) REVERT: B 1557 LYS cc_start: 0.8121 (tptt) cc_final: 0.7913 (tttt) REVERT: B 1562 MET cc_start: 0.7832 (ptp) cc_final: 0.7450 (ptp) REVERT: B 1564 TYR cc_start: 0.7424 (t80) cc_final: 0.7224 (t80) REVERT: B 1590 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 1646 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.4835 (m-80) REVERT: B 1679 ILE cc_start: 0.7635 (mm) cc_final: 0.7242 (mt) REVERT: B 1779 MET cc_start: 0.5636 (pmm) cc_final: 0.4929 (ptt) outliers start: 88 outliers final: 63 residues processed: 422 average time/residue: 0.4389 time to fit residues: 302.8483 Evaluate side-chains 427 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 359 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 SER Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 55 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 276 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 177 ASN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.169902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.132612 restraints weight = 54186.075| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.40 r_work: 0.3636 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33570 Z= 0.144 Angle : 0.540 11.977 45370 Z= 0.273 Chirality : 0.040 0.137 5052 Planarity : 0.004 0.046 5722 Dihedral : 3.810 25.159 4412 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.54 % Allowed : 12.98 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4036 helix: 1.80 (0.11), residues: 2126 sheet: 0.65 (0.27), residues: 360 loop : -0.82 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1116 HIS 0.011 0.001 HIS B 140 PHE 0.022 0.001 PHE B1655 TYR 0.021 0.001 TYR B 339 ARG 0.011 0.000 ARG A 316 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1761) hydrogen bonds : angle 4.28278 ( 5145) covalent geometry : bond 0.00347 (33570) covalent geometry : angle 0.54022 (45370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 366 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 HIS cc_start: 0.8667 (t70) cc_final: 0.8412 (t70) REVERT: A 184 MET cc_start: 0.7036 (ptm) cc_final: 0.6587 (ptm) REVERT: A 645 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: A 650 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7412 (ttm110) REVERT: A 1040 PHE cc_start: 0.7525 (t80) cc_final: 0.6954 (t80) REVERT: A 1322 PHE cc_start: 0.6840 (m-80) cc_final: 0.6556 (m-80) REVERT: A 1536 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7900 (mmtm) REVERT: A 1562 MET cc_start: 0.7814 (ptp) cc_final: 0.7409 (ptp) REVERT: A 1646 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.4815 (m-80) REVERT: A 1767 MET cc_start: 0.9373 (ptp) cc_final: 0.8841 (ptp) REVERT: A 1768 ASP cc_start: 0.9223 (m-30) cc_final: 0.8989 (m-30) REVERT: A 1779 MET cc_start: 0.5780 (pmm) cc_final: 0.4793 (ppp) REVERT: B 650 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7411 (ttm110) REVERT: B 791 GLU cc_start: 0.7428 (tp30) cc_final: 0.7225 (tm-30) REVERT: B 1040 PHE cc_start: 0.7508 (t80) cc_final: 0.6940 (t80) REVERT: B 1469 ASN cc_start: 0.7573 (m110) cc_final: 0.7220 (m110) REVERT: B 1536 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7918 (mmtm) REVERT: B 1557 LYS cc_start: 0.8118 (tptt) cc_final: 0.7909 (tttt) REVERT: B 1562 MET cc_start: 0.7736 (ptp) cc_final: 0.7352 (ptp) REVERT: B 1590 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 1646 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: B 1679 ILE cc_start: 0.7650 (mm) cc_final: 0.7242 (mt) REVERT: B 1779 MET cc_start: 0.5606 (pmm) cc_final: 0.4902 (ptt) outliers start: 92 outliers final: 69 residues processed: 416 average time/residue: 0.4465 time to fit residues: 301.5556 Evaluate side-chains 429 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 354 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1604 HIS Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1753 LEU Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 SER Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1753 LEU Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 266 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 356 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 181 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 316 optimal weight: 0.9980 chunk 398 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS A 824 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.169720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.132181 restraints weight = 54197.244| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.41 r_work: 0.3634 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33570 Z= 0.145 Angle : 0.558 12.863 45370 Z= 0.281 Chirality : 0.040 0.145 5052 Planarity : 0.004 0.047 5722 Dihedral : 3.860 25.465 4412 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.48 % Allowed : 13.22 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4036 helix: 1.76 (0.11), residues: 2128 sheet: 0.60 (0.27), residues: 360 loop : -0.83 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B1116 HIS 0.005 0.001 HIS B 140 PHE 0.021 0.001 PHE A1655 TYR 0.042 0.001 TYR A 662 ARG 0.014 0.000 ARG A 316 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 1761) hydrogen bonds : angle 4.28369 ( 5145) covalent geometry : bond 0.00349 (33570) covalent geometry : angle 0.55828 (45370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 371 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 184 MET cc_start: 0.7132 (ptm) cc_final: 0.6654 (ptm) REVERT: A 456 GLN cc_start: 0.8550 (mt0) cc_final: 0.8216 (mp10) REVERT: A 645 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: A 650 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7373 (ttm110) REVERT: A 735 MET cc_start: 0.7293 (tpp) cc_final: 0.7028 (tpp) REVERT: A 905 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8378 (mt) REVERT: A 1038 LYS cc_start: 0.8879 (mmpt) cc_final: 0.8665 (tppt) REVERT: A 1040 PHE cc_start: 0.7538 (t80) cc_final: 0.7112 (t80) REVERT: A 1322 PHE cc_start: 0.6861 (m-80) cc_final: 0.6569 (m-80) REVERT: A 1536 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7896 (mmtm) REVERT: A 1562 MET cc_start: 0.7721 (ptp) cc_final: 0.7362 (ptp) REVERT: A 1605 LYS cc_start: 0.7996 (mppt) cc_final: 0.7594 (mtmm) REVERT: A 1646 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: A 1768 ASP cc_start: 0.9212 (m-30) cc_final: 0.8918 (t0) REVERT: A 1779 MET cc_start: 0.5743 (pmm) cc_final: 0.4747 (ppp) REVERT: B 23 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7991 (mt-10) REVERT: B 88 LEU cc_start: 0.7790 (mm) cc_final: 0.7362 (tp) REVERT: B 650 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7384 (ttm110) REVERT: B 735 MET cc_start: 0.7320 (tpp) cc_final: 0.7045 (tpp) REVERT: B 905 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8384 (mt) REVERT: B 1040 PHE cc_start: 0.7579 (t80) cc_final: 0.7034 (t80) REVERT: B 1469 ASN cc_start: 0.7546 (m110) cc_final: 0.7206 (m110) REVERT: B 1536 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7896 (mmtm) REVERT: B 1562 MET cc_start: 0.7707 (ptp) cc_final: 0.7341 (ptp) REVERT: B 1590 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 1605 LYS cc_start: 0.7971 (mppt) cc_final: 0.7574 (mtmm) REVERT: B 1646 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.4791 (m-80) REVERT: B 1679 ILE cc_start: 0.7710 (mm) cc_final: 0.7275 (mt) REVERT: B 1737 LEU cc_start: 0.7786 (tp) cc_final: 0.7561 (tp) REVERT: B 1779 MET cc_start: 0.5572 (pmm) cc_final: 0.4886 (ptt) outliers start: 90 outliers final: 65 residues processed: 419 average time/residue: 0.4544 time to fit residues: 308.7392 Evaluate side-chains 423 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 350 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1604 HIS Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 SER Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1604 HIS Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 125 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 314 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 313 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 373 optimal weight: 40.0000 chunk 296 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130882 restraints weight = 54181.291| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.44 r_work: 0.3612 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33570 Z= 0.182 Angle : 0.596 13.595 45370 Z= 0.301 Chirality : 0.042 0.218 5052 Planarity : 0.004 0.051 5722 Dihedral : 3.993 26.942 4412 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.21 % Allowed : 13.56 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4036 helix: 1.60 (0.11), residues: 2126 sheet: 0.55 (0.27), residues: 348 loop : -0.88 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A1116 HIS 0.004 0.001 HIS B1365 PHE 0.018 0.002 PHE A 585 TYR 0.053 0.002 TYR A 662 ARG 0.013 0.000 ARG A 316 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1761) hydrogen bonds : angle 4.38195 ( 5145) covalent geometry : bond 0.00442 (33570) covalent geometry : angle 0.59593 (45370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 359 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7138 (ptm) cc_final: 0.6709 (ptm) REVERT: A 456 GLN cc_start: 0.8580 (mt0) cc_final: 0.8234 (mp10) REVERT: A 645 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 691 ASP cc_start: 0.6985 (m-30) cc_final: 0.6531 (m-30) REVERT: A 735 MET cc_start: 0.7379 (tpp) cc_final: 0.7135 (tpp) REVERT: A 905 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 1040 PHE cc_start: 0.7567 (t80) cc_final: 0.7185 (t80) REVERT: A 1536 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7927 (mmtm) REVERT: A 1562 MET cc_start: 0.7697 (ptp) cc_final: 0.7298 (ptp) REVERT: A 1646 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.4867 (m-80) REVERT: A 1768 ASP cc_start: 0.9160 (m-30) cc_final: 0.8878 (m-30) REVERT: A 1779 MET cc_start: 0.5789 (pmm) cc_final: 0.4713 (ppp) REVERT: B 88 LEU cc_start: 0.7847 (mm) cc_final: 0.7362 (tp) REVERT: B 185 ARG cc_start: 0.7485 (tpp-160) cc_final: 0.7144 (mmt180) REVERT: B 456 GLN cc_start: 0.8583 (mt0) cc_final: 0.8242 (mp10) REVERT: B 735 MET cc_start: 0.7325 (tpp) cc_final: 0.7048 (tpp) REVERT: B 905 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 1536 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7928 (mmtm) REVERT: B 1562 MET cc_start: 0.7708 (ptp) cc_final: 0.7338 (ptp) REVERT: B 1605 LYS cc_start: 0.8061 (mppt) cc_final: 0.7682 (mtmm) REVERT: B 1646 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.4851 (m-80) REVERT: B 1679 ILE cc_start: 0.7730 (mm) cc_final: 0.7306 (mt) REVERT: B 1737 LEU cc_start: 0.7926 (tp) cc_final: 0.7680 (tp) REVERT: B 1779 MET cc_start: 0.5632 (pmm) cc_final: 0.4868 (ptt) REVERT: B 1872 ASP cc_start: 0.8209 (t0) cc_final: 0.7921 (t70) outliers start: 80 outliers final: 64 residues processed: 402 average time/residue: 0.4651 time to fit residues: 307.9632 Evaluate side-chains 418 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 349 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1604 HIS Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 SER Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 1604 HIS Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 151 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 272 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 314 optimal weight: 0.3980 chunk 129 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1469 ASN ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.170085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133121 restraints weight = 54052.255| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.78 r_work: 0.3624 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33570 Z= 0.123 Angle : 0.577 13.607 45370 Z= 0.289 Chirality : 0.040 0.221 5052 Planarity : 0.004 0.058 5722 Dihedral : 3.900 25.650 4412 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.96 % Allowed : 14.16 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.13), residues: 4036 helix: 1.72 (0.11), residues: 2126 sheet: 0.41 (0.27), residues: 352 loop : -0.87 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B1116 HIS 0.008 0.001 HIS B 140 PHE 0.016 0.001 PHE A 585 TYR 0.014 0.001 TYR A 662 ARG 0.014 0.000 ARG A 316 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1761) hydrogen bonds : angle 4.26179 ( 5145) covalent geometry : bond 0.00290 (33570) covalent geometry : angle 0.57714 (45370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 185 ARG cc_start: 0.7722 (mmt180) cc_final: 0.7240 (mmt180) REVERT: A 645 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: A 735 MET cc_start: 0.7284 (tpp) cc_final: 0.7060 (tpp) REVERT: A 905 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 1040 PHE cc_start: 0.7515 (t80) cc_final: 0.7032 (t80) REVERT: A 1093 PHE cc_start: 0.8524 (p90) cc_final: 0.8120 (p90) REVERT: A 1536 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7893 (mmtm) REVERT: A 1562 MET cc_start: 0.7680 (ptp) cc_final: 0.7314 (ptp) REVERT: A 1646 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.4829 (m-80) REVERT: A 1753 LEU cc_start: 0.9189 (mm) cc_final: 0.8952 (mm) REVERT: A 1768 ASP cc_start: 0.9137 (m-30) cc_final: 0.8862 (m-30) REVERT: A 1779 MET cc_start: 0.5751 (pmm) cc_final: 0.5204 (ppp) REVERT: B 23 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 88 LEU cc_start: 0.7916 (mm) cc_final: 0.7384 (tp) REVERT: B 183 TYR cc_start: 0.7919 (m-80) cc_final: 0.7706 (m-80) REVERT: B 735 MET cc_start: 0.7276 (tpp) cc_final: 0.7043 (tpp) REVERT: B 905 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8341 (mt) REVERT: B 963 LYS cc_start: 0.8366 (ttmm) cc_final: 0.7892 (tptt) REVERT: B 1040 PHE cc_start: 0.7383 (t80) cc_final: 0.7149 (t80) REVERT: B 1093 PHE cc_start: 0.8524 (p90) cc_final: 0.8091 (p90) REVERT: B 1536 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7882 (mmtm) REVERT: B 1605 LYS cc_start: 0.8150 (mppt) cc_final: 0.7527 (mppt) REVERT: B 1646 TYR cc_start: 0.6199 (OUTLIER) cc_final: 0.4820 (m-80) REVERT: B 1779 MET cc_start: 0.5600 (pmm) cc_final: 0.4839 (ptt) outliers start: 71 outliers final: 57 residues processed: 399 average time/residue: 0.4605 time to fit residues: 301.6845 Evaluate side-chains 418 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 356 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain A residue 1604 HIS Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 SER Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1558 ARG Chi-restraints excluded: chain B residue 1604 HIS Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 356 optimal weight: 2.9990 chunk 347 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 182 optimal weight: 0.1980 chunk 135 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 345 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS B 824 GLN B 875 GLN ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.171210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130402 restraints weight = 53953.672| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.71 r_work: 0.3647 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33570 Z= 0.111 Angle : 0.566 13.225 45370 Z= 0.283 Chirality : 0.040 0.203 5052 Planarity : 0.004 0.060 5722 Dihedral : 3.801 24.068 4412 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.93 % Allowed : 14.22 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4036 helix: 1.82 (0.11), residues: 2126 sheet: 0.39 (0.27), residues: 352 loop : -0.82 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B1116 HIS 0.005 0.001 HIS A1761 PHE 0.014 0.001 PHE B 585 TYR 0.024 0.001 TYR B 339 ARG 0.014 0.000 ARG A 316 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 1761) hydrogen bonds : angle 4.18344 ( 5145) covalent geometry : bond 0.00258 (33570) covalent geometry : angle 0.56633 (45370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19073.58 seconds wall clock time: 330 minutes 38.45 seconds (19838.45 seconds total)