Starting phenix.real_space_refine on Tue Aug 26 04:04:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qgu_18391/08_2025/8qgu_18391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qgu_18391/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qgu_18391/08_2025/8qgu_18391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qgu_18391/08_2025/8qgu_18391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qgu_18391/08_2025/8qgu_18391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qgu_18391/08_2025/8qgu_18391.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 26.77, per 1000 atoms: 0.82 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: 3.21 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.90 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: 10.53 Time building geometry restraints manager: 4.16 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: 0.04 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: 4.560 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: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 53.930 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.610 ------------------------------------------------------------------------------- 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 : 7.83 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.010 0.000 ARG B 289 TYR 0.022 0.001 TYR B 32 PHE 0.022 0.001 PHE B 371 TRP 0.022 0.001 TRP B1423 HIS 0.004 0.000 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00249 (33570) covalent geometry : angle 0.50349 (45370) hydrogen bonds : bond 0.15013 ( 1761) hydrogen bonds : angle 5.90974 ( 5145) *********************** 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 : 1.423 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: 0.2324 time to fit residues: 274.1470 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 : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A1287 ASN A1365 HIS A1575 GLN A1881 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 ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1287 ASN B1365 HIS B1575 GLN B1881 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.171732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130441 restraints weight = 54403.310| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.74 r_work: 0.3629 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2250 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= 0.186 Angle : 0.616 12.559 45370 Z= 0.315 Chirality : 0.043 0.178 5052 Planarity : 0.005 0.054 5722 Dihedral : 3.888 21.917 4412 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.52 % Allowed : 9.22 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.13), residues: 4036 helix: 1.67 (0.11), residues: 2122 sheet: 0.84 (0.28), residues: 378 loop : -0.85 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1703 TYR 0.020 0.002 TYR A 869 PHE 0.025 0.002 PHE A 91 TRP 0.015 0.002 TRP A1423 HIS 0.005 0.001 HIS A 742 Details of bonding type rmsd covalent geometry : bond 0.00443 (33570) covalent geometry : angle 0.61556 (45370) hydrogen bonds : bond 0.04052 ( 1761) hydrogen bonds : angle 4.72389 ( 5145) *********************** 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 517 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 462 time to evaluate : 1.050 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: A 1 MET cc_start: 0.7383 (mmm) cc_final: 0.7161 (mmm) REVERT: A 27 TYR cc_start: 0.8507 (m-80) cc_final: 0.8284 (m-80) REVERT: A 140 HIS cc_start: 0.8894 (t70) cc_final: 0.8608 (t70) REVERT: A 184 MET cc_start: 0.7241 (ptm) cc_final: 0.6598 (ptm) REVERT: A 884 LYS cc_start: 0.7152 (mtmm) cc_final: 0.6675 (mttm) REVERT: A 1093 PHE cc_start: 0.8575 (p90) cc_final: 0.8137 (p90) REVERT: A 1322 PHE cc_start: 0.6931 (m-80) cc_final: 0.6626 (m-80) REVERT: A 1469 ASN cc_start: 0.7605 (m110) cc_final: 0.7362 (m-40) REVERT: A 1536 LYS cc_start: 0.8329 (mmtm) cc_final: 0.7934 (mmtm) REVERT: A 1562 MET cc_start: 0.7909 (ptp) cc_final: 0.7545 (ptp) REVERT: A 1605 LYS cc_start: 0.8089 (mppt) cc_final: 0.7729 (mtmm) REVERT: A 1654 TRP cc_start: 0.7981 (t-100) cc_final: 0.7680 (t-100) REVERT: A 1679 ILE cc_start: 0.7498 (mm) cc_final: 0.7294 (mt) REVERT: A 1763 LEU cc_start: 0.9335 (mt) cc_final: 0.8930 (mp) REVERT: A 1768 ASP cc_start: 0.9360 (m-30) cc_final: 0.9065 (t70) REVERT: A 1779 MET cc_start: 0.6159 (pmm) cc_final: 0.5330 (tmm) REVERT: A 2111 ASN cc_start: 0.8608 (t0) cc_final: 0.8011 (t0) REVERT: A 2135 MET cc_start: 0.8347 (mmt) cc_final: 0.7847 (mmt) REVERT: A 2151 TYR cc_start: 0.7242 (m-80) cc_final: 0.6949 (m-80) REVERT: B 184 MET cc_start: 0.7477 (ptm) cc_final: 0.6834 (ptm) REVERT: B 650 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7369 (mtm110) REVERT: B 884 LYS cc_start: 0.7156 (mtmm) cc_final: 0.6689 (mttm) REVERT: B 1026 TYR cc_start: 0.8905 (t80) cc_final: 0.8691 (t80) REVERT: B 1093 PHE cc_start: 0.8573 (p90) cc_final: 0.8150 (p90) REVERT: B 1138 MET cc_start: 0.6691 (ptt) cc_final: 0.6447 (ptt) REVERT: B 1322 PHE cc_start: 0.7022 (m-80) cc_final: 0.6744 (m-80) REVERT: B 1469 ASN cc_start: 0.7613 (m110) cc_final: 0.7378 (m-40) REVERT: B 1536 LYS cc_start: 0.8355 (mmtm) cc_final: 0.7964 (mmtm) REVERT: B 1562 MET cc_start: 0.7902 (ptp) cc_final: 0.7533 (ptp) REVERT: B 1605 LYS cc_start: 0.8057 (mppt) cc_final: 0.7686 (mtmm) REVERT: B 1654 TRP cc_start: 0.8008 (t-100) cc_final: 0.7706 (t-100) REVERT: B 1679 ILE cc_start: 0.7599 (mm) cc_final: 0.7288 (mt) REVERT: B 1763 LEU cc_start: 0.9382 (mt) cc_final: 0.8969 (mp) REVERT: B 1768 ASP cc_start: 0.9371 (m-30) cc_final: 0.9068 (t70) REVERT: B 1779 MET cc_start: 0.5997 (pmm) cc_final: 0.5440 (ptt) REVERT: B 1792 MET cc_start: 0.5053 (tmm) cc_final: 0.4830 (tmm) REVERT: B 2111 ASN cc_start: 0.8636 (t0) cc_final: 0.8016 (t0) REVERT: B 2135 MET cc_start: 0.8359 (mmt) cc_final: 0.7845 (mmt) REVERT: B 2151 TYR cc_start: 0.7139 (m-80) cc_final: 0.6894 (m-10) outliers start: 55 outliers final: 36 residues processed: 493 average time/residue: 0.2014 time to fit residues: 159.6143 Evaluate side-chains 432 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 395 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 613 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 664 ILE 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 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1558 ARG Chi-restraints excluded: chain B residue 62 LEU 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 314 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 634 THR 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 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 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 77 optimal weight: 0.0670 chunk 176 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 284 optimal weight: 0.4980 chunk 225 optimal weight: 8.9990 chunk 121 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 413 GLN A 824 GLN A1125 GLN A1298 HIS B 82 HIS B 140 HIS B 363 GLN B 406 ASN B 413 GLN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 GLN B1298 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.173138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.135720 restraints weight = 53909.965| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.43 r_work: 0.3688 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33570 Z= 0.113 Angle : 0.530 9.803 45370 Z= 0.270 Chirality : 0.040 0.208 5052 Planarity : 0.004 0.053 5722 Dihedral : 3.733 21.943 4412 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.49 % Allowed : 11.04 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.13), residues: 4036 helix: 1.82 (0.11), residues: 2120 sheet: 0.77 (0.28), residues: 374 loop : -0.74 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1703 TYR 0.017 0.001 TYR A 339 PHE 0.046 0.001 PHE A 63 TRP 0.012 0.001 TRP B1139 HIS 0.008 0.001 HIS A1298 Details of bonding type rmsd covalent geometry : bond 0.00247 (33570) covalent geometry : angle 0.52967 (45370) hydrogen bonds : bond 0.03489 ( 1761) hydrogen bonds : angle 4.47090 ( 5145) *********************** 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 482 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 428 time to evaluate : 1.642 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: A 62 LEU cc_start: 0.9287 (mm) cc_final: 0.8992 (mt) REVERT: A 140 HIS cc_start: 0.8743 (t70) cc_final: 0.8488 (t70) REVERT: A 184 MET cc_start: 0.7161 (ptm) cc_final: 0.6721 (ptm) REVERT: A 884 LYS cc_start: 0.7129 (mtmm) cc_final: 0.6602 (mttm) REVERT: A 1322 PHE cc_start: 0.6874 (m-80) cc_final: 0.6606 (m-80) REVERT: A 1355 SER cc_start: 0.8200 (t) cc_final: 0.7815 (p) REVERT: A 1387 LEU cc_start: 0.8588 (tt) cc_final: 0.8284 (tp) REVERT: A 1469 ASN cc_start: 0.7475 (m110) cc_final: 0.7229 (m110) REVERT: A 1536 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7856 (mmtm) REVERT: A 1562 MET cc_start: 0.7889 (ptp) cc_final: 0.7486 (ptp) REVERT: A 1679 ILE cc_start: 0.7486 (mm) cc_final: 0.7219 (mt) REVERT: A 1768 ASP cc_start: 0.9097 (m-30) cc_final: 0.8877 (m-30) REVERT: A 1779 MET cc_start: 0.5713 (pmm) cc_final: 0.4718 (tmm) REVERT: A 2111 ASN cc_start: 0.8580 (t0) cc_final: 0.7933 (t0) REVERT: A 2135 MET cc_start: 0.8356 (mmt) cc_final: 0.7893 (mmt) REVERT: B 184 MET cc_start: 0.7414 (ptm) cc_final: 0.6933 (ptm) REVERT: B 884 LYS cc_start: 0.7111 (mtmm) cc_final: 0.6600 (mttm) REVERT: B 1093 PHE cc_start: 0.8398 (p90) cc_final: 0.8016 (p90) REVERT: B 1138 MET cc_start: 0.6536 (ptt) cc_final: 0.6320 (ptt) REVERT: B 1355 SER cc_start: 0.8183 (t) cc_final: 0.7804 (p) REVERT: B 1387 LEU cc_start: 0.8591 (tt) cc_final: 0.8305 (tp) REVERT: B 1469 ASN cc_start: 0.7506 (m110) cc_final: 0.7253 (m110) REVERT: B 1536 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7859 (mmtm) REVERT: B 1562 MET cc_start: 0.7872 (ptp) cc_final: 0.7523 (ptp) REVERT: B 1768 ASP cc_start: 0.9120 (m-30) cc_final: 0.8905 (m-30) REVERT: B 1779 MET cc_start: 0.5616 (pmm) cc_final: 0.4902 (ptt) REVERT: B 1792 MET cc_start: 0.5339 (tmm) cc_final: 0.5042 (tmm) REVERT: B 2135 MET cc_start: 0.8349 (mmt) cc_final: 0.7862 (mmt) outliers start: 54 outliers final: 23 residues processed: 460 average time/residue: 0.1972 time to fit residues: 147.5513 Evaluate side-chains 403 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 380 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 645 GLU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 747 GLU 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 B residue 140 HIS Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 1164 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 188 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 399 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN A1125 GLN ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 GLN A2115 ASN B 8 HIS B 323 ASN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN B1125 GLN ** B1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4291 r_free = 0.4291 target = 0.167085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.129459 restraints weight = 53971.293| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.46 r_work: 0.3588 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 33570 Z= 0.255 Angle : 0.638 10.407 45370 Z= 0.329 Chirality : 0.044 0.257 5052 Planarity : 0.005 0.053 5722 Dihedral : 4.152 27.307 4412 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.71 % Allowed : 12.07 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.13), residues: 4036 helix: 1.36 (0.11), residues: 2130 sheet: 0.68 (0.28), residues: 364 loop : -0.86 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1702 TYR 0.023 0.002 TYR A 662 PHE 0.028 0.002 PHE A 63 TRP 0.033 0.002 TRP B1116 HIS 0.019 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00616 (33570) covalent geometry : angle 0.63807 (45370) hydrogen bonds : bond 0.04332 ( 1761) hydrogen bonds : angle 4.74386 ( 5145) *********************** 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 484 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 386 time to evaluate : 1.330 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: A 62 LEU cc_start: 0.9205 (mm) cc_final: 0.8927 (mt) REVERT: A 140 HIS cc_start: 0.8620 (t70) cc_final: 0.8358 (t70) REVERT: A 184 MET cc_start: 0.7092 (ptm) cc_final: 0.6596 (ptm) REVERT: A 691 ASP cc_start: 0.7158 (m-30) cc_final: 0.6698 (m-30) REVERT: A 1322 PHE cc_start: 0.6909 (m-80) cc_final: 0.6620 (m-80) REVERT: A 1469 ASN cc_start: 0.7471 (m110) cc_final: 0.7160 (m-40) REVERT: A 1518 MET cc_start: 0.7982 (tpp) cc_final: 0.7765 (tpp) REVERT: A 1562 MET cc_start: 0.7937 (ptp) cc_final: 0.7515 (ptp) REVERT: A 1605 LYS cc_start: 0.8073 (mppt) cc_final: 0.7686 (mtmm) REVERT: A 1646 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5119 (m-80) REVERT: A 1679 ILE cc_start: 0.7651 (mm) cc_final: 0.7279 (mt) REVERT: A 1768 ASP cc_start: 0.9073 (m-30) cc_final: 0.8873 (m-30) REVERT: A 1779 MET cc_start: 0.5783 (pmm) cc_final: 0.4876 (tmm) REVERT: A 2135 MET cc_start: 0.8420 (mmt) cc_final: 0.7918 (mmt) REVERT: B 1093 PHE cc_start: 0.8584 (p90) cc_final: 0.8157 (p90) REVERT: B 1138 MET cc_start: 0.7032 (ptt) cc_final: 0.6782 (ptt) REVERT: B 1469 ASN cc_start: 0.7533 (m110) cc_final: 0.7205 (m-40) REVERT: B 1518 MET cc_start: 0.7993 (tpp) cc_final: 0.7779 (tpp) REVERT: B 1562 MET cc_start: 0.7937 (ptp) cc_final: 0.7515 (ptp) REVERT: B 1564 TYR cc_start: 0.7434 (t80) cc_final: 0.7194 (t80) REVERT: B 1605 LYS cc_start: 0.8068 (mppt) cc_final: 0.7679 (mtmm) REVERT: B 1646 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5118 (m-80) REVERT: B 1767 MET cc_start: 0.9325 (mtm) cc_final: 0.8875 (ptp) REVERT: B 1779 MET cc_start: 0.5636 (pmm) cc_final: 0.4922 (ptt) REVERT: B 2135 MET cc_start: 0.8411 (mmt) cc_final: 0.7897 (mmt) outliers start: 98 outliers final: 57 residues processed: 446 average time/residue: 0.1919 time to fit residues: 141.1220 Evaluate side-chains 420 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE 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 634 THR 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 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 1242 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1340 ILE Chi-restraints excluded: chain A residue 1456 CYS 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 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 510 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU 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 915 ILE 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 1242 THR Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1340 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 208 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 342 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 289 optimal weight: 0.6980 chunk 394 optimal weight: 4.9990 chunk 303 optimal weight: 0.8980 chunk 376 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** 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** ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS B 824 GLN B1125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.170111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.132472 restraints weight = 54051.440| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.74 r_work: 0.3625 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33570 Z= 0.123 Angle : 0.543 10.910 45370 Z= 0.275 Chirality : 0.040 0.232 5052 Planarity : 0.004 0.051 5722 Dihedral : 3.922 25.219 4412 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.13 % Allowed : 12.92 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.13), residues: 4036 helix: 1.67 (0.11), residues: 2122 sheet: 0.67 (0.27), residues: 360 loop : -0.80 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 185 TYR 0.016 0.001 TYR B 713 PHE 0.025 0.001 PHE A 63 TRP 0.032 0.001 TRP A1116 HIS 0.006 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00283 (33570) covalent geometry : angle 0.54293 (45370) hydrogen bonds : bond 0.03454 ( 1761) hydrogen bonds : angle 4.40768 ( 5145) *********************** 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 451 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 374 time to evaluate : 1.323 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 62 LEU cc_start: 0.9320 (mm) cc_final: 0.9057 (mt) REVERT: A 140 HIS cc_start: 0.8784 (t70) cc_final: 0.8513 (t70) REVERT: A 184 MET cc_start: 0.7117 (ptm) cc_final: 0.6450 (ptm) REVERT: A 735 MET cc_start: 0.7337 (tpp) cc_final: 0.6987 (tpp) REVERT: A 905 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 1469 ASN cc_start: 0.7618 (m110) cc_final: 0.7269 (m-40) REVERT: A 1518 MET cc_start: 0.7917 (tpp) cc_final: 0.7694 (tpp) REVERT: A 1557 LYS cc_start: 0.8083 (tptt) cc_final: 0.7807 (tttt) REVERT: A 1562 MET cc_start: 0.7898 (ptp) cc_final: 0.7499 (ptp) REVERT: A 1646 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.4904 (m-80) REVERT: A 1679 ILE cc_start: 0.7540 (mm) cc_final: 0.7153 (mt) REVERT: A 1767 MET cc_start: 0.9411 (ptp) cc_final: 0.8909 (ptp) REVERT: A 1768 ASP cc_start: 0.9179 (m-30) cc_final: 0.8913 (m-30) REVERT: A 1779 MET cc_start: 0.5715 (pmm) cc_final: 0.4753 (ppp) REVERT: A 2111 ASN cc_start: 0.8548 (t0) cc_final: 0.7986 (t0) REVERT: A 2135 MET cc_start: 0.8434 (mmt) cc_final: 0.8005 (mmt) REVERT: B 735 MET cc_start: 0.7308 (tpp) cc_final: 0.7002 (tpp) REVERT: B 905 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 1040 PHE cc_start: 0.7614 (t80) cc_final: 0.7077 (t80) REVERT: B 1093 PHE cc_start: 0.8598 (p90) cc_final: 0.8100 (p90) REVERT: B 1138 MET cc_start: 0.6859 (ptt) cc_final: 0.6639 (ptt) REVERT: B 1469 ASN cc_start: 0.7618 (m110) cc_final: 0.7263 (m-40) REVERT: B 1518 MET cc_start: 0.7908 (tpp) cc_final: 0.7696 (tpp) REVERT: B 1562 MET cc_start: 0.7890 (ptp) cc_final: 0.7480 (ptp) REVERT: B 1564 TYR cc_start: 0.7406 (t80) cc_final: 0.7191 (t80) REVERT: B 1590 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8474 (mp) REVERT: B 1646 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.4899 (m-80) REVERT: B 1679 ILE cc_start: 0.7724 (mt) cc_final: 0.7230 (mm) REVERT: B 1763 LEU cc_start: 0.9450 (mt) cc_final: 0.9233 (mt) REVERT: B 1779 MET cc_start: 0.5563 (pmm) cc_final: 0.4771 (ptt) REVERT: B 1792 MET cc_start: 0.5342 (tmm) cc_final: 0.4827 (tmm) REVERT: B 2135 MET cc_start: 0.8430 (mmt) cc_final: 0.7982 (mmt) outliers start: 77 outliers final: 40 residues processed: 418 average time/residue: 0.1934 time to fit residues: 133.0513 Evaluate side-chains 397 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 352 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE 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 629 LEU 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 1164 VAL Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1294 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 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 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 629 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 905 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1006 ILE 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 1456 CYS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1548 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 297 optimal weight: 1.9990 chunk 368 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 375 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 361 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 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** B1130 HIS ** B1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.166273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128823 restraints weight = 54291.574| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.53 r_work: 0.3566 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 33570 Z= 0.255 Angle : 0.634 9.295 45370 Z= 0.324 Chirality : 0.044 0.218 5052 Planarity : 0.005 0.054 5722 Dihedral : 4.185 27.754 4412 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.68 % Allowed : 12.98 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.13), residues: 4036 helix: 1.36 (0.11), residues: 2130 sheet: 0.63 (0.29), residues: 340 loop : -0.94 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1702 TYR 0.019 0.002 TYR B 339 PHE 0.022 0.002 PHE A 585 TRP 0.047 0.002 TRP B1116 HIS 0.019 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00619 (33570) covalent geometry : angle 0.63438 (45370) hydrogen bonds : bond 0.04228 ( 1761) hydrogen bonds : angle 4.64382 ( 5145) *********************** 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 447 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 350 time to evaluate : 0.887 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: A 140 HIS cc_start: 0.8693 (t70) cc_final: 0.8433 (t70) REVERT: A 645 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 691 ASP cc_start: 0.7059 (m-30) cc_final: 0.6590 (m-30) REVERT: A 1322 PHE cc_start: 0.6851 (m-80) cc_final: 0.6576 (m-80) REVERT: A 1376 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8098 (tmt170) REVERT: A 1557 LYS cc_start: 0.8150 (tptt) cc_final: 0.7887 (tttt) REVERT: A 1562 MET cc_start: 0.7939 (ptp) cc_final: 0.7464 (ptp) REVERT: A 1646 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: A 1679 ILE cc_start: 0.7698 (mm) cc_final: 0.7237 (mt) REVERT: A 1768 ASP cc_start: 0.9210 (m-30) cc_final: 0.8942 (t0) REVERT: A 1779 MET cc_start: 0.5735 (pmm) cc_final: 0.4793 (ppp) REVERT: B 662 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: B 691 ASP cc_start: 0.7065 (m-30) cc_final: 0.6587 (m-30) REVERT: B 1376 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8100 (tmt170) REVERT: B 1562 MET cc_start: 0.7961 (ptp) cc_final: 0.7504 (ptp) REVERT: B 1564 TYR cc_start: 0.7427 (t80) cc_final: 0.7222 (t80) REVERT: B 1624 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7854 (mmmm) REVERT: B 1646 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.5092 (m-80) REVERT: B 1779 MET cc_start: 0.5607 (pmm) cc_final: 0.4866 (ptt) REVERT: B 1792 MET cc_start: 0.5193 (tmm) cc_final: 0.4680 (tmm) outliers start: 97 outliers final: 60 residues processed: 417 average time/residue: 0.1874 time to fit residues: 128.4806 Evaluate side-chains 399 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 332 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 180 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 563 ASP Chi-restraints excluded: chain A residue 622 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 1242 THR Chi-restraints excluded: chain A residue 1257 LYS Chi-restraints excluded: chain A residue 1340 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1456 CYS 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 2071 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 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 370 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 731 LEU 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 1006 ILE 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 1257 LYS Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1376 ARG 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 1624 LYS Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2071 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 237 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 170 optimal weight: 40.0000 chunk 329 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 389 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 290 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 A 875 GLN ** A1298 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 875 GLN ** B1125 GLN ** 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 = 0.4319 r_free = 0.4319 target = 0.170098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.132995 restraints weight = 54511.221| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.44 r_work: 0.3629 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33570 Z= 0.122 Angle : 0.549 11.428 45370 Z= 0.277 Chirality : 0.040 0.165 5052 Planarity : 0.004 0.048 5722 Dihedral : 3.956 26.535 4412 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.46 % Allowed : 13.91 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.13), residues: 4036 helix: 1.67 (0.11), residues: 2122 sheet: 0.57 (0.27), residues: 360 loop : -0.86 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.014 0.001 TYR B 713 PHE 0.017 0.001 PHE A 63 TRP 0.036 0.001 TRP B1116 HIS 0.003 0.001 HIS A1761 Details of bonding type rmsd covalent geometry : bond 0.00285 (33570) covalent geometry : angle 0.54948 (45370) hydrogen bonds : bond 0.03434 ( 1761) hydrogen bonds : angle 4.34714 ( 5145) *********************** 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 446 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 357 time to evaluate : 1.424 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: A 140 HIS cc_start: 0.8626 (t70) cc_final: 0.8384 (t70) REVERT: A 645 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: A 691 ASP cc_start: 0.6987 (m-30) cc_final: 0.6542 (m-30) REVERT: A 735 MET cc_start: 0.7333 (tpp) cc_final: 0.7088 (tpp) REVERT: A 905 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8372 (mt) REVERT: A 1040 PHE cc_start: 0.7542 (t80) cc_final: 0.7114 (t80) REVERT: A 1322 PHE cc_start: 0.6872 (m-80) cc_final: 0.6591 (m-80) REVERT: A 1646 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.4972 (m-80) REVERT: A 1679 ILE cc_start: 0.7695 (mm) cc_final: 0.7260 (mt) REVERT: A 1767 MET cc_start: 0.9289 (ptp) cc_final: 0.8789 (ptp) REVERT: A 1768 ASP cc_start: 0.9218 (m-30) cc_final: 0.8952 (m-30) REVERT: A 1779 MET cc_start: 0.5731 (pmm) cc_final: 0.4768 (ppp) REVERT: B 732 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6304 (m90) REVERT: B 735 MET cc_start: 0.7319 (tpp) cc_final: 0.7073 (tpp) REVERT: B 905 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8376 (mt) REVERT: B 1040 PHE cc_start: 0.7568 (t80) cc_final: 0.7139 (t80) REVERT: B 1093 PHE cc_start: 0.8557 (p90) cc_final: 0.8101 (p90) REVERT: B 1322 PHE cc_start: 0.6941 (m-80) cc_final: 0.6676 (m-80) REVERT: B 1562 MET cc_start: 0.7815 (ptp) cc_final: 0.7473 (ptp) REVERT: B 1590 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8471 (mp) REVERT: B 1646 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5006 (m-80) REVERT: B 1679 ILE cc_start: 0.7716 (mt) cc_final: 0.7262 (mm) REVERT: B 1779 MET cc_start: 0.5543 (pmm) cc_final: 0.4795 (ptt) REVERT: B 1792 MET cc_start: 0.5142 (tmm) cc_final: 0.4648 (tmm) outliers start: 89 outliers final: 54 residues processed: 416 average time/residue: 0.2316 time to fit residues: 157.7202 Evaluate side-chains 400 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 339 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 559 VAL 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 664 ILE Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 875 GLN 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 1118 LEU Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1242 THR 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 1753 LEU Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain B residue 40 ASP 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 629 LEU 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 732 HIS Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 875 GLN 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 1006 ILE Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 393 optimal weight: 0.9980 chunk 202 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** A1298 HIS ** 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** ** B1125 GLN ** 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 = 0.4316 r_free = 0.4316 target = 0.169125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.132262 restraints weight = 54028.643| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.76 r_work: 0.3611 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33570 Z= 0.124 Angle : 0.554 11.748 45370 Z= 0.278 Chirality : 0.040 0.228 5052 Planarity : 0.004 0.048 5722 Dihedral : 3.912 25.993 4412 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 2.18 % Allowed : 14.30 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.13), residues: 4036 helix: 1.72 (0.11), residues: 2124 sheet: 0.51 (0.27), residues: 360 loop : -0.82 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1867 TYR 0.020 0.001 TYR A 339 PHE 0.016 0.001 PHE A 585 TRP 0.031 0.001 TRP B1116 HIS 0.010 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00293 (33570) covalent geometry : angle 0.55404 (45370) hydrogen bonds : bond 0.03418 ( 1761) hydrogen bonds : angle 4.29570 ( 5145) *********************** 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 421 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 342 time to evaluate : 1.384 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: A 645 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: A 691 ASP cc_start: 0.6953 (m-30) cc_final: 0.6499 (m-30) REVERT: A 732 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6382 (m90) REVERT: A 735 MET cc_start: 0.7333 (tpp) cc_final: 0.7066 (tpp) REVERT: A 905 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 1040 PHE cc_start: 0.7510 (t80) cc_final: 0.7068 (t80) REVERT: A 1322 PHE cc_start: 0.6823 (m-80) cc_final: 0.6517 (m-80) REVERT: A 1447 MET cc_start: 0.8348 (mmt) cc_final: 0.8066 (mmt) REVERT: A 1605 LYS cc_start: 0.8040 (mppt) cc_final: 0.7658 (mtmm) REVERT: A 1646 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.4892 (m-80) REVERT: A 1753 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9119 (mt) REVERT: A 1768 ASP cc_start: 0.9226 (m-30) cc_final: 0.8930 (m-30) REVERT: A 1779 MET cc_start: 0.5756 (pmm) cc_final: 0.4763 (ppp) REVERT: B 88 LEU cc_start: 0.7921 (mm) cc_final: 0.7400 (tp) REVERT: B 732 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.5989 (m-70) REVERT: B 735 MET cc_start: 0.7293 (tpp) cc_final: 0.7042 (tpp) REVERT: B 905 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8372 (mt) REVERT: B 1040 PHE cc_start: 0.7507 (t80) cc_final: 0.7054 (t80) REVERT: B 1093 PHE cc_start: 0.8604 (p90) cc_final: 0.8146 (p90) REVERT: B 1447 MET cc_start: 0.8351 (mmt) cc_final: 0.8068 (mmt) REVERT: B 1562 MET cc_start: 0.7771 (ptp) cc_final: 0.7402 (ptp) REVERT: B 1590 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8423 (mp) REVERT: B 1605 LYS cc_start: 0.8032 (mppt) cc_final: 0.7658 (mtmm) REVERT: B 1646 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.4885 (m-80) REVERT: B 1679 ILE cc_start: 0.7711 (mt) cc_final: 0.7276 (mm) REVERT: B 1779 MET cc_start: 0.5563 (pmm) cc_final: 0.4550 (ppp) REVERT: B 1792 MET cc_start: 0.5178 (tmm) cc_final: 0.4671 (tmm) outliers start: 79 outliers final: 51 residues processed: 393 average time/residue: 0.2255 time to fit residues: 146.7732 Evaluate side-chains 394 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 559 VAL Chi-restraints excluded: chain A residue 622 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 664 ILE Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 732 HIS 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 1164 VAL Chi-restraints excluded: chain A residue 1242 THR 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 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 B residue 40 ASP Chi-restraints excluded: chain B residue 106 ILE 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 622 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 664 ILE Chi-restraints excluded: chain B residue 732 HIS 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 1006 ILE Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 297 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 875 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 HIS ** 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 B 875 GLN ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.168185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131110 restraints weight = 54016.392| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.79 r_work: 0.3594 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33570 Z= 0.155 Angle : 0.574 13.115 45370 Z= 0.289 Chirality : 0.041 0.210 5052 Planarity : 0.004 0.047 5722 Dihedral : 3.969 26.676 4412 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.41 % Rotamer: Outliers : 2.13 % Allowed : 14.58 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.13), residues: 4036 helix: 1.67 (0.11), residues: 2122 sheet: 0.52 (0.27), residues: 348 loop : -0.86 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1867 TYR 0.014 0.001 TYR B1705 PHE 0.017 0.001 PHE B 585 TRP 0.030 0.001 TRP B1116 HIS 0.013 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00377 (33570) covalent geometry : angle 0.57370 (45370) hydrogen bonds : bond 0.03609 ( 1761) hydrogen bonds : angle 4.35076 ( 5145) *********************** 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 420 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 343 time to evaluate : 1.414 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: A 645 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 691 ASP cc_start: 0.6955 (m-30) cc_final: 0.6511 (m-30) REVERT: A 732 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6607 (m-70) REVERT: A 735 MET cc_start: 0.7356 (tpp) cc_final: 0.7104 (tpp) REVERT: A 905 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 1040 PHE cc_start: 0.7521 (t80) cc_final: 0.7094 (t80) REVERT: A 1322 PHE cc_start: 0.6765 (m-80) cc_final: 0.6452 (m-80) REVERT: A 1447 MET cc_start: 0.8405 (mmt) cc_final: 0.8080 (mmt) REVERT: A 1605 LYS cc_start: 0.8064 (mppt) cc_final: 0.7705 (mtmm) REVERT: A 1646 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5007 (m-80) REVERT: A 1753 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9196 (mm) REVERT: A 1768 ASP cc_start: 0.9234 (m-30) cc_final: 0.8959 (m-30) REVERT: A 1779 MET cc_start: 0.5767 (pmm) cc_final: 0.4791 (ppp) REVERT: B 735 MET cc_start: 0.7320 (tpp) cc_final: 0.7058 (tpp) REVERT: B 905 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8371 (mt) REVERT: B 1040 PHE cc_start: 0.7505 (t80) cc_final: 0.7061 (t80) REVERT: B 1093 PHE cc_start: 0.8614 (p90) cc_final: 0.8138 (p90) REVERT: B 1447 MET cc_start: 0.8396 (mmt) cc_final: 0.8069 (mmt) REVERT: B 1562 MET cc_start: 0.7765 (ptp) cc_final: 0.7351 (ptp) REVERT: B 1605 LYS cc_start: 0.8063 (mppt) cc_final: 0.7703 (mtmm) REVERT: B 1646 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.4983 (m-80) REVERT: B 1737 LEU cc_start: 0.8104 (tp) cc_final: 0.7819 (tp) REVERT: B 1779 MET cc_start: 0.5631 (pmm) cc_final: 0.4618 (ppp) REVERT: B 1792 MET cc_start: 0.5252 (tmm) cc_final: 0.4769 (tmm) outliers start: 77 outliers final: 54 residues processed: 396 average time/residue: 0.2239 time to fit residues: 146.5525 Evaluate side-chains 398 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 337 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 559 VAL Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 622 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 732 HIS Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 875 GLN 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 1164 VAL Chi-restraints excluded: chain A residue 1242 THR 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 1549 ASP 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 B residue 40 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 106 ILE 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 563 ASP Chi-restraints excluded: chain B residue 622 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 875 GLN 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 1006 ILE Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR 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 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 2071 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 84 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 232 optimal weight: 0.0040 chunk 194 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 327 optimal weight: 0.6980 chunk 372 optimal weight: 30.0000 chunk 329 optimal weight: 0.1980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 875 GLN ** A1125 GLN ** 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 B 824 GLN B 875 GLN ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.170053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133157 restraints weight = 54271.067| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.37 r_work: 0.3651 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33570 Z= 0.109 Angle : 0.557 12.939 45370 Z= 0.279 Chirality : 0.040 0.208 5052 Planarity : 0.004 0.048 5722 Dihedral : 3.867 25.587 4412 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 1.77 % Allowed : 15.02 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.13), residues: 4036 helix: 1.78 (0.11), residues: 2124 sheet: 0.45 (0.27), residues: 342 loop : -0.84 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 873 TYR 0.021 0.001 TYR B 339 PHE 0.015 0.001 PHE A 63 TRP 0.028 0.001 TRP B1116 HIS 0.006 0.001 HIS A1761 Details of bonding type rmsd covalent geometry : bond 0.00248 (33570) covalent geometry : angle 0.55727 (45370) hydrogen bonds : bond 0.03291 ( 1761) hydrogen bonds : angle 4.23638 ( 5145) ********************** 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 427 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 363 time to evaluate : 1.367 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: A 23 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 645 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 735 MET cc_start: 0.7294 (tpp) cc_final: 0.7063 (tpp) REVERT: A 791 GLU cc_start: 0.7381 (tp30) cc_final: 0.6986 (tp30) REVERT: A 905 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8350 (mt) REVERT: A 1040 PHE cc_start: 0.7443 (t80) cc_final: 0.7046 (t80) REVERT: A 1322 PHE cc_start: 0.6801 (m-80) cc_final: 0.6488 (m-80) REVERT: A 1447 MET cc_start: 0.8420 (mmt) cc_final: 0.8172 (mmt) REVERT: A 1605 LYS cc_start: 0.8006 (mppt) cc_final: 0.7643 (mtmm) REVERT: A 1646 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.4860 (m-80) REVERT: A 1768 ASP cc_start: 0.9197 (m-30) cc_final: 0.8936 (m-30) REVERT: A 1779 MET cc_start: 0.5740 (pmm) cc_final: 0.4765 (ppp) REVERT: B 23 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 735 MET cc_start: 0.7267 (tpp) cc_final: 0.7049 (tpp) REVERT: B 905 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 1040 PHE cc_start: 0.7428 (t80) cc_final: 0.7019 (t80) REVERT: B 1093 PHE cc_start: 0.8567 (p90) cc_final: 0.8132 (p90) REVERT: B 1387 LEU cc_start: 0.8693 (tt) cc_final: 0.8420 (tp) REVERT: B 1447 MET cc_start: 0.8429 (mmt) cc_final: 0.8112 (mmt) REVERT: B 1562 MET cc_start: 0.7674 (ptp) cc_final: 0.7346 (ptp) REVERT: B 1590 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8421 (mp) REVERT: B 1605 LYS cc_start: 0.8012 (mppt) cc_final: 0.7664 (mtmm) REVERT: B 1646 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.4851 (m-80) REVERT: B 1737 LEU cc_start: 0.8119 (tp) cc_final: 0.7852 (tp) REVERT: B 1779 MET cc_start: 0.5520 (pmm) cc_final: 0.4940 (ppp) REVERT: B 1792 MET cc_start: 0.5216 (tmm) cc_final: 0.4754 (tmm) outliers start: 64 outliers final: 46 residues processed: 403 average time/residue: 0.2267 time to fit residues: 150.6829 Evaluate side-chains 404 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 352 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 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 559 VAL Chi-restraints excluded: chain A residue 622 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 664 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1604 HIS Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1742 LEU Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 106 ILE 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 622 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 905 LEU Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1419 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 218 optimal weight: 5.9990 chunk 168 optimal weight: 30.0000 chunk 369 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 185 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 A 732 HIS A 875 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 875 GLN ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.166296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.129717 restraints weight = 54301.947| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.59 r_work: 0.3572 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33570 Z= 0.215 Angle : 0.627 13.930 45370 Z= 0.318 Chirality : 0.043 0.220 5052 Planarity : 0.004 0.049 5722 Dihedral : 4.125 28.191 4412 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 1.96 % Allowed : 15.21 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.13), residues: 4036 helix: 1.50 (0.11), residues: 2140 sheet: 0.43 (0.28), residues: 332 loop : -0.94 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1702 TYR 0.014 0.002 TYR A1564 PHE 0.020 0.002 PHE A 585 TRP 0.032 0.002 TRP B1116 HIS 0.005 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00520 (33570) covalent geometry : angle 0.62733 (45370) hydrogen bonds : bond 0.03985 ( 1761) hydrogen bonds : angle 4.48667 ( 5145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9161.74 seconds wall clock time: 157 minutes 52.78 seconds (9472.78 seconds total)