Starting phenix.real_space_refine on Sat May 24 08:56:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8b_42020/05_2025/8u8b_42020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8b_42020/05_2025/8u8b_42020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8b_42020/05_2025/8u8b_42020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8b_42020/05_2025/8u8b_42020.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8b_42020/05_2025/8u8b_42020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8b_42020/05_2025/8u8b_42020.cif" } resolution = 3.7 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= 0.002 sd= 0.061 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 144 5.16 5 C 15924 2.51 5 N 4204 2.21 5 O 4416 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.95s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24694 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1712, 12278 Classifications: {'peptide': 1712} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'PCIS': 2, 'PTRANS': 71, 'TRANS': 1638} Chain breaks: 14 Unresolved non-hydrogen bonds: 1345 Unresolved non-hydrogen angles: 1638 Unresolved non-hydrogen dihedrals: 1101 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 36, 'GLU%COO:plan': 1, 'ASP:plan': 46, 'TYR:plan': 5, 'ASN:plan1': 18, 'HIS:plan': 13, 'PHE:plan': 4, 'GLU:plan': 68, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 896 Chain: "B" Number of atoms: 12278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1712, 12278 Classifications: {'peptide': 1712} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'PCIS': 2, 'PTRANS': 71, 'TRANS': 1638} Chain breaks: 14 Unresolved non-hydrogen bonds: 1345 Unresolved non-hydrogen angles: 1638 Unresolved non-hydrogen dihedrals: 1101 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 36, 'GLU%COO:plan': 1, 'ASP:plan': 46, 'TYR:plan': 5, 'ASN:plan1': 18, 'HIS:plan': 13, 'PHE:plan': 4, 'GLU:plan': 68, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 896 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'919': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'919': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.41, per 1000 atoms: 0.54 Number of scatterers: 24694 At special positions: 0 Unit cell: (175.095, 128.403, 147.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 4 15.00 F 2 9.00 O 4416 8.00 N 4204 7.00 C 15924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 3.2 seconds 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6536 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 34 sheets defined 36.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 585 through 596 Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.666A pdb=" N GLN A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.802A pdb=" N ALA A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 removed outlier: 3.507A pdb=" N THR A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 4.209A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.666A pdb=" N VAL A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.747A pdb=" N VAL A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS A 727 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.501A pdb=" N LYS A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 783 through 795 removed outlier: 4.055A pdb=" N ARG A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 853 Processing helix chain 'A' and resid 1006 through 1011 removed outlier: 3.612A pdb=" N GLU A1011 " --> pdb=" O SER A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1240 through 1245 removed outlier: 3.621A pdb=" N TRP A1244 " --> pdb=" O ALA A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 4.052A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 Processing helix chain 'A' and resid 1314 through 1328 removed outlier: 3.931A pdb=" N LYS A1327 " --> pdb=" O GLN A1323 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A1328 " --> pdb=" O GLN A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1355 Processing helix chain 'A' and resid 1398 through 1402 removed outlier: 3.658A pdb=" N PHE A1401 " --> pdb=" O ARG A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 4.005A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1463 through 1465 No H-bonds generated for 'chain 'A' and resid 1463 through 1465' Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1538 Processing helix chain 'A' and resid 1550 through 1560 Processing helix chain 'A' and resid 1565 through 1567 No H-bonds generated for 'chain 'A' and resid 1565 through 1567' Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 4.166A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1613 Processing helix chain 'A' and resid 1645 through 1656 Processing helix chain 'A' and resid 1703 through 1712 Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1793 through 1796 Processing helix chain 'A' and resid 1829 through 1835 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1914 through 1926 removed outlier: 3.561A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.522A pdb=" N LEU A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1966 Processing helix chain 'A' and resid 1967 through 1988 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2040 through 2046 Processing helix chain 'A' and resid 2053 through 2069 removed outlier: 3.996A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A2058 " --> pdb=" O ALA A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 removed outlier: 3.580A pdb=" N TYR A2099 " --> pdb=" O PRO A2095 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.838A pdb=" N GLU A2108 " --> pdb=" O TRP A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2118 through 2122 Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 4.019A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2282 Processing helix chain 'A' and resid 2308 through 2312 removed outlier: 3.613A pdb=" N ARG A2312 " --> pdb=" O SER A2309 " (cutoff:3.500A) Processing helix chain 'A' and resid 2339 through 2344 removed outlier: 4.261A pdb=" N GLN A2342 " --> pdb=" O ARG A2339 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A2343 " --> pdb=" O THR A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2396 removed outlier: 3.759A pdb=" N VAL A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2527 Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 585 through 596 Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.693A pdb=" N GLN B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 607 Processing helix chain 'B' and resid 624 through 639 removed outlier: 3.784A pdb=" N ALA B 628 " --> pdb=" O GLY B 624 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.506A pdb=" N THR B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 670 removed outlier: 4.218A pdb=" N LYS B 664 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.667A pdb=" N VAL B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 Processing helix chain 'B' and resid 706 through 719 Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.732A pdb=" N VAL B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU B 726 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS B 727 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 754 through 764 Processing helix chain 'B' and resid 767 through 781 Processing helix chain 'B' and resid 783 through 795 removed outlier: 4.049A pdb=" N ARG B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.728A pdb=" N LEU B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 853 Processing helix chain 'B' and resid 1006 through 1011 removed outlier: 3.620A pdb=" N GLU B1011 " --> pdb=" O SER B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1034 Processing helix chain 'B' and resid 1051 through 1057 Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1240 through 1245 removed outlier: 3.629A pdb=" N TRP B1244 " --> pdb=" O ALA B1241 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1267 removed outlier: 4.055A pdb=" N GLY B1265 " --> pdb=" O PRO B1262 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1291 Processing helix chain 'B' and resid 1314 through 1328 removed outlier: 3.949A pdb=" N LYS B1327 " --> pdb=" O GLN B1323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B1328 " --> pdb=" O GLN B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1347 through 1355 Processing helix chain 'B' and resid 1398 through 1402 removed outlier: 3.628A pdb=" N PHE B1401 " --> pdb=" O ARG B1398 " (cutoff:3.500A) Processing helix chain 'B' and resid 1404 through 1409 removed outlier: 4.020A pdb=" N MET B1409 " --> pdb=" O PRO B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1442 Processing helix chain 'B' and resid 1463 through 1465 No H-bonds generated for 'chain 'B' and resid 1463 through 1465' Processing helix chain 'B' and resid 1466 through 1473 Processing helix chain 'B' and resid 1494 through 1510 Processing helix chain 'B' and resid 1517 through 1520 Processing helix chain 'B' and resid 1525 through 1538 Processing helix chain 'B' and resid 1550 through 1560 Processing helix chain 'B' and resid 1565 through 1567 No H-bonds generated for 'chain 'B' and resid 1565 through 1567' Processing helix chain 'B' and resid 1568 through 1579 Processing helix chain 'B' and resid 1599 through 1608 removed outlier: 4.145A pdb=" N LEU B1603 " --> pdb=" O GLU B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1613 Processing helix chain 'B' and resid 1645 through 1656 Processing helix chain 'B' and resid 1703 through 1712 Processing helix chain 'B' and resid 1770 through 1792 Processing helix chain 'B' and resid 1793 through 1796 Processing helix chain 'B' and resid 1829 through 1835 Processing helix chain 'B' and resid 1853 through 1855 No H-bonds generated for 'chain 'B' and resid 1853 through 1855' Processing helix chain 'B' and resid 1914 through 1926 removed outlier: 3.601A pdb=" N HIS B1926 " --> pdb=" O VAL B1922 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1962 removed outlier: 3.516A pdb=" N LEU B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1963 through 1966 Processing helix chain 'B' and resid 1967 through 1988 Processing helix chain 'B' and resid 1996 through 1998 No H-bonds generated for 'chain 'B' and resid 1996 through 1998' Processing helix chain 'B' and resid 2040 through 2046 Processing helix chain 'B' and resid 2053 through 2069 removed outlier: 4.009A pdb=" N TYR B2057 " --> pdb=" O GLN B2053 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B2058 " --> pdb=" O ALA B2054 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2099 removed outlier: 3.593A pdb=" N TYR B2099 " --> pdb=" O PRO B2095 " (cutoff:3.500A) Processing helix chain 'B' and resid 2104 through 2115 removed outlier: 3.912A pdb=" N GLU B2108 " --> pdb=" O TRP B2104 " (cutoff:3.500A) Processing helix chain 'B' and resid 2118 through 2122 Processing helix chain 'B' and resid 2124 through 2133 Processing helix chain 'B' and resid 2134 through 2139 removed outlier: 4.090A pdb=" N VAL B2138 " --> pdb=" O SER B2134 " (cutoff:3.500A) Processing helix chain 'B' and resid 2278 through 2282 Processing helix chain 'B' and resid 2308 through 2312 removed outlier: 3.612A pdb=" N ARG B2312 " --> pdb=" O SER B2309 " (cutoff:3.500A) Processing helix chain 'B' and resid 2339 through 2344 removed outlier: 4.279A pdb=" N GLN B2342 " --> pdb=" O ARG B2339 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B2343 " --> pdb=" O THR B2340 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2351 Processing helix chain 'B' and resid 2389 through 2396 removed outlier: 3.835A pdb=" N VAL B2396 " --> pdb=" O PHE B2392 " (cutoff:3.500A) Processing helix chain 'B' and resid 2499 through 2527 Processing sheet with id=AA1, first strand: chain 'A' and resid 796 through 797 removed outlier: 6.689A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1015 through 1017 removed outlier: 6.738A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A1088 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 6.947A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A1225 " --> pdb=" O HIS A1251 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU A1250 " --> pdb=" O ASP A1274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1329 through 1331 Processing sheet with id=AA5, first strand: chain 'A' and resid 1376 through 1378 removed outlier: 3.574A pdb=" N MET A1335 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE A1448 " --> pdb=" O ALA A1413 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A1447 " --> pdb=" O ILE A1482 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A1484 " --> pdb=" O VAL A1447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1548 through 1549 removed outlier: 3.700A pdb=" N ILE A1548 " --> pdb=" O TYR A1596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1679 through 1681 removed outlier: 3.698A pdb=" N VAL A1679 " --> pdb=" O TYR B1733 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B1731 " --> pdb=" O GLU A1681 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1747 " --> pdb=" O PRO B1768 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE B1692 " --> pdb=" O LEU B1813 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B1813 " --> pdb=" O ILE B1692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1825 through 1828 removed outlier: 3.645A pdb=" N LEU A1813 " --> pdb=" O ILE A1692 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A1731 " --> pdb=" O GLU B1681 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B1679 " --> pdb=" O TYR A1733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB1, first strand: chain 'A' and resid 1893 through 1898 removed outlier: 6.512A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB3, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.843A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A2469 " --> pdb=" O THR A2460 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR A2460 " --> pdb=" O VAL A2469 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A2471 " --> pdb=" O MET A2458 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET A2458 " --> pdb=" O LEU A2471 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A2473 " --> pdb=" O ARG A2456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2166 through 2167 removed outlier: 3.690A pdb=" N GLY A2188 " --> pdb=" O ASP A2183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 4.916A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A2218 " --> pdb=" O CYS A2201 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A2236 " --> pdb=" O VAL A2226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2245 through 2251 removed outlier: 4.498A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A2289 " --> pdb=" O ILE A2274 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2304 through 2305 removed outlier: 6.479A pdb=" N ILE A2323 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A2335 " --> pdb=" O ILE A2323 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER A2325 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2354 through 2358 removed outlier: 5.023A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A2373 " --> pdb=" O LEU A2386 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A2386 " --> pdb=" O VAL A2373 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A2375 " --> pdb=" O CYS A2384 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 6.821A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A2419 " --> pdb=" O ALA A2424 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA A2424 " --> pdb=" O LEU A2419 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A2434 " --> pdb=" O VAL A2447 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A2447 " --> pdb=" O ILE A2434 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A2436 " --> pdb=" O ILE A2445 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A2443 " --> pdb=" O ASP A2438 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 796 through 797 removed outlier: 6.685A pdb=" N ILE B 803 " --> pdb=" O ASP B 988 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1015 through 1017 removed outlier: 6.701A pdb=" N LEU B1016 " --> pdb=" O ASP B1041 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU B1063 " --> pdb=" O ASN B1089 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE B1088 " --> pdb=" O ILE B1113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1177 through 1179 removed outlier: 6.981A pdb=" N LEU B1178 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B1225 " --> pdb=" O HIS B1251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B1250 " --> pdb=" O ASP B1274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1329 through 1331 Processing sheet with id=AC5, first strand: chain 'B' and resid 1376 through 1378 removed outlier: 3.555A pdb=" N MET B1335 " --> pdb=" O VAL B1389 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N ILE B1448 " --> pdb=" O ALA B1413 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B1415 " --> pdb=" O ILE B1448 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL B1450 " --> pdb=" O TYR B1415 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA B1417 " --> pdb=" O VAL B1450 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B1447 " --> pdb=" O ILE B1482 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B1484 " --> pdb=" O VAL B1447 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1548 through 1549 removed outlier: 3.687A pdb=" N ILE B1548 " --> pdb=" O TYR B1596 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AC8, first strand: chain 'B' and resid 1896 through 1898 removed outlier: 6.510A pdb=" N GLU B1948 " --> pdb=" O LEU B1935 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU B1935 " --> pdb=" O GLU B1948 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 2000 through 2002 Processing sheet with id=AD1, first strand: chain 'B' and resid 2140 through 2145 removed outlier: 6.818A pdb=" N LEU B2140 " --> pdb=" O ASP B2497 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP B2497 " --> pdb=" O LEU B2140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B2142 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B2469 " --> pdb=" O THR B2460 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR B2460 " --> pdb=" O VAL B2469 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B2471 " --> pdb=" O MET B2458 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET B2458 " --> pdb=" O LEU B2471 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B2473 " --> pdb=" O ARG B2456 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 2166 through 2167 removed outlier: 3.686A pdb=" N GLY B2188 " --> pdb=" O ASP B2183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 2199 through 2207 removed outlier: 4.964A pdb=" N CYS B2201 " --> pdb=" O GLY B2218 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B2218 " --> pdb=" O CYS B2201 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B2236 " --> pdb=" O VAL B2226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 2245 through 2251 removed outlier: 4.514A pdb=" N LYS B2271 " --> pdb=" O THR B2267 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B2289 " --> pdb=" O ILE B2274 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2304 through 2305 removed outlier: 6.446A pdb=" N ILE B2323 " --> pdb=" O LEU B2335 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B2335 " --> pdb=" O ILE B2323 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B2325 " --> pdb=" O GLN B2333 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 2354 through 2358 removed outlier: 5.017A pdb=" N LYS B2367 " --> pdb=" O VAL B2372 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B2372 " --> pdb=" O LYS B2367 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B2373 " --> pdb=" O LEU B2386 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B2386 " --> pdb=" O VAL B2373 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B2375 " --> pdb=" O CYS B2384 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 2414 through 2419 removed outlier: 6.804A pdb=" N GLY B2428 " --> pdb=" O LYS B2415 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B2417 " --> pdb=" O TRP B2426 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TRP B2426 " --> pdb=" O LEU B2417 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B2419 " --> pdb=" O ALA B2424 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA B2424 " --> pdb=" O LEU B2419 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE B2434 " --> pdb=" O VAL B2447 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B2447 " --> pdb=" O ILE B2434 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B2436 " --> pdb=" O ILE B2445 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B2443 " --> pdb=" O ASP B2438 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2649 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: 12.37 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3926 1.31 - 1.44: 6318 1.44 - 1.56: 14707 1.56 - 1.69: 7 1.69 - 1.81: 206 Bond restraints: 25164 Sorted by residual: bond pdb=" C70 919 A2602 " pdb=" N74 919 A2602 " ideal model delta sigma weight residual 1.332 1.450 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C70 919 B2602 " pdb=" N74 919 B2602 " ideal model delta sigma weight residual 1.332 1.449 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C58 919 A2602 " pdb=" N60 919 A2602 " ideal model delta sigma weight residual 1.367 1.468 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C58 919 B2602 " pdb=" N60 919 B2602 " ideal model delta sigma weight residual 1.367 1.466 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C58 919 B2602 " pdb=" N56 919 B2602 " ideal model delta sigma weight residual 1.372 1.470 -0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 25159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 33373 1.91 - 3.82: 819 3.82 - 5.73: 149 5.73 - 7.64: 50 7.64 - 9.55: 13 Bond angle restraints: 34404 Sorted by residual: angle pdb=" C GLY B1886 " pdb=" N ASP B1887 " pdb=" CA ASP B1887 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" N LYS A1184 " pdb=" CA LYS A1184 " pdb=" C LYS A1184 " ideal model delta sigma weight residual 111.39 117.57 -6.18 1.38e+00 5.25e-01 2.01e+01 angle pdb=" N LYS B1184 " pdb=" CA LYS B1184 " pdb=" C LYS B1184 " ideal model delta sigma weight residual 111.39 117.55 -6.16 1.38e+00 5.25e-01 1.99e+01 angle pdb=" N GLY A1891 " pdb=" CA GLY A1891 " pdb=" C GLY A1891 " ideal model delta sigma weight residual 113.18 104.12 9.06 2.37e+00 1.78e-01 1.46e+01 angle pdb=" CA MET A2458 " pdb=" CB MET A2458 " pdb=" CG MET A2458 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.43e+00 ... (remaining 34399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13666 17.79 - 35.57: 1098 35.57 - 53.36: 206 53.36 - 71.15: 32 71.15 - 88.93: 6 Dihedral angle restraints: 15008 sinusoidal: 5002 harmonic: 10006 Sorted by residual: dihedral pdb=" CA TRP B2104 " pdb=" C TRP B2104 " pdb=" N PRO B2105 " pdb=" CA PRO B2105 " ideal model delta harmonic sigma weight residual -180.00 -149.63 -30.37 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA TRP A2104 " pdb=" C TRP A2104 " pdb=" N PRO A2105 " pdb=" CA PRO A2105 " ideal model delta harmonic sigma weight residual -180.00 -149.69 -30.31 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA HIS B1926 " pdb=" C HIS B1926 " pdb=" N LEU B1927 " pdb=" CA LEU B1927 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 15005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3822 0.078 - 0.156: 441 0.156 - 0.233: 11 0.233 - 0.311: 6 0.311 - 0.389: 2 Chirality restraints: 4282 Sorted by residual: chirality pdb=" CB ILE B1868 " pdb=" CA ILE B1868 " pdb=" CG1 ILE B1868 " pdb=" CG2 ILE B1868 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE A1868 " pdb=" CA ILE A1868 " pdb=" CG1 ILE A1868 " pdb=" CG2 ILE A1868 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB THR A2298 " pdb=" CA THR A2298 " pdb=" OG1 THR A2298 " pdb=" CG2 THR A2298 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4279 not shown) Planarity restraints: 4292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2104 " 0.028 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP A2104 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A2104 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A2104 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2104 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A2104 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2104 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2104 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A2104 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B2104 " -0.027 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP B2104 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B2104 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B2104 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B2104 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B2104 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B2104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B2104 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B2104 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B2104 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1434 " -0.008 2.00e-02 2.50e+03 1.21e-02 3.65e+00 pdb=" CG TRP B1434 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP B1434 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B1434 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1434 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1434 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1434 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1434 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1434 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B1434 " -0.008 2.00e-02 2.50e+03 ... (remaining 4289 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4162 2.77 - 3.30: 23817 3.30 - 3.84: 39124 3.84 - 4.37: 44745 4.37 - 4.90: 76942 Nonbonded interactions: 188790 Sorted by model distance: nonbonded pdb=" OG SER A2134 " pdb=" OE1 GLU A2136 " model vdw 2.238 3.040 nonbonded pdb=" OG SER B2134 " pdb=" OE1 GLU B2136 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR B1368 " pdb=" O1B GDP B2601 " model vdw 2.276 3.040 nonbonded pdb=" O ARG B1161 " pdb=" ND2 ASN B1163 " model vdw 2.283 3.120 nonbonded pdb=" O ARG A1161 " pdb=" ND2 ASN A1163 " model vdw 2.290 3.120 ... (remaining 188785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 55.640 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 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 : 0.004 0.118 25164 Z= 0.188 Angle : 0.773 9.550 34404 Z= 0.387 Chirality : 0.049 0.389 4282 Planarity : 0.005 0.046 4292 Dihedral : 13.633 88.935 8472 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.62 % Allowed : 12.73 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -2.19 (0.14), residues: 3364 helix: -0.52 (0.16), residues: 1042 sheet: -2.14 (0.21), residues: 598 loop : -1.74 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A2104 HIS 0.005 0.001 HIS A2510 PHE 0.025 0.002 PHE B1185 TYR 0.017 0.001 TYR A1649 ARG 0.003 0.000 ARG B1693 Details of bonding type rmsd hydrogen bonds : bond 0.20293 ( 972) hydrogen bonds : angle 6.67959 ( 2649) covalent geometry : bond 0.00386 (25164) covalent geometry : angle 0.77276 (34404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 300 time to evaluate : 2.591 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: A 1947 MET cc_start: 0.6192 (mmm) cc_final: 0.5925 (mmm) REVERT: A 2241 MET cc_start: 0.5387 (mpp) cc_final: 0.4134 (ptp) REVERT: B 1947 MET cc_start: 0.6733 (mmm) cc_final: 0.6388 (mmm) REVERT: B 2241 MET cc_start: 0.0382 (mpp) cc_final: -0.0306 (mmp) REVERT: B 2470 MET cc_start: 0.6755 (mmm) cc_final: 0.6535 (mmm) outliers start: 15 outliers final: 3 residues processed: 307 average time/residue: 0.3445 time to fit residues: 168.8112 Evaluate side-chains 159 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1892 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 268 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS A1043 HIS ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS A2353 ASN ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1333 ASN ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.114392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.078537 restraints weight = 82098.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.080015 restraints weight = 52402.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.080253 restraints weight = 34421.845| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25164 Z= 0.202 Angle : 0.686 9.762 34404 Z= 0.341 Chirality : 0.046 0.215 4282 Planarity : 0.005 0.044 4292 Dihedral : 5.723 59.576 3604 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 2.12 % Allowed : 16.56 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.41 (0.15), residues: 3364 helix: 0.33 (0.16), residues: 1062 sheet: -1.85 (0.21), residues: 634 loop : -1.35 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A2104 HIS 0.011 0.002 HIS A1043 PHE 0.018 0.002 PHE A1284 TYR 0.016 0.002 TYR A1695 ARG 0.006 0.001 ARG B1483 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 972) hydrogen bonds : angle 5.00545 ( 2649) covalent geometry : bond 0.00459 (25164) covalent geometry : angle 0.68636 (34404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 2.855 Fit side-chains revert: symmetry clash REVERT: A 676 PHE cc_start: 0.8086 (m-80) cc_final: 0.6447 (m-10) REVERT: A 712 MET cc_start: 0.9100 (mmt) cc_final: 0.8499 (tpp) REVERT: A 724 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8011 (ttt) REVERT: A 1045 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6941 (t0) REVERT: A 1175 MET cc_start: 0.8505 (tpp) cc_final: 0.8201 (mmm) REVERT: A 1244 TRP cc_start: 0.8671 (m-10) cc_final: 0.8415 (m-10) REVERT: A 2417 LEU cc_start: 0.7253 (tp) cc_final: 0.6732 (tp) REVERT: B 712 MET cc_start: 0.9158 (mmt) cc_final: 0.8244 (tpp) REVERT: B 713 LEU cc_start: 0.9251 (tp) cc_final: 0.8965 (mm) REVERT: B 842 MET cc_start: 0.9451 (mpp) cc_final: 0.9221 (mpp) REVERT: B 1159 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 1947 MET cc_start: 0.6834 (mmm) cc_final: 0.6423 (mmm) REVERT: B 2241 MET cc_start: 0.3487 (mpp) cc_final: 0.1679 (mmp) REVERT: B 2292 ASN cc_start: 0.8205 (m-40) cc_final: 0.7810 (p0) REVERT: B 2470 MET cc_start: 0.7012 (mmm) cc_final: 0.6735 (mmm) outliers start: 51 outliers final: 26 residues processed: 198 average time/residue: 0.3286 time to fit residues: 108.5578 Evaluate side-chains 158 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2396 VAL Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2439 LEU Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1333 ASN Chi-restraints excluded: chain B residue 1340 VAL Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 1860 ILE Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2396 VAL Chi-restraints excluded: chain B residue 2459 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 159 optimal weight: 20.0000 chunk 222 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 127 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS B 678 GLN ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1986 HIS B1999 ASN B2251 ASN B2333 GLN ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.109062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.075952 restraints weight = 82376.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.076938 restraints weight = 56562.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.077048 restraints weight = 38909.499| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25164 Z= 0.241 Angle : 0.691 9.072 34404 Z= 0.349 Chirality : 0.046 0.186 4282 Planarity : 0.005 0.045 4292 Dihedral : 5.836 59.518 3602 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 2.91 % Allowed : 18.51 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.26 (0.15), residues: 3364 helix: 0.40 (0.16), residues: 1090 sheet: -1.67 (0.21), residues: 632 loop : -1.29 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B2104 HIS 0.050 0.002 HIS A1043 PHE 0.021 0.002 PHE A1436 TYR 0.030 0.002 TYR B 846 ARG 0.007 0.001 ARG A1483 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 972) hydrogen bonds : angle 4.91022 ( 2649) covalent geometry : bond 0.00553 (25164) covalent geometry : angle 0.69141 (34404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 125 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 676 PHE cc_start: 0.8104 (m-80) cc_final: 0.7437 (m-10) REVERT: A 712 MET cc_start: 0.9130 (mmt) cc_final: 0.8592 (tpp) REVERT: A 1057 MET cc_start: 0.7435 (mmt) cc_final: 0.7032 (mmt) REVERT: A 1162 MET cc_start: 0.9349 (mpp) cc_final: 0.9131 (mmm) REVERT: A 1175 MET cc_start: 0.8525 (tpp) cc_final: 0.8109 (mmm) REVERT: A 1244 TRP cc_start: 0.8822 (m-10) cc_final: 0.8515 (m-10) REVERT: A 2240 LYS cc_start: 0.8159 (tptt) cc_final: 0.7860 (tptt) REVERT: A 2241 MET cc_start: 0.5621 (mpp) cc_final: 0.4705 (ptp) REVERT: A 2315 MET cc_start: 0.3701 (tpt) cc_final: 0.3493 (tpt) REVERT: A 2470 MET cc_start: 0.7409 (mmm) cc_final: 0.6694 (mtt) REVERT: B 676 PHE cc_start: 0.8180 (m-80) cc_final: 0.7338 (m-10) REVERT: B 712 MET cc_start: 0.9198 (mmt) cc_final: 0.8419 (tpp) REVERT: B 842 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.9042 (mmm) REVERT: B 1065 VAL cc_start: 0.6949 (OUTLIER) cc_final: 0.6725 (m) REVERT: B 1088 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8111 (t80) REVERT: B 1607 MET cc_start: 0.7417 (tpp) cc_final: 0.6993 (mmp) REVERT: B 1947 MET cc_start: 0.6914 (mmm) cc_final: 0.6584 (mmm) REVERT: B 2241 MET cc_start: 0.3751 (mpp) cc_final: 0.2357 (mmp) REVERT: B 2292 ASN cc_start: 0.8256 (m-40) cc_final: 0.7905 (p0) REVERT: B 2301 MET cc_start: 0.5372 (mmm) cc_final: 0.5057 (mmm) REVERT: B 2437 LEU cc_start: 0.8671 (pp) cc_final: 0.8436 (mt) REVERT: B 2470 MET cc_start: 0.7495 (mmm) cc_final: 0.7000 (mmm) outliers start: 70 outliers final: 38 residues processed: 182 average time/residue: 0.2827 time to fit residues: 89.3918 Evaluate side-chains 163 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1889 SER Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1388 LEU Chi-restraints excluded: chain B residue 1488 VAL Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1613 VAL Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1738 ILE Chi-restraints excluded: chain B residue 1860 ILE Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1999 ASN Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 199 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 306 optimal weight: 4.9990 chunk 104 optimal weight: 0.0000 chunk 119 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1043 HIS ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1999 ASN ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.110443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.077615 restraints weight = 82394.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.079007 restraints weight = 54691.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.079113 restraints weight = 38284.341| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25164 Z= 0.115 Angle : 0.567 10.494 34404 Z= 0.283 Chirality : 0.042 0.168 4282 Planarity : 0.004 0.036 4292 Dihedral : 5.484 59.017 3602 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 1.91 % Allowed : 19.72 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3364 helix: 0.81 (0.17), residues: 1080 sheet: -1.54 (0.22), residues: 626 loop : -1.14 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B2104 HIS 0.004 0.001 HIS B 572 PHE 0.012 0.001 PHE A1436 TYR 0.025 0.001 TYR B1485 ARG 0.002 0.000 ARG A1386 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 972) hydrogen bonds : angle 4.53223 ( 2649) covalent geometry : bond 0.00261 (25164) covalent geometry : angle 0.56655 (34404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 676 PHE cc_start: 0.8080 (m-80) cc_final: 0.7372 (m-10) REVERT: A 712 MET cc_start: 0.9108 (mmt) cc_final: 0.8555 (tpp) REVERT: A 1057 MET cc_start: 0.7096 (mmt) cc_final: 0.6692 (mmt) REVERT: A 1088 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 1175 MET cc_start: 0.8636 (tpp) cc_final: 0.8401 (mmm) REVERT: A 1244 TRP cc_start: 0.8825 (m-10) cc_final: 0.8517 (m-10) REVERT: A 2240 LYS cc_start: 0.8173 (tptt) cc_final: 0.7846 (tptt) REVERT: A 2241 MET cc_start: 0.5428 (mpp) cc_final: 0.4691 (ptp) REVERT: A 2425 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7040 (mt) REVERT: B 724 MET cc_start: 0.8786 (ttm) cc_final: 0.8572 (ttm) REVERT: B 1088 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8188 (t80) REVERT: B 1175 MET cc_start: 0.7990 (tpp) cc_final: 0.7726 (tpp) REVERT: B 1203 MET cc_start: 0.8895 (mmm) cc_final: 0.8098 (mmm) REVERT: B 1607 MET cc_start: 0.7120 (tpp) cc_final: 0.6668 (mmp) REVERT: B 1947 MET cc_start: 0.6538 (mmm) cc_final: 0.6246 (mmm) REVERT: B 2241 MET cc_start: 0.3494 (mpp) cc_final: 0.2235 (mmp) REVERT: B 2292 ASN cc_start: 0.8264 (m-40) cc_final: 0.7887 (p0) REVERT: B 2301 MET cc_start: 0.5247 (mmm) cc_final: 0.4910 (mmm) REVERT: B 2437 LEU cc_start: 0.8668 (pp) cc_final: 0.8410 (mm) REVERT: B 2459 MET cc_start: 0.5148 (pmm) cc_final: 0.4557 (pmm) REVERT: B 2470 MET cc_start: 0.7303 (mmm) cc_final: 0.6905 (mmm) outliers start: 46 outliers final: 27 residues processed: 166 average time/residue: 0.2981 time to fit residues: 85.9845 Evaluate side-chains 149 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2396 VAL Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1738 ILE Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1999 ASN Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 92 optimal weight: 1.9990 chunk 266 optimal weight: 0.5980 chunk 96 optimal weight: 0.0270 chunk 321 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.109851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.078209 restraints weight = 82230.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.078216 restraints weight = 55844.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.078098 restraints weight = 41913.479| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25164 Z= 0.137 Angle : 0.567 8.933 34404 Z= 0.282 Chirality : 0.042 0.160 4282 Planarity : 0.004 0.038 4292 Dihedral : 5.389 58.866 3602 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 2.66 % Allowed : 19.84 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3364 helix: 1.09 (0.17), residues: 1052 sheet: -1.46 (0.21), residues: 640 loop : -1.09 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2104 HIS 0.007 0.001 HIS A1043 PHE 0.012 0.001 PHE A1436 TYR 0.022 0.001 TYR B1485 ARG 0.003 0.000 ARG B1483 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 972) hydrogen bonds : angle 4.45562 ( 2649) covalent geometry : bond 0.00315 (25164) covalent geometry : angle 0.56735 (34404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 LEU cc_start: 0.7612 (mm) cc_final: 0.7194 (pp) REVERT: A 676 PHE cc_start: 0.8024 (m-80) cc_final: 0.7324 (m-10) REVERT: A 712 MET cc_start: 0.9060 (mmt) cc_final: 0.8523 (tpp) REVERT: A 1057 MET cc_start: 0.7171 (mmt) cc_final: 0.6968 (mmt) REVERT: A 1088 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7976 (t80) REVERT: A 1175 MET cc_start: 0.8643 (tpp) cc_final: 0.8411 (mmm) REVERT: A 1244 TRP cc_start: 0.8862 (m-10) cc_final: 0.8557 (m-10) REVERT: A 1335 MET cc_start: 0.7804 (ttp) cc_final: 0.7590 (ttp) REVERT: A 2240 LYS cc_start: 0.8336 (tptt) cc_final: 0.8053 (tptt) REVERT: A 2241 MET cc_start: 0.5412 (mpp) cc_final: 0.5035 (ptp) REVERT: A 2425 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6946 (mt) REVERT: B 712 MET cc_start: 0.9201 (mmt) cc_final: 0.8425 (tpp) REVERT: B 724 MET cc_start: 0.8749 (ttm) cc_final: 0.8433 (ttm) REVERT: B 1013 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.6000 (tp) REVERT: B 1088 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8218 (t80) REVERT: B 1175 MET cc_start: 0.8138 (tpp) cc_final: 0.7842 (tpp) REVERT: B 1203 MET cc_start: 0.8964 (mmm) cc_final: 0.8140 (mmm) REVERT: B 1607 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6674 (mmp) REVERT: B 2241 MET cc_start: 0.3535 (mpp) cc_final: 0.2394 (mmp) REVERT: B 2292 ASN cc_start: 0.8222 (m-40) cc_final: 0.7838 (p0) REVERT: B 2301 MET cc_start: 0.5080 (mmm) cc_final: 0.4755 (mmm) REVERT: B 2437 LEU cc_start: 0.8607 (pp) cc_final: 0.8288 (mt) REVERT: B 2470 MET cc_start: 0.7464 (mmm) cc_final: 0.6978 (mmm) outliers start: 64 outliers final: 38 residues processed: 180 average time/residue: 0.2773 time to fit residues: 88.7253 Evaluate side-chains 162 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2396 VAL Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1607 MET Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1738 ILE Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1999 ASN Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2396 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 141 optimal weight: 20.0000 chunk 296 optimal weight: 0.0970 chunk 321 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 279 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2499 ASN ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1730 ASN B1999 ASN ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.110296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.079146 restraints weight = 81774.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.079256 restraints weight = 54722.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.078912 restraints weight = 42805.310| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25164 Z= 0.110 Angle : 0.546 10.886 34404 Z= 0.270 Chirality : 0.042 0.311 4282 Planarity : 0.003 0.037 4292 Dihedral : 5.245 59.066 3602 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 2.25 % Allowed : 20.47 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3364 helix: 1.18 (0.17), residues: 1058 sheet: -1.36 (0.22), residues: 640 loop : -1.00 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1376 HIS 0.006 0.001 HIS A1043 PHE 0.017 0.001 PHE B1816 TYR 0.020 0.001 TYR B1485 ARG 0.002 0.000 ARG A1735 Details of bonding type rmsd hydrogen bonds : bond 0.02839 ( 972) hydrogen bonds : angle 4.28951 ( 2649) covalent geometry : bond 0.00252 (25164) covalent geometry : angle 0.54571 (34404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 LEU cc_start: 0.7558 (mm) cc_final: 0.7230 (pp) REVERT: A 676 PHE cc_start: 0.7954 (m-80) cc_final: 0.7248 (m-10) REVERT: A 712 MET cc_start: 0.9033 (mmt) cc_final: 0.8523 (tpp) REVERT: A 1088 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7855 (t80) REVERT: A 1175 MET cc_start: 0.8642 (tpp) cc_final: 0.8420 (mmm) REVERT: A 1244 TRP cc_start: 0.8783 (m-10) cc_final: 0.8459 (m100) REVERT: A 2240 LYS cc_start: 0.8327 (tptt) cc_final: 0.8027 (tptt) REVERT: A 2241 MET cc_start: 0.5277 (mpp) cc_final: 0.4872 (ptp) REVERT: A 2245 VAL cc_start: 0.2992 (OUTLIER) cc_final: 0.2773 (p) REVERT: A 2425 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7168 (mt) REVERT: A 2448 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6461 (mm) REVERT: B 712 MET cc_start: 0.9172 (mmt) cc_final: 0.8283 (tpp) REVERT: B 724 MET cc_start: 0.8666 (ttm) cc_final: 0.8281 (ttm) REVERT: B 1088 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8187 (t80) REVERT: B 1175 MET cc_start: 0.8171 (tpp) cc_final: 0.7839 (tpp) REVERT: B 1203 MET cc_start: 0.9041 (mmm) cc_final: 0.8250 (mmm) REVERT: B 1607 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6703 (mmp) REVERT: B 2241 MET cc_start: 0.3399 (mpp) cc_final: 0.2359 (mmp) REVERT: B 2292 ASN cc_start: 0.8186 (m-40) cc_final: 0.7799 (p0) REVERT: B 2301 MET cc_start: 0.5023 (mmm) cc_final: 0.4684 (mmm) REVERT: B 2437 LEU cc_start: 0.8607 (pp) cc_final: 0.8293 (mt) REVERT: B 2470 MET cc_start: 0.7411 (mmm) cc_final: 0.6995 (mmm) outliers start: 54 outliers final: 35 residues processed: 166 average time/residue: 0.2851 time to fit residues: 84.3017 Evaluate side-chains 157 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2245 VAL Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2396 VAL Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1180 LEU Chi-restraints excluded: chain B residue 1488 VAL Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1607 MET Chi-restraints excluded: chain B residue 1613 VAL Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1999 ASN Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2338 THR Chi-restraints excluded: chain B residue 2396 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 173 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 301 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1043 HIS ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.108693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.076656 restraints weight = 82010.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.076711 restraints weight = 55010.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.076510 restraints weight = 42683.146| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25164 Z= 0.168 Angle : 0.585 8.342 34404 Z= 0.291 Chirality : 0.043 0.251 4282 Planarity : 0.004 0.044 4292 Dihedral : 5.358 59.674 3602 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 2.70 % Allowed : 20.22 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3364 helix: 1.05 (0.17), residues: 1074 sheet: -1.27 (0.22), residues: 630 loop : -0.98 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1734 HIS 0.005 0.001 HIS A1407 PHE 0.023 0.001 PHE B1816 TYR 0.017 0.001 TYR B 846 ARG 0.004 0.000 ARG A1483 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 972) hydrogen bonds : angle 4.37910 ( 2649) covalent geometry : bond 0.00391 (25164) covalent geometry : angle 0.58488 (34404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 119 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 LEU cc_start: 0.7660 (mm) cc_final: 0.7323 (pp) REVERT: A 676 PHE cc_start: 0.7966 (m-80) cc_final: 0.7598 (m-10) REVERT: A 712 MET cc_start: 0.9025 (mmt) cc_final: 0.8543 (tpp) REVERT: A 1057 MET cc_start: 0.7000 (mmt) cc_final: 0.6656 (mmt) REVERT: A 1088 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8064 (t80) REVERT: A 1175 MET cc_start: 0.8647 (tpp) cc_final: 0.8249 (tpp) REVERT: A 1244 TRP cc_start: 0.8844 (m-10) cc_final: 0.8515 (m100) REVERT: A 1947 MET cc_start: 0.6131 (mmm) cc_final: 0.5923 (mmm) REVERT: A 2240 LYS cc_start: 0.8260 (tptt) cc_final: 0.7980 (tptt) REVERT: A 2241 MET cc_start: 0.5315 (mpp) cc_final: 0.4954 (ptp) REVERT: A 2425 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7135 (mt) REVERT: A 2448 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6454 (mm) REVERT: B 712 MET cc_start: 0.9214 (mmt) cc_final: 0.8368 (tpp) REVERT: B 1088 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8208 (t80) REVERT: B 1175 MET cc_start: 0.8239 (tpp) cc_final: 0.7946 (tpp) REVERT: B 1203 MET cc_start: 0.9127 (mmm) cc_final: 0.8374 (mmm) REVERT: B 2241 MET cc_start: 0.4255 (mpp) cc_final: 0.3169 (mmp) REVERT: B 2292 ASN cc_start: 0.8185 (m-40) cc_final: 0.7843 (p0) REVERT: B 2301 MET cc_start: 0.5004 (mmm) cc_final: 0.4683 (mmm) REVERT: B 2437 LEU cc_start: 0.8610 (pp) cc_final: 0.8292 (mt) REVERT: B 2470 MET cc_start: 0.7610 (mmm) cc_final: 0.7127 (mmm) outliers start: 65 outliers final: 45 residues processed: 177 average time/residue: 0.2942 time to fit residues: 91.4134 Evaluate side-chains 167 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2396 VAL Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1180 LEU Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1488 VAL Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1613 VAL Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2099 TYR Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2338 THR Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2396 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 35 optimal weight: 0.8980 chunk 176 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 219 optimal weight: 0.0980 chunk 271 optimal weight: 0.3980 chunk 110 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 ASN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2353 ASN ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.110011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.078036 restraints weight = 82039.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.078514 restraints weight = 51737.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.078700 restraints weight = 39771.199| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25164 Z= 0.100 Angle : 0.539 8.662 34404 Z= 0.267 Chirality : 0.041 0.263 4282 Planarity : 0.003 0.036 4292 Dihedral : 5.191 60.381 3602 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.00 % Allowed : 21.26 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3364 helix: 1.25 (0.17), residues: 1072 sheet: -1.33 (0.22), residues: 650 loop : -0.92 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2104 HIS 0.004 0.001 HIS B 572 PHE 0.020 0.001 PHE B1816 TYR 0.018 0.001 TYR B1485 ARG 0.003 0.000 ARG A1735 Details of bonding type rmsd hydrogen bonds : bond 0.02751 ( 972) hydrogen bonds : angle 4.21865 ( 2649) covalent geometry : bond 0.00226 (25164) covalent geometry : angle 0.53904 (34404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 LEU cc_start: 0.7580 (mm) cc_final: 0.7286 (pp) REVERT: A 676 PHE cc_start: 0.8290 (m-80) cc_final: 0.7645 (m-10) REVERT: A 712 MET cc_start: 0.9084 (mmt) cc_final: 0.8584 (tpp) REVERT: A 1088 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7918 (t80) REVERT: A 1175 MET cc_start: 0.8630 (tpp) cc_final: 0.8206 (tpp) REVERT: A 1203 MET cc_start: 0.9233 (mmm) cc_final: 0.8628 (mmm) REVERT: A 1244 TRP cc_start: 0.8920 (m-10) cc_final: 0.8516 (m100) REVERT: A 1338 MET cc_start: 0.8778 (mpp) cc_final: 0.7717 (mpp) REVERT: A 1947 MET cc_start: 0.5832 (mmm) cc_final: 0.5593 (mmm) REVERT: A 2240 LYS cc_start: 0.8280 (tptt) cc_final: 0.7993 (tptt) REVERT: A 2241 MET cc_start: 0.5044 (mpp) cc_final: 0.4757 (ptp) REVERT: A 2448 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6428 (mm) REVERT: B 1088 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8173 (t80) REVERT: B 1175 MET cc_start: 0.8202 (tpp) cc_final: 0.7897 (tpp) REVERT: B 1203 MET cc_start: 0.9067 (mmm) cc_final: 0.8352 (mmm) REVERT: B 1371 ILE cc_start: 0.8555 (pt) cc_final: 0.8295 (mt) REVERT: B 1407 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7795 (t70) REVERT: B 1552 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7466 (ttt90) REVERT: B 1658 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7731 (mm) REVERT: B 2241 MET cc_start: 0.4160 (mpp) cc_final: 0.3139 (mmp) REVERT: B 2292 ASN cc_start: 0.8232 (m-40) cc_final: 0.7938 (p0) REVERT: B 2301 MET cc_start: 0.4887 (mmm) cc_final: 0.4635 (mmm) REVERT: B 2437 LEU cc_start: 0.8635 (pp) cc_final: 0.8315 (mt) REVERT: B 2470 MET cc_start: 0.7510 (mmm) cc_final: 0.7048 (mmm) outliers start: 48 outliers final: 36 residues processed: 164 average time/residue: 0.2971 time to fit residues: 84.9058 Evaluate side-chains 162 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1180 LEU Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1407 HIS Chi-restraints excluded: chain B residue 1488 VAL Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1552 ARG Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1658 ILE Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2338 THR Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2396 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 296 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 330 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 217 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.109584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077739 restraints weight = 82245.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078184 restraints weight = 52267.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.077867 restraints weight = 41638.192| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25164 Z= 0.117 Angle : 0.553 11.125 34404 Z= 0.273 Chirality : 0.042 0.270 4282 Planarity : 0.004 0.037 4292 Dihedral : 5.137 60.034 3602 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.25 % Allowed : 21.34 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3364 helix: 1.28 (0.17), residues: 1072 sheet: -1.29 (0.22), residues: 650 loop : -0.91 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1734 HIS 0.004 0.001 HIS A1043 PHE 0.016 0.001 PHE B1816 TYR 0.017 0.001 TYR B 846 ARG 0.008 0.000 ARG A1866 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 972) hydrogen bonds : angle 4.20233 ( 2649) covalent geometry : bond 0.00270 (25164) covalent geometry : angle 0.55333 (34404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 LEU cc_start: 0.7593 (mm) cc_final: 0.7317 (pp) REVERT: A 676 PHE cc_start: 0.8268 (m-80) cc_final: 0.7623 (m-10) REVERT: A 712 MET cc_start: 0.9062 (mmt) cc_final: 0.8567 (tpp) REVERT: A 1057 MET cc_start: 0.6873 (mmt) cc_final: 0.6642 (mmt) REVERT: A 1088 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7965 (t80) REVERT: A 1175 MET cc_start: 0.8674 (tpp) cc_final: 0.8262 (tpp) REVERT: A 1203 MET cc_start: 0.9239 (mmm) cc_final: 0.8628 (mmm) REVERT: A 1244 TRP cc_start: 0.8939 (m-10) cc_final: 0.8536 (m100) REVERT: A 1338 MET cc_start: 0.8630 (mpp) cc_final: 0.8304 (mpp) REVERT: A 1416 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 1702 MET cc_start: 0.8386 (mmm) cc_final: 0.7977 (mmm) REVERT: A 1947 MET cc_start: 0.6011 (mmm) cc_final: 0.5784 (mmm) REVERT: A 2240 LYS cc_start: 0.8263 (tptt) cc_final: 0.7975 (tptt) REVERT: A 2241 MET cc_start: 0.5103 (mpp) cc_final: 0.4790 (ptp) REVERT: A 2425 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7362 (mt) REVERT: A 2448 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6417 (mm) REVERT: B 712 MET cc_start: 0.9243 (mmt) cc_final: 0.8510 (tpp) REVERT: B 1088 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 1175 MET cc_start: 0.8229 (tpp) cc_final: 0.7926 (tpp) REVERT: B 1203 MET cc_start: 0.9106 (mmm) cc_final: 0.8392 (mmm) REVERT: B 1371 ILE cc_start: 0.8627 (pt) cc_final: 0.8310 (mt) REVERT: B 1407 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7737 (t70) REVERT: B 1552 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7544 (ttt90) REVERT: B 1658 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7622 (mm) REVERT: B 2224 LEU cc_start: 0.8031 (mp) cc_final: 0.7728 (tt) REVERT: B 2241 MET cc_start: 0.4179 (mpp) cc_final: 0.3078 (mmp) REVERT: B 2292 ASN cc_start: 0.8213 (m-40) cc_final: 0.7950 (p0) REVERT: B 2301 MET cc_start: 0.4940 (mmm) cc_final: 0.4700 (mmm) REVERT: B 2437 LEU cc_start: 0.8639 (pp) cc_final: 0.8325 (mt) REVERT: B 2470 MET cc_start: 0.7598 (mmm) cc_final: 0.7174 (mmm) outliers start: 54 outliers final: 40 residues processed: 166 average time/residue: 0.2979 time to fit residues: 86.7304 Evaluate side-chains 166 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1180 LEU Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1407 HIS Chi-restraints excluded: chain B residue 1488 VAL Chi-restraints excluded: chain B residue 1552 ARG Chi-restraints excluded: chain B residue 1607 MET Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1658 ILE Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2099 TYR Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2338 THR Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2396 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 167 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 253 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1043 HIS ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1609 GLN A1928 HIS ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 ASN B1928 HIS B1999 ASN ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.109464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.076049 restraints weight = 81859.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.077593 restraints weight = 53809.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.077867 restraints weight = 39983.767| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25164 Z= 0.121 Angle : 0.566 14.757 34404 Z= 0.277 Chirality : 0.042 0.245 4282 Planarity : 0.004 0.037 4292 Dihedral : 5.179 60.851 3602 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.20 % Allowed : 21.46 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3364 helix: 1.29 (0.17), residues: 1074 sheet: -1.18 (0.21), residues: 660 loop : -0.92 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1734 HIS 0.004 0.001 HIS A1043 PHE 0.015 0.001 PHE B1816 TYR 0.016 0.001 TYR B 846 ARG 0.002 0.000 ARG B1866 Details of bonding type rmsd hydrogen bonds : bond 0.02763 ( 972) hydrogen bonds : angle 4.21519 ( 2649) covalent geometry : bond 0.00279 (25164) covalent geometry : angle 0.56596 (34404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 LEU cc_start: 0.7670 (mm) cc_final: 0.7378 (pp) REVERT: A 676 PHE cc_start: 0.8344 (m-80) cc_final: 0.7716 (m-10) REVERT: A 712 MET cc_start: 0.9113 (mmt) cc_final: 0.8610 (tpp) REVERT: A 1057 MET cc_start: 0.6917 (mmt) cc_final: 0.6634 (mmt) REVERT: A 1088 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7931 (t80) REVERT: A 1175 MET cc_start: 0.8692 (tpp) cc_final: 0.8312 (tpp) REVERT: A 1203 MET cc_start: 0.9219 (mmm) cc_final: 0.8613 (mmm) REVERT: A 1244 TRP cc_start: 0.8955 (m-10) cc_final: 0.8536 (m100) REVERT: A 1338 MET cc_start: 0.8684 (mpp) cc_final: 0.8382 (mpp) REVERT: A 1416 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8137 (mp) REVERT: A 1702 MET cc_start: 0.8368 (mmm) cc_final: 0.8021 (mmm) REVERT: A 1947 MET cc_start: 0.6086 (mmm) cc_final: 0.5817 (mmm) REVERT: A 2240 LYS cc_start: 0.8246 (tptt) cc_final: 0.7950 (tptt) REVERT: A 2241 MET cc_start: 0.5204 (mpp) cc_final: 0.4829 (ptp) REVERT: A 2425 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7318 (mt) REVERT: A 2448 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6434 (mm) REVERT: B 712 MET cc_start: 0.9264 (mmt) cc_final: 0.8597 (tpp) REVERT: B 1088 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 1175 MET cc_start: 0.8345 (tpp) cc_final: 0.8110 (tpp) REVERT: B 1177 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7590 (mm) REVERT: B 1203 MET cc_start: 0.9130 (mmm) cc_final: 0.8592 (mmm) REVERT: B 1371 ILE cc_start: 0.8678 (pt) cc_final: 0.8323 (mt) REVERT: B 1407 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7729 (t70) REVERT: B 1552 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7519 (ttt90) REVERT: B 1658 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7613 (mm) REVERT: B 2224 LEU cc_start: 0.8119 (mp) cc_final: 0.7785 (tt) REVERT: B 2241 MET cc_start: 0.3811 (mpp) cc_final: 0.3118 (mmp) REVERT: B 2292 ASN cc_start: 0.8248 (m-40) cc_final: 0.8009 (p0) REVERT: B 2301 MET cc_start: 0.4969 (mmm) cc_final: 0.4757 (mmm) REVERT: B 2437 LEU cc_start: 0.8645 (pp) cc_final: 0.8286 (mp) REVERT: B 2470 MET cc_start: 0.7596 (mmm) cc_final: 0.7149 (mmm) REVERT: B 2521 MET cc_start: 0.8520 (ptt) cc_final: 0.8061 (ptm) outliers start: 53 outliers final: 39 residues processed: 164 average time/residue: 0.2954 time to fit residues: 84.6509 Evaluate side-chains 167 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1043 HIS Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2197 SER Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2396 VAL Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1088 PHE Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1368 THR Chi-restraints excluded: chain B residue 1407 HIS Chi-restraints excluded: chain B residue 1488 VAL Chi-restraints excluded: chain B residue 1552 ARG Chi-restraints excluded: chain B residue 1607 MET Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1658 ILE Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2099 TYR Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2338 THR Chi-restraints excluded: chain B residue 2356 THR Chi-restraints excluded: chain B residue 2396 VAL Chi-restraints excluded: chain B residue 2425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 306 optimal weight: 1.9990 chunk 188 optimal weight: 0.0470 chunk 263 optimal weight: 0.1980 chunk 109 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.109910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.076847 restraints weight = 81985.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.079154 restraints weight = 49659.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078735 restraints weight = 32702.256| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25164 Z= 0.097 Angle : 0.547 12.450 34404 Z= 0.267 Chirality : 0.041 0.233 4282 Planarity : 0.003 0.037 4292 Dihedral : 5.084 60.982 3602 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.04 % Allowed : 21.55 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3364 helix: 1.30 (0.17), residues: 1088 sheet: -1.18 (0.22), residues: 654 loop : -0.84 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2104 HIS 0.009 0.001 HIS A1043 PHE 0.014 0.001 PHE B1816 TYR 0.017 0.001 TYR B1485 ARG 0.002 0.000 ARG A1735 Details of bonding type rmsd hydrogen bonds : bond 0.02624 ( 972) hydrogen bonds : angle 4.14729 ( 2649) covalent geometry : bond 0.00220 (25164) covalent geometry : angle 0.54744 (34404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7068.01 seconds wall clock time: 124 minutes 52.92 seconds (7492.92 seconds total)