Starting phenix.real_space_refine on Fri Jul 26 13:56:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgu_18391/07_2024/8qgu_18391.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgu_18391/07_2024/8qgu_18391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgu_18391/07_2024/8qgu_18391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgu_18391/07_2024/8qgu_18391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgu_18391/07_2024/8qgu_18391.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgu_18391/07_2024/8qgu_18391.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 21138 2.51 5 N 5532 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 772": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "A PHE 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1422": "OE1" <-> "OE2" Residue "A ASP 1446": "OD1" <-> "OD2" Residue "A PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1523": "OD1" <-> "OD2" Residue "A TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2086": "OE1" <-> "OE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 728": "OE1" <-> "OE2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B GLU 796": "OE1" <-> "OE2" Residue "B ASP 910": "OD1" <-> "OD2" Residue "B TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1016": "OD1" <-> "OD2" Residue "B PHE 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1422": "OE1" <-> "OE2" Residue "B ASP 1446": "OD1" <-> "OD2" Residue "B PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1523": "OD1" <-> "OD2" Residue "B TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2086": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32838 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "B" 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 Time building chain proxies: 17.87, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.31 Conformation dependent library (CDL) restraints added in 6.3 seconds 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7760 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 38 sheets defined 57.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 20 through 48 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.714A pdb=" N ILE A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 116 through 146 removed outlier: 5.115A pdb=" N ALA A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 176 through 197 removed outlier: 3.578A pdb=" N VAL A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.740A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 282 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.882A pdb=" N ARG A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.309A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.938A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 4.747A pdb=" N LYS A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 635 removed outlier: 3.867A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.636A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 675 removed outlier: 3.647A pdb=" N VAL A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 4.001A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 733 Processing helix chain 'A' and resid 734 through 760 Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.586A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.809A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.557A pdb=" N SER A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 824 " --> pdb=" O TYR A 821 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR A 825 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 826 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 827 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 930 through 948 removed outlier: 4.273A pdb=" N ALA A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 991 removed outlier: 4.312A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1013 removed outlier: 3.814A pdb=" N ASN A1003 " --> pdb=" O ASN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.690A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1114 through 1126 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 5.878A pdb=" N HIS A1130 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP A1131 " --> pdb=" O HIS A1128 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1127 through 1132' Processing helix chain 'A' and resid 1138 through 1153 removed outlier: 3.535A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 4.032A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER A1194 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP A1195 " --> pdb=" O GLY A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1297 Processing helix chain 'A' and resid 1302 through 1319 Processing helix chain 'A' and resid 1322 through 1326 Processing helix chain 'A' and resid 1349 through 1353 removed outlier: 3.636A pdb=" N MET A1352 " --> pdb=" O PHE A1349 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A1353 " --> pdb=" O ALA A1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1349 through 1353' Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 4.026A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 4.404A pdb=" N PHE A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.728A pdb=" N ASN A1439 " --> pdb=" O SER A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1455 Processing helix chain 'A' and resid 1463 through 1470 Processing helix chain 'A' and resid 1502 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1546 Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing helix chain 'A' and resid 1616 through 1642 Processing helix chain 'A' and resid 1645 through 1651 Processing helix chain 'A' and resid 1660 through 1671 Processing helix chain 'A' and resid 1675 through 1677 No H-bonds generated for 'chain 'A' and resid 1675 through 1677' Processing helix chain 'A' and resid 1678 through 1690 Processing helix chain 'A' and resid 1693 through 1704 removed outlier: 3.595A pdb=" N GLN A1697 " --> pdb=" O TYR A1693 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1778 removed outlier: 3.501A pdb=" N LEU A1763 " --> pdb=" O GLN A1759 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1823 Processing helix chain 'A' and resid 1867 through 1871 Processing helix chain 'A' and resid 1888 through 1894 Processing helix chain 'A' and resid 1896 through 1903 Processing helix chain 'A' and resid 1909 through 1918 Processing helix chain 'A' and resid 1923 through 1937 Processing helix chain 'A' and resid 2034 through 2041 Processing helix chain 'A' and resid 2054 through 2069 removed outlier: 3.685A pdb=" N ILE A2059 " --> pdb=" O PRO A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2092 removed outlier: 3.517A pdb=" N GLU A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 removed outlier: 3.766A pdb=" N VAL A2098 " --> pdb=" O TRP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2116 removed outlier: 3.614A pdb=" N ASN A2115 " --> pdb=" O ASN A2111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A2116 " --> pdb=" O MET A2112 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2142 Processing helix chain 'A' and resid 2146 through 2151 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 20 through 48 Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.715A pdb=" N ILE B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 116 through 146 removed outlier: 5.115A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 176 through 197 removed outlier: 3.578A pdb=" N VAL B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 239 through 252 removed outlier: 3.740A pdb=" N LEU B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.881A pdb=" N ARG B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 343 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 379 through 391 Processing helix chain 'B' and resid 409 through 429 Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 463 through 469 removed outlier: 4.309A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 490 removed outlier: 3.936A pdb=" N HIS B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.747A pdb=" N LYS B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 572 through 593 Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 616 through 635 removed outlier: 3.866A pdb=" N TYR B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Proline residue: B 631 - end of helix Processing helix chain 'B' and resid 639 through 649 removed outlier: 3.636A pdb=" N LEU B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 675 removed outlier: 3.647A pdb=" N VAL B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 726 removed outlier: 4.000A pdb=" N LEU B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 734 through 760 Processing helix chain 'B' and resid 760 through 767 removed outlier: 3.586A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 777 Processing helix chain 'B' and resid 786 through 802 removed outlier: 3.809A pdb=" N VAL B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 814 Processing helix chain 'B' and resid 820 through 828 removed outlier: 3.557A pdb=" N SER B 823 " --> pdb=" O PRO B 820 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 824 " --> pdb=" O TYR B 821 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N THR B 825 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG B 826 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 827 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 859 Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'B' and resid 898 through 917 Processing helix chain 'B' and resid 918 through 920 No H-bonds generated for 'chain 'B' and resid 918 through 920' Processing helix chain 'B' and resid 930 through 948 removed outlier: 4.273A pdb=" N ALA B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 948 " --> pdb=" O ARG B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 991 removed outlier: 4.312A pdb=" N ARG B 987 " --> pdb=" O ALA B 983 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 988 " --> pdb=" O LYS B 984 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET B 991 " --> pdb=" O ARG B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1013 removed outlier: 3.814A pdb=" N ASN B1003 " --> pdb=" O ASN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1029 Processing helix chain 'B' and resid 1034 through 1044 removed outlier: 3.690A pdb=" N PHE B1044 " --> pdb=" O PHE B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1084 Processing helix chain 'B' and resid 1114 through 1126 Processing helix chain 'B' and resid 1127 through 1132 removed outlier: 5.878A pdb=" N HIS B1130 " --> pdb=" O GLY B1127 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP B1131 " --> pdb=" O HIS B1128 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B1132 " --> pdb=" O LEU B1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1127 through 1132' Processing helix chain 'B' and resid 1138 through 1153 removed outlier: 3.536A pdb=" N GLY B1153 " --> pdb=" O ILE B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1168 through 1181 Processing helix chain 'B' and resid 1184 through 1195 removed outlier: 4.031A pdb=" N ILE B1188 " --> pdb=" O PRO B1184 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B1193 " --> pdb=" O LEU B1189 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B1194 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP B1195 " --> pdb=" O GLY B1191 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1219 Processing helix chain 'B' and resid 1221 through 1241 Processing helix chain 'B' and resid 1249 through 1253 Processing helix chain 'B' and resid 1272 through 1279 Processing helix chain 'B' and resid 1282 through 1297 Processing helix chain 'B' and resid 1302 through 1319 Processing helix chain 'B' and resid 1322 through 1326 Processing helix chain 'B' and resid 1349 through 1353 removed outlier: 3.636A pdb=" N MET B1352 " --> pdb=" O PHE B1349 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR B1353 " --> pdb=" O ALA B1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1349 through 1353' Processing helix chain 'B' and resid 1354 through 1365 Processing helix chain 'B' and resid 1366 through 1370 Processing helix chain 'B' and resid 1375 through 1388 removed outlier: 4.027A pdb=" N ILE B1381 " --> pdb=" O ASP B1377 " (cutoff:3.500A) Processing helix chain 'B' and resid 1389 through 1397 Processing helix chain 'B' and resid 1402 through 1412 removed outlier: 4.403A pdb=" N PHE B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B1407 " --> pdb=" O GLN B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1425 through 1439 removed outlier: 3.728A pdb=" N ASN B1439 " --> pdb=" O SER B1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1455 Processing helix chain 'B' and resid 1463 through 1470 Processing helix chain 'B' and resid 1502 through 1512 Processing helix chain 'B' and resid 1514 through 1525 Processing helix chain 'B' and resid 1527 through 1529 No H-bonds generated for 'chain 'B' and resid 1527 through 1529' Processing helix chain 'B' and resid 1530 through 1546 Processing helix chain 'B' and resid 1552 through 1564 Proline residue: B1561 - end of helix Processing helix chain 'B' and resid 1581 through 1592 Processing helix chain 'B' and resid 1616 through 1642 Processing helix chain 'B' and resid 1645 through 1651 Processing helix chain 'B' and resid 1660 through 1671 Processing helix chain 'B' and resid 1675 through 1677 No H-bonds generated for 'chain 'B' and resid 1675 through 1677' Processing helix chain 'B' and resid 1678 through 1690 Processing helix chain 'B' and resid 1693 through 1704 removed outlier: 3.595A pdb=" N GLN B1697 " --> pdb=" O TYR B1693 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B1704 " --> pdb=" O ALA B1700 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1778 removed outlier: 3.501A pdb=" N LEU B1763 " --> pdb=" O GLN B1759 " (cutoff:3.500A) Processing helix chain 'B' and resid 1820 through 1823 Processing helix chain 'B' and resid 1867 through 1871 Processing helix chain 'B' and resid 1888 through 1894 Processing helix chain 'B' and resid 1896 through 1903 Processing helix chain 'B' and resid 1909 through 1918 Processing helix chain 'B' and resid 1923 through 1937 Processing helix chain 'B' and resid 2034 through 2041 Processing helix chain 'B' and resid 2054 through 2069 removed outlier: 3.685A pdb=" N ILE B2059 " --> pdb=" O PRO B2055 " (cutoff:3.500A) Processing helix chain 'B' and resid 2080 through 2092 removed outlier: 3.517A pdb=" N GLU B2086 " --> pdb=" O TYR B2082 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2099 removed outlier: 3.767A pdb=" N VAL B2098 " --> pdb=" O TRP B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2102 through 2116 removed outlier: 3.614A pdb=" N ASN B2115 " --> pdb=" O ASN B2111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B2116 " --> pdb=" O MET B2112 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2142 Processing helix chain 'B' and resid 2146 through 2151 Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 102 removed outlier: 3.983A pdb=" N ASN A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 109 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 159 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 112 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.608A pdb=" N PHE A1090 " --> pdb=" O GLY A1105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.710A pdb=" N SER A 950 " --> pdb=" O MET A 962 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.657A pdb=" N PHE A 527 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 683 through 685 Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA9, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.158A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 895 through 897 removed outlier: 4.874A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1417 through 1419 removed outlier: 3.734A pdb=" N GLU A1422 " --> pdb=" O LEU A1419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1473 through 1476 removed outlier: 4.207A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1486 through 1490 removed outlier: 3.613A pdb=" N ARG A1570 " --> pdb=" O PHE A1490 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1658 through 1659 Processing sheet with id=AB6, first strand: chain 'A' and resid 1706 through 1710 removed outlier: 4.854A pdb=" N GLY A1707 " --> pdb=" O ASN A1734 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN A1734 " --> pdb=" O GLY A1707 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A1729 " --> pdb=" O ILE A1744 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A1738 " --> pdb=" O PHE A1735 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL A1817 " --> pdb=" O TYR A1751 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A1753 " --> pdb=" O VAL A1817 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1717 through 1719 Processing sheet with id=AB8, first strand: chain 'A' and resid 1783 through 1786 removed outlier: 3.552A pdb=" N VAL A1786 " --> pdb=" O CYS A1810 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A1811 " --> pdb=" O LYS A1796 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A1794 " --> pdb=" O TYR A1813 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A1804 " --> pdb=" O VAL A1793 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1833 through 1837 removed outlier: 3.632A pdb=" N MET A1833 " --> pdb=" O GLN A1846 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A1846 " --> pdb=" O MET A1833 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA A1845 " --> pdb=" O LEU A1855 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU A1855 " --> pdb=" O ALA A1845 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AC2, first strand: chain 'B' and resid 98 through 102 removed outlier: 3.982A pdb=" N ASN B 98 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 109 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 159 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 112 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 260 through 261 removed outlier: 3.609A pdb=" N PHE B1090 " --> pdb=" O GLY B1105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 260 through 261 removed outlier: 3.710A pdb=" N SER B 950 " --> pdb=" O MET B 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AC7, first strand: chain 'B' and resid 499 through 503 removed outlier: 3.657A pdb=" N PHE B 527 " --> pdb=" O MET B 560 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 Processing sheet with id=AD1, first strand: chain 'B' and resid 832 through 837 removed outlier: 5.158A pdb=" N SER B 844 " --> pdb=" O GLY B 835 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 895 through 897 removed outlier: 4.874A pdb=" N ILE B 881 " --> pdb=" O PHE B1018 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1417 through 1419 removed outlier: 3.734A pdb=" N GLU B1422 " --> pdb=" O LEU B1419 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1473 through 1476 removed outlier: 4.207A pdb=" N THR B1598 " --> pdb=" O ILE B1476 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1486 through 1490 removed outlier: 3.613A pdb=" N ARG B1570 " --> pdb=" O PHE B1490 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1658 through 1659 Processing sheet with id=AD7, first strand: chain 'B' and resid 1706 through 1710 removed outlier: 4.855A pdb=" N GLY B1707 " --> pdb=" O ASN B1734 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B1734 " --> pdb=" O GLY B1707 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B1729 " --> pdb=" O ILE B1744 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B1738 " --> pdb=" O PHE B1735 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL B1817 " --> pdb=" O TYR B1751 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B1753 " --> pdb=" O VAL B1817 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1717 through 1719 Processing sheet with id=AD9, first strand: chain 'B' and resid 1783 through 1786 removed outlier: 3.551A pdb=" N VAL B1786 " --> pdb=" O CYS B1810 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B1811 " --> pdb=" O LYS B1796 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU B1794 " --> pdb=" O TYR B1813 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B1804 " --> pdb=" O VAL B1793 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1833 through 1837 removed outlier: 3.632A pdb=" N MET B1833 " --> pdb=" O GLN B1846 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B1846 " --> pdb=" O MET B1833 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA B1845 " --> pdb=" O LEU B1855 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B1855 " --> pdb=" O ALA B1845 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1878 through 1881 1797 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.80 Time building geometry restraints manager: 14.88 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: 98.69 - 105.76: 565 105.76 - 112.83: 18061 112.83 - 119.90: 11032 119.90 - 126.97: 15338 126.97 - 134.04: 374 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 2.440 nonbonded pdb=" O SER A1133 " pdb=" OG SER A1141 " model vdw 2.105 2.440 nonbonded pdb=" ND2 ASN A 351 " pdb=" O LYS A 360 " model vdw 2.138 2.520 nonbonded pdb=" ND2 ASN B 351 " pdb=" O LYS B 360 " model vdw 2.138 2.520 nonbonded pdb=" OH TYR B 341 " pdb=" OH TYR B 353 " model vdw 2.188 2.440 ... (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 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.230 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 94.380 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.380 ------------------------------------------------------------------------------- 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= 0.162 Angle : 0.503 9.832 45370 Z= 0.265 Chirality : 0.039 0.211 5052 Planarity : 0.004 0.104 5722 Dihedral : 13.812 89.992 12470 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.13), residues: 4036 helix: 1.92 (0.11), residues: 2106 sheet: 0.63 (0.28), residues: 368 loop : -0.74 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1423 HIS 0.004 0.000 HIS B 742 PHE 0.022 0.001 PHE B 371 TYR 0.022 0.001 TYR B 32 ARG 0.010 0.000 ARG B 289 *********************** 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 fitting. rotamer outliers: 0 poor density : 754 time to evaluate : 3.581 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: 0.4904 time to fit residues: 577.0358 Evaluate side-chains 456 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 318 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 368 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 406 ASN A 457 ASN A 827 ASN A1287 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1365 HIS A1575 GLN A1881 HIS A2070 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 363 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN B1287 ASN ** B1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1365 HIS B1575 GLN B1881 HIS B2070 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33570 Z= 0.227 Angle : 0.571 12.528 45370 Z= 0.290 Chirality : 0.041 0.230 5052 Planarity : 0.004 0.055 5722 Dihedral : 3.715 21.929 4412 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.57 % Allowed : 9.08 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.13), residues: 4036 helix: 1.92 (0.11), residues: 2112 sheet: 0.86 (0.28), residues: 378 loop : -0.79 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1423 HIS 0.006 0.001 HIS B 82 PHE 0.024 0.002 PHE B 91 TYR 0.018 0.001 TYR B 32 ARG 0.015 0.001 ARG B1703 *********************** 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 509 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 3.532 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: A 88 LEU cc_start: 0.8288 (mt) cc_final: 0.8054 (tp) REVERT: A 140 HIS cc_start: 0.9275 (t70) cc_final: 0.8957 (t70) REVERT: A 184 MET cc_start: 0.7064 (ptm) cc_final: 0.6451 (ptm) REVERT: A 650 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7384 (mtm110) REVERT: A 884 LYS cc_start: 0.6871 (mtmm) cc_final: 0.6484 (mttm) REVERT: A 1355 SER cc_start: 0.7904 (t) cc_final: 0.7551 (p) REVERT: A 1536 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7852 (mmtm) REVERT: A 1679 ILE cc_start: 0.7591 (mm) cc_final: 0.7277 (mt) REVERT: A 1763 LEU cc_start: 0.9326 (mt) cc_final: 0.8946 (mp) REVERT: A 1768 ASP cc_start: 0.9416 (m-30) cc_final: 0.9100 (t70) REVERT: A 1779 MET cc_start: 0.6017 (pmm) cc_final: 0.5458 (ptt) REVERT: A 2111 ASN cc_start: 0.7802 (t0) cc_final: 0.7302 (t0) REVERT: A 2135 MET cc_start: 0.7988 (mmt) cc_final: 0.7583 (mmt) REVERT: B 63 PHE cc_start: 0.9214 (m-80) cc_final: 0.9014 (m-80) REVERT: B 88 LEU cc_start: 0.8387 (mt) cc_final: 0.8105 (tp) REVERT: B 150 GLN cc_start: 0.9259 (mm-40) cc_final: 0.9055 (tp40) REVERT: B 184 MET cc_start: 0.7272 (ptm) cc_final: 0.7045 (ptm) REVERT: B 884 LYS cc_start: 0.6896 (mtmm) cc_final: 0.6489 (mttm) REVERT: B 1138 MET cc_start: 0.6434 (ptt) cc_final: 0.6139 (ptt) REVERT: B 1355 SER cc_start: 0.7872 (t) cc_final: 0.7508 (p) REVERT: B 1536 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7854 (mmtm) REVERT: B 1679 ILE cc_start: 0.7687 (mm) cc_final: 0.7417 (mt) REVERT: B 1763 LEU cc_start: 0.9366 (mt) cc_final: 0.9003 (mp) REVERT: B 1768 ASP cc_start: 0.9437 (m-30) cc_final: 0.9119 (t70) REVERT: B 1779 MET cc_start: 0.5863 (pmm) cc_final: 0.5277 (ptt) REVERT: B 2111 ASN cc_start: 0.7828 (t0) cc_final: 0.7226 (t0) REVERT: B 2135 MET cc_start: 0.7968 (mmt) cc_final: 0.7563 (mmt) outliers start: 57 outliers final: 35 residues processed: 488 average time/residue: 0.4634 time to fit residues: 365.1404 Evaluate side-chains 434 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 398 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 247 SER 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 314 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 909 GLU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1293 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 2 ASP Chi-restraints excluded: chain B residue 247 SER 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 634 THR Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 909 GLU Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1066 SER 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 204 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 306 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 101 optimal weight: 0.0270 chunk 369 optimal weight: 6.9990 chunk 399 optimal weight: 0.0170 chunk 328 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN A 363 GLN A 413 GLN A 824 GLN A1298 HIS ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 323 ASN B 363 GLN B 406 ASN B 413 GLN B1298 HIS B2070 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33570 Z= 0.154 Angle : 0.514 9.585 45370 Z= 0.259 Chirality : 0.039 0.207 5052 Planarity : 0.004 0.050 5722 Dihedral : 3.626 21.862 4412 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.63 % Allowed : 10.93 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.13), residues: 4036 helix: 2.00 (0.11), residues: 2116 sheet: 0.78 (0.28), residues: 374 loop : -0.74 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1139 HIS 0.007 0.001 HIS A1298 PHE 0.020 0.001 PHE A1093 TYR 0.018 0.001 TYR A 339 ARG 0.017 0.000 ARG A1703 *********************** 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 487 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 428 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.8172 (m-80) cc_final: 0.7960 (m-80) REVERT: A 62 LEU cc_start: 0.9468 (mm) cc_final: 0.9162 (mt) REVERT: A 88 LEU cc_start: 0.8214 (mt) cc_final: 0.7984 (tp) REVERT: A 140 HIS cc_start: 0.9278 (t70) cc_final: 0.8968 (t70) REVERT: A 184 MET cc_start: 0.7047 (ptm) cc_final: 0.6376 (ptm) REVERT: A 884 LYS cc_start: 0.6830 (mtmm) cc_final: 0.6436 (mttm) REVERT: A 1355 SER cc_start: 0.7879 (t) cc_final: 0.7526 (p) REVERT: A 1387 LEU cc_start: 0.8303 (tt) cc_final: 0.8100 (tp) REVERT: A 1654 TRP cc_start: 0.7630 (t-100) cc_final: 0.7192 (t-100) REVERT: A 1679 ILE cc_start: 0.7544 (mm) cc_final: 0.7127 (mt) REVERT: A 1768 ASP cc_start: 0.9223 (m-30) cc_final: 0.8986 (m-30) REVERT: A 1779 MET cc_start: 0.6103 (pmm) cc_final: 0.5455 (ptt) REVERT: A 1834 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6738 (mm) REVERT: A 2111 ASN cc_start: 0.7772 (t0) cc_final: 0.7221 (t0) REVERT: A 2135 MET cc_start: 0.7992 (mmt) cc_final: 0.7625 (mmt) REVERT: B 27 TYR cc_start: 0.8149 (m-80) cc_final: 0.7934 (m-80) REVERT: B 63 PHE cc_start: 0.9204 (m-10) cc_final: 0.9002 (m-80) REVERT: B 184 MET cc_start: 0.7211 (ptm) cc_final: 0.6930 (ptm) REVERT: B 884 LYS cc_start: 0.6856 (mtmm) cc_final: 0.6436 (mttm) REVERT: B 1355 SER cc_start: 0.7863 (t) cc_final: 0.7487 (p) REVERT: B 1654 TRP cc_start: 0.7625 (t-100) cc_final: 0.7218 (t-100) REVERT: B 1679 ILE cc_start: 0.7583 (mm) cc_final: 0.7263 (mt) REVERT: B 1753 LEU cc_start: 0.9623 (tp) cc_final: 0.9381 (mm) REVERT: B 1768 ASP cc_start: 0.9246 (m-30) cc_final: 0.9013 (m-30) REVERT: B 1779 MET cc_start: 0.5963 (pmm) cc_final: 0.5310 (ptt) REVERT: B 2135 MET cc_start: 0.7966 (mmt) cc_final: 0.7589 (mmt) outliers start: 59 outliers final: 30 residues processed: 466 average time/residue: 0.4486 time to fit residues: 339.9363 Evaluate side-chains 426 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 395 time to evaluate : 3.444 ------------------------------------------------------------------------------- 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 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 818 GLU Chi-restraints excluded: chain A residue 909 GLU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 247 SER 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 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 364 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 370 optimal weight: 30.0000 chunk 392 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 351 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 137 GLN A1125 GLN ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33570 Z= 0.260 Angle : 0.545 9.883 45370 Z= 0.276 Chirality : 0.041 0.272 5052 Planarity : 0.004 0.052 5722 Dihedral : 3.776 24.247 4412 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.13 % Allowed : 12.01 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4036 helix: 1.82 (0.11), residues: 2138 sheet: 0.70 (0.28), residues: 364 loop : -0.79 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 473 HIS 0.013 0.001 HIS B 140 PHE 0.017 0.002 PHE A 951 TYR 0.018 0.001 TYR A 662 ARG 0.005 0.000 ARG A1238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 405 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9476 (mm) cc_final: 0.9174 (mt) REVERT: A 88 LEU cc_start: 0.8193 (mt) cc_final: 0.7979 (tp) REVERT: A 140 HIS cc_start: 0.9282 (t70) cc_final: 0.8953 (t70) REVERT: A 184 MET cc_start: 0.7016 (ptm) cc_final: 0.6542 (ptm) REVERT: A 926 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6642 (m-10) REVERT: A 1646 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4676 (m-80) REVERT: A 1679 ILE cc_start: 0.7568 (mm) cc_final: 0.7165 (mt) REVERT: A 1768 ASP cc_start: 0.9237 (m-30) cc_final: 0.9012 (m-30) REVERT: A 1779 MET cc_start: 0.6100 (pmm) cc_final: 0.5537 (ppp) REVERT: A 1834 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6742 (mm) REVERT: A 2135 MET cc_start: 0.8040 (mmt) cc_final: 0.7630 (mmt) REVERT: B 88 LEU cc_start: 0.8067 (mp) cc_final: 0.7353 (tp) REVERT: B 650 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7489 (ttm110) REVERT: B 1093 PHE cc_start: 0.8268 (p90) cc_final: 0.7974 (p90) REVERT: B 1469 ASN cc_start: 0.6702 (m110) cc_final: 0.6483 (m-40) REVERT: B 1518 MET cc_start: 0.7617 (tpp) cc_final: 0.7343 (tpp) REVERT: B 1646 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.4675 (m-80) REVERT: B 1679 ILE cc_start: 0.7709 (mm) cc_final: 0.7328 (mt) REVERT: B 1767 MET cc_start: 0.9553 (mtm) cc_final: 0.9323 (ptp) REVERT: B 1779 MET cc_start: 0.5965 (pmm) cc_final: 0.5244 (ptt) REVERT: B 2135 MET cc_start: 0.8019 (mmt) cc_final: 0.7658 (mmt) outliers start: 77 outliers final: 49 residues processed: 445 average time/residue: 0.4549 time to fit residues: 329.5627 Evaluate side-chains 435 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 381 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER 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 413 GLN Chi-restraints excluded: chain A residue 510 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 747 GLU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 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 1646 TYR Chi-restraints excluded: chain A residue 1834 ILE 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 62 LEU Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 650 ARG 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 1294 LEU 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 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 326 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 271 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 0.5980 chunk 352 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 838 GLN A 875 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 GLN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 140 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN B 875 GLN ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1497 GLN ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33570 Z= 0.227 Angle : 0.532 10.173 45370 Z= 0.267 Chirality : 0.040 0.221 5052 Planarity : 0.004 0.050 5722 Dihedral : 3.773 24.540 4412 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.40 % Allowed : 12.48 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4036 helix: 1.80 (0.11), residues: 2138 sheet: 0.73 (0.28), residues: 360 loop : -0.78 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1056 HIS 0.006 0.001 HIS B 140 PHE 0.016 0.002 PHE B 951 TYR 0.021 0.001 TYR A 339 ARG 0.007 0.000 ARG B1702 *********************** 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 483 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 396 time to evaluate : 3.673 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 88 LEU cc_start: 0.8247 (mt) cc_final: 0.8030 (tp) REVERT: A 140 HIS cc_start: 0.9283 (t70) cc_final: 0.8962 (t70) REVERT: A 184 MET cc_start: 0.7020 (ptm) cc_final: 0.6801 (ptm) REVERT: A 691 ASP cc_start: 0.7155 (m-30) cc_final: 0.6760 (m-30) REVERT: A 1557 LYS cc_start: 0.8153 (tptt) cc_final: 0.7953 (tttt) REVERT: A 1646 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.4637 (m-80) REVERT: A 1679 ILE cc_start: 0.7690 (mm) cc_final: 0.7256 (mt) REVERT: A 1767 MET cc_start: 0.9633 (ptp) cc_final: 0.9015 (ptp) REVERT: A 1768 ASP cc_start: 0.9303 (m-30) cc_final: 0.9063 (m-30) REVERT: A 1779 MET cc_start: 0.6070 (pmm) cc_final: 0.5502 (ppp) REVERT: A 1834 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6784 (mm) REVERT: B 1093 PHE cc_start: 0.8303 (p90) cc_final: 0.8017 (p90) REVERT: B 1469 ASN cc_start: 0.6725 (m110) cc_final: 0.6520 (m-40) REVERT: B 1518 MET cc_start: 0.7593 (tpp) cc_final: 0.7351 (tpp) REVERT: B 1557 LYS cc_start: 0.8255 (tptt) cc_final: 0.7993 (tttt) REVERT: B 1646 TYR cc_start: 0.5773 (OUTLIER) cc_final: 0.4619 (m-80) REVERT: B 1679 ILE cc_start: 0.7762 (mm) cc_final: 0.7318 (mt) REVERT: B 1753 LEU cc_start: 0.9616 (tp) cc_final: 0.9356 (mm) REVERT: B 1779 MET cc_start: 0.5918 (pmm) cc_final: 0.5184 (ptt) outliers start: 87 outliers final: 51 residues processed: 452 average time/residue: 0.4426 time to fit residues: 327.3900 Evaluate side-chains 419 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 365 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 875 GLN 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 1294 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1834 ILE 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 247 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR 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 613 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 747 GLU Chi-restraints excluded: chain B residue 875 GLN Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1646 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 132 optimal weight: 0.8980 chunk 353 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 230 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 392 optimal weight: 4.9990 chunk 326 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1469 ASN ** B 82 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** B2070 ASN ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33570 Z= 0.272 Angle : 0.553 11.160 45370 Z= 0.278 Chirality : 0.041 0.206 5052 Planarity : 0.004 0.080 5722 Dihedral : 3.843 25.685 4412 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.54 % Allowed : 13.22 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4036 helix: 1.75 (0.11), residues: 2130 sheet: 0.66 (0.27), residues: 374 loop : -0.85 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1056 HIS 0.008 0.001 HIS B 140 PHE 0.017 0.002 PHE B 585 TYR 0.013 0.001 TYR A 662 ARG 0.011 0.000 ARG A 316 *********************** 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 465 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 373 time to evaluate : 3.556 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 140 HIS cc_start: 0.9297 (t70) cc_final: 0.8970 (t70) REVERT: A 184 MET cc_start: 0.6972 (ptm) cc_final: 0.6722 (ptm) REVERT: A 735 MET cc_start: 0.7261 (tpp) cc_final: 0.7019 (tpp) REVERT: A 905 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8173 (mt) REVERT: A 1646 TYR cc_start: 0.5929 (OUTLIER) cc_final: 0.4630 (m-80) REVERT: A 1679 ILE cc_start: 0.7708 (mm) cc_final: 0.7274 (mt) REVERT: A 1768 ASP cc_start: 0.9313 (m-30) cc_final: 0.9069 (m-30) REVERT: A 1779 MET cc_start: 0.6041 (pmm) cc_final: 0.5465 (ppp) REVERT: A 1834 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6837 (mm) REVERT: A 2111 ASN cc_start: 0.7856 (t0) cc_final: 0.7458 (t0) REVERT: B 905 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8139 (mt) REVERT: B 1093 PHE cc_start: 0.8337 (p90) cc_final: 0.8016 (p90) REVERT: B 1469 ASN cc_start: 0.6796 (m110) cc_final: 0.6592 (m110) REVERT: B 1518 MET cc_start: 0.7624 (tpp) cc_final: 0.7413 (tpp) REVERT: B 1557 LYS cc_start: 0.8231 (tptt) cc_final: 0.8013 (tttt) REVERT: B 1646 TYR cc_start: 0.5870 (OUTLIER) cc_final: 0.4611 (m-80) REVERT: B 1679 ILE cc_start: 0.7801 (mm) cc_final: 0.7337 (mt) REVERT: B 1767 MET cc_start: 0.9536 (ptp) cc_final: 0.8856 (ptp) REVERT: B 1779 MET cc_start: 0.5885 (pmm) cc_final: 0.5067 (ptt) outliers start: 92 outliers final: 65 residues processed: 432 average time/residue: 0.4421 time to fit residues: 312.4602 Evaluate side-chains 429 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 359 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 247 SER 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 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 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 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1753 LEU Chi-restraints excluded: chain A residue 1834 ILE 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 158 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 875 GLN Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1242 THR Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 378 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 286 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 chunk 330 optimal weight: 0.5980 chunk 219 optimal weight: 0.8980 chunk 391 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS B 177 ASN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33570 Z= 0.173 Angle : 0.524 11.654 45370 Z= 0.262 Chirality : 0.039 0.184 5052 Planarity : 0.004 0.049 5722 Dihedral : 3.744 24.942 4412 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.91 % Allowed : 14.25 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.13), residues: 4036 helix: 1.89 (0.11), residues: 2130 sheet: 0.62 (0.27), residues: 374 loop : -0.80 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A1116 HIS 0.005 0.001 HIS B1761 PHE 0.014 0.001 PHE B 585 TYR 0.015 0.001 TYR B 662 ARG 0.012 0.000 ARG A 316 *********************** 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 454 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 385 time to evaluate : 3.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8138 (mp) cc_final: 0.7612 (tp) REVERT: A 140 HIS cc_start: 0.9293 (t70) cc_final: 0.8966 (t70) REVERT: A 184 MET cc_start: 0.6935 (ptm) cc_final: 0.6561 (ptm) REVERT: A 1646 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.4620 (m-80) REVERT: A 1679 ILE cc_start: 0.7710 (mm) cc_final: 0.7266 (mt) REVERT: A 1768 ASP cc_start: 0.9326 (m-30) cc_final: 0.9007 (t0) REVERT: A 1779 MET cc_start: 0.6014 (pmm) cc_final: 0.5448 (ppp) REVERT: B 735 MET cc_start: 0.7245 (tpp) cc_final: 0.6980 (tpp) REVERT: B 1040 PHE cc_start: 0.7388 (t80) cc_final: 0.7132 (t80) REVERT: B 1093 PHE cc_start: 0.8312 (p90) cc_final: 0.7987 (p90) REVERT: B 1469 ASN cc_start: 0.6783 (m110) cc_final: 0.6576 (m110) REVERT: B 1518 MET cc_start: 0.7544 (tpp) cc_final: 0.7329 (tpp) REVERT: B 1646 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.4610 (m-80) REVERT: B 1679 ILE cc_start: 0.7864 (mm) cc_final: 0.7419 (mt) REVERT: B 1753 LEU cc_start: 0.9619 (tp) cc_final: 0.9339 (mm) REVERT: B 1779 MET cc_start: 0.5875 (pmm) cc_final: 0.5051 (ptt) outliers start: 69 outliers final: 55 residues processed: 424 average time/residue: 0.4491 time to fit residues: 310.5764 Evaluate side-chains 419 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 362 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 247 SER 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 563 ASP Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP 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 247 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 972 ASP 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 1271 MET Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 242 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 413 GLN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS A 875 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 GLN ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33570 Z= 0.243 Angle : 0.563 12.761 45370 Z= 0.282 Chirality : 0.040 0.195 5052 Planarity : 0.004 0.049 5722 Dihedral : 3.825 25.862 4412 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.37 % Allowed : 14.05 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 4036 helix: 1.80 (0.11), residues: 2130 sheet: 0.75 (0.27), residues: 362 loop : -0.88 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1116 HIS 0.004 0.001 HIS B1761 PHE 0.016 0.001 PHE B 585 TYR 0.021 0.001 TYR A 339 ARG 0.013 0.000 ARG A 316 *********************** 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 452 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 366 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8192 (mp) cc_final: 0.7658 (tp) REVERT: A 184 MET cc_start: 0.6979 (ptm) cc_final: 0.6504 (ptm) REVERT: A 691 ASP cc_start: 0.7059 (m-30) cc_final: 0.6668 (m-30) REVERT: A 735 MET cc_start: 0.7238 (tpp) cc_final: 0.7004 (tpp) REVERT: A 905 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 1040 PHE cc_start: 0.7431 (t80) cc_final: 0.7108 (t80) REVERT: A 1646 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.4633 (m-80) REVERT: A 1654 TRP cc_start: 0.7711 (t-100) cc_final: 0.7255 (t-100) REVERT: A 1679 ILE cc_start: 0.7714 (mm) cc_final: 0.7290 (mt) REVERT: A 1753 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9337 (mt) REVERT: A 1768 ASP cc_start: 0.9249 (m-30) cc_final: 0.8962 (m-30) REVERT: A 1779 MET cc_start: 0.6048 (pmm) cc_final: 0.5448 (ppp) REVERT: B 905 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8155 (mt) REVERT: B 1040 PHE cc_start: 0.7423 (t80) cc_final: 0.7190 (t80) REVERT: B 1093 PHE cc_start: 0.8335 (p90) cc_final: 0.8015 (p90) REVERT: B 1646 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.4630 (m-80) REVERT: B 1654 TRP cc_start: 0.7748 (t-100) cc_final: 0.7371 (t-100) REVERT: B 1679 ILE cc_start: 0.7811 (mm) cc_final: 0.7315 (mt) REVERT: B 1779 MET cc_start: 0.5896 (pmm) cc_final: 0.5061 (ptt) outliers start: 86 outliers final: 66 residues processed: 417 average time/residue: 0.4535 time to fit residues: 309.7150 Evaluate side-chains 426 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 355 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 247 SER 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 629 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 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 1015 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP 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 2 ASP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR 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 613 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 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 915 ILE Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 972 ASP 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 1271 MET Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 0.9980 chunk 374 optimal weight: 0.3980 chunk 342 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 219 optimal weight: 0.0270 chunk 158 optimal weight: 0.0030 chunk 286 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 329 optimal weight: 0.9980 chunk 344 optimal weight: 0.9980 chunk 363 optimal weight: 4.9990 overall best weight: 0.4248 ------------------------------------------------------------------------------- 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** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 GLN B1039 GLN ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1469 ASN ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 33570 Z= 0.151 Angle : 0.540 12.886 45370 Z= 0.269 Chirality : 0.039 0.190 5052 Planarity : 0.004 0.057 5722 Dihedral : 3.720 24.561 4412 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.79 % Allowed : 14.66 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4036 helix: 1.99 (0.11), residues: 2116 sheet: 0.70 (0.26), residues: 362 loop : -0.84 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP A1116 HIS 0.006 0.001 HIS B1761 PHE 0.013 0.001 PHE B 585 TYR 0.014 0.001 TYR B 662 ARG 0.014 0.000 ARG A 316 *********************** 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 444 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 379 time to evaluate : 3.606 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 88 LEU cc_start: 0.8199 (mp) cc_final: 0.7670 (tp) REVERT: A 184 MET cc_start: 0.6861 (ptm) cc_final: 0.6433 (ptm) REVERT: A 1040 PHE cc_start: 0.7341 (t80) cc_final: 0.7032 (t80) REVERT: A 1093 PHE cc_start: 0.8265 (p90) cc_final: 0.7980 (p90) REVERT: A 1646 TYR cc_start: 0.5826 (OUTLIER) cc_final: 0.4529 (m-80) REVERT: A 1654 TRP cc_start: 0.7664 (t-100) cc_final: 0.7176 (t-100) REVERT: A 1679 ILE cc_start: 0.7765 (mm) cc_final: 0.7302 (mt) REVERT: A 1753 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9355 (mm) REVERT: A 1768 ASP cc_start: 0.9249 (m-30) cc_final: 0.8983 (m-30) REVERT: A 1779 MET cc_start: 0.6028 (pmm) cc_final: 0.5421 (ppp) REVERT: B 735 MET cc_start: 0.7168 (tpp) cc_final: 0.6927 (tpp) REVERT: B 1093 PHE cc_start: 0.8287 (p90) cc_final: 0.7987 (p90) REVERT: B 1469 ASN cc_start: 0.6989 (m-40) cc_final: 0.6750 (m110) REVERT: B 1646 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.4526 (m-80) REVERT: B 1654 TRP cc_start: 0.7672 (t-100) cc_final: 0.7319 (t-100) REVERT: B 1679 ILE cc_start: 0.7882 (mm) cc_final: 0.7413 (mt) REVERT: B 1779 MET cc_start: 0.5853 (pmm) cc_final: 0.5211 (ppp) outliers start: 65 outliers final: 49 residues processed: 415 average time/residue: 0.4348 time to fit residues: 294.3795 Evaluate side-chains 415 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 363 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 247 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 662 TYR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 972 ASP 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 1271 MET Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1540 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1646 TYR Chi-restraints excluded: chain A residue 1753 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 926 TYR Chi-restraints excluded: chain B residue 972 ASP 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 1271 MET Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 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 239 optimal weight: 0.8980 chunk 385 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 chunk 372 optimal weight: 30.0000 chunk 322 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 836 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 ** B1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33570 Z= 0.293 Angle : 0.601 13.833 45370 Z= 0.301 Chirality : 0.042 0.207 5052 Planarity : 0.004 0.062 5722 Dihedral : 3.934 27.387 4412 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.88 % Allowed : 14.58 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 4036 helix: 1.75 (0.11), residues: 2116 sheet: 0.74 (0.27), residues: 352 loop : -0.88 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A1116 HIS 0.005 0.001 HIS B 742 PHE 0.020 0.002 PHE A1458 TYR 0.020 0.002 TYR B 339 ARG 0.014 0.000 ARG A 316 ********************** 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 419 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 351 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8216 (mp) cc_final: 0.7716 (tp) REVERT: A 691 ASP cc_start: 0.7050 (m-30) cc_final: 0.6650 (m-30) REVERT: A 875 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: A 905 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8184 (mt) REVERT: A 1040 PHE cc_start: 0.7444 (t80) cc_final: 0.7078 (t80) REVERT: A 1326 ARG cc_start: 0.7126 (mtp85) cc_final: 0.6688 (mtp85) REVERT: A 1646 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: A 1654 TRP cc_start: 0.7762 (t-100) cc_final: 0.7296 (t-100) REVERT: A 1679 ILE cc_start: 0.7809 (mm) cc_final: 0.7290 (mt) REVERT: A 1753 LEU cc_start: 0.9617 (tp) cc_final: 0.9407 (mm) REVERT: A 1779 MET cc_start: 0.6071 (pmm) cc_final: 0.5482 (ppp) REVERT: B 732 HIS cc_start: 0.6909 (OUTLIER) cc_final: 0.6506 (m90) REVERT: B 735 MET cc_start: 0.7267 (tpp) cc_final: 0.7021 (tpp) REVERT: B 905 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8139 (mt) REVERT: B 1093 PHE cc_start: 0.8383 (p90) cc_final: 0.8057 (p90) REVERT: B 1646 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.4621 (m-80) REVERT: B 1654 TRP cc_start: 0.7785 (t-100) cc_final: 0.7443 (t-100) REVERT: B 1753 LEU cc_start: 0.9586 (tp) cc_final: 0.9350 (mm) REVERT: B 1779 MET cc_start: 0.5893 (pmm) cc_final: 0.5246 (ppp) outliers start: 68 outliers final: 53 residues processed: 396 average time/residue: 0.4373 time to fit residues: 283.6819 Evaluate side-chains 404 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 345 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 247 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 613 ILE Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 972 ASP 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 1271 MET Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1456 CYS Chi-restraints excluded: chain A residue 1549 ASP 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 140 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 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 972 ASP 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 1271 MET Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1456 CYS Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1549 ASP Chi-restraints excluded: chain B residue 1646 TYR Chi-restraints excluded: chain B residue 1944 LEU Chi-restraints excluded: chain B residue 2128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 255 optimal weight: 0.9980 chunk 343 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 331 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 59 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN ** 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** ** B2115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.170134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.132650 restraints weight = 54070.109| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.61 r_work: 0.3634 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33570 Z= 0.169 Angle : 0.561 13.111 45370 Z= 0.279 Chirality : 0.040 0.228 5052 Planarity : 0.004 0.062 5722 Dihedral : 3.810 25.720 4412 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.66 % Allowed : 14.88 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.13), residues: 4036 helix: 1.84 (0.11), residues: 2124 sheet: 0.68 (0.27), residues: 352 loop : -0.83 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1116 HIS 0.011 0.001 HIS B 732 PHE 0.016 0.001 PHE B1667 TYR 0.013 0.001 TYR B1705 ARG 0.015 0.000 ARG B 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8228.21 seconds wall clock time: 146 minutes 56.60 seconds (8816.60 seconds total)