Starting phenix.real_space_refine on Mon Aug 25 04:33:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8b_42020/08_2025/8u8b_42020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8b_42020/08_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_42020/08_2025/8u8b_42020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8b_42020/08_2025/8u8b_42020.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8b_42020/08_2025/8u8b_42020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8b_42020/08_2025/8u8b_42020.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 46, 'HIS:plan': 13, 'GLN:plan1': 36, 'TYR:plan': 5, 'GLU:plan': 68, 'ARG:plan': 32, 'PHE:plan': 4, 'ASN:plan1': 18, 'GLU%COO:plan': 1} 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: {'ASP:plan': 46, 'HIS:plan': 13, 'GLN:plan1': 36, 'TYR:plan': 5, 'GLU:plan': 68, 'ARG:plan': 32, 'PHE:plan': 4, 'ASN:plan1': 18, 'GLU%COO:plan': 1} 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: 5.09, per 1000 atoms: 0.21 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: 1.52 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.40 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: 5.25 Time building geometry restraints manager: 2.07 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: 0.05 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.220 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- 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 : 4.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (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 ARG 0.003 0.000 ARG B1693 TYR 0.017 0.001 TYR A1649 PHE 0.025 0.002 PHE B1185 TRP 0.055 0.002 TRP A2104 HIS 0.005 0.001 HIS A2510 Details of bonding type rmsd covalent geometry : bond 0.00386 (25164) covalent geometry : angle 0.77276 (34404) hydrogen bonds : bond 0.20293 ( 972) hydrogen bonds : angle 6.67959 ( 2649) *********************** 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 : 0.954 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: 0.5928 (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: 0.6389 (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: 0.6534 (mmm) outliers start: 15 outliers final: 3 residues processed: 307 average time/residue: 0.1435 time to fit residues: 70.8515 Evaluate side-chains 158 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ** B1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1574 HIS B2353 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.117515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.082619 restraints weight = 82544.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.084164 restraints weight = 48272.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.084599 restraints weight = 32707.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.085144 restraints weight = 30320.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.085312 restraints weight = 27518.457| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25164 Z= 0.125 Angle : 0.617 9.589 34404 Z= 0.306 Chirality : 0.044 0.205 4282 Planarity : 0.004 0.039 4292 Dihedral : 5.535 59.135 3604 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 2.00 % Allowed : 15.27 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 3364 helix: 0.44 (0.16), residues: 1078 sheet: -1.82 (0.21), residues: 638 loop : -1.26 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1386 TYR 0.018 0.001 TYR B1485 PHE 0.017 0.001 PHE A1284 TRP 0.042 0.002 TRP A2104 HIS 0.009 0.001 HIS A1043 Details of bonding type rmsd covalent geometry : bond 0.00283 (25164) covalent geometry : angle 0.61705 (34404) hydrogen bonds : bond 0.03582 ( 972) hydrogen bonds : angle 4.93079 ( 2649) *********************** 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 208 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 PHE cc_start: 0.8102 (m-80) cc_final: 0.7062 (m-10) REVERT: A 712 MET cc_start: 0.9083 (mmt) cc_final: 0.8457 (tpp) REVERT: A 1045 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6854 (t0) REVERT: A 1175 MET cc_start: 0.8385 (tpp) cc_final: 0.8075 (mmm) REVERT: A 1947 MET cc_start: 0.6023 (mmm) cc_final: 0.5752 (mmm) REVERT: A 2240 LYS cc_start: 0.8277 (tppt) cc_final: 0.7952 (tptt) REVERT: A 2241 MET cc_start: 0.5263 (mpp) cc_final: 0.4886 (ptp) REVERT: A 2360 ASP cc_start: 0.7970 (t0) cc_final: 0.7768 (t70) REVERT: A 2417 LEU cc_start: 0.7228 (tp) cc_final: 0.6684 (tp) REVERT: A 2459 MET cc_start: 0.4455 (mpp) cc_final: 0.4185 (pmm) REVERT: B 712 MET cc_start: 0.9177 (mmt) cc_final: 0.8370 (tpp) REVERT: B 842 MET cc_start: 0.9467 (mpp) cc_final: 0.9233 (mpp) REVERT: B 1333 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7326 (t0) REVERT: B 1947 MET cc_start: 0.6571 (mmm) cc_final: 0.6096 (mmm) REVERT: B 2241 MET cc_start: 0.3439 (mpp) cc_final: 0.1687 (mmp) outliers start: 48 outliers final: 20 residues processed: 196 average time/residue: 0.1426 time to fit residues: 45.4907 Evaluate side-chains 153 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 HIS 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 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 1066 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 1488 VAL Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL 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 278 optimal weight: 0.0770 chunk 52 optimal weight: 4.9990 chunk 321 optimal weight: 9.9990 chunk 166 optimal weight: 0.0970 chunk 265 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 134 optimal weight: 0.0670 chunk 280 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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** ** A1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2420 GLN B 572 HIS B 678 GLN B1251 HIS B1310 HIS B1999 ASN B2251 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.122884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.086473 restraints weight = 83545.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.089226 restraints weight = 47859.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.089477 restraints weight = 30388.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.089916 restraints weight = 30405.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.090147 restraints weight = 28375.591| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2200 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= 0.106 Angle : 0.560 8.496 34404 Z= 0.280 Chirality : 0.042 0.162 4282 Planarity : 0.004 0.056 4292 Dihedral : 5.261 56.928 3602 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.17 % Favored : 94.77 % Rotamer: Outliers : 1.54 % Allowed : 17.85 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.15), residues: 3364 helix: 0.80 (0.17), residues: 1080 sheet: -1.53 (0.21), residues: 628 loop : -1.12 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1973 TYR 0.028 0.001 TYR B 846 PHE 0.010 0.001 PHE B1308 TRP 0.026 0.001 TRP B2104 HIS 0.014 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00232 (25164) covalent geometry : angle 0.56045 (34404) hydrogen bonds : bond 0.03254 ( 972) hydrogen bonds : angle 4.61840 ( 2649) *********************** 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 174 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 PHE cc_start: 0.8136 (m-80) cc_final: 0.7077 (m-10) REVERT: A 712 MET cc_start: 0.9124 (mmt) cc_final: 0.8496 (tpp) REVERT: A 1045 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6699 (t0) REVERT: A 1162 MET cc_start: 0.9344 (mpp) cc_final: 0.9134 (mmm) REVERT: A 1175 MET cc_start: 0.8422 (tpp) cc_final: 0.8055 (mmm) REVERT: A 1947 MET cc_start: 0.6305 (mmm) cc_final: 0.5959 (mmm) REVERT: A 2315 MET cc_start: 0.3822 (tpt) cc_final: 0.3428 (tpt) REVERT: A 2459 MET cc_start: 0.4756 (mpp) cc_final: 0.4465 (pmm) REVERT: A 2470 MET cc_start: 0.6241 (mmm) cc_final: 0.5005 (mtt) REVERT: B 712 MET cc_start: 0.9171 (mmt) cc_final: 0.8390 (tpp) REVERT: B 724 MET cc_start: 0.8694 (ttt) cc_final: 0.8419 (ttm) REVERT: B 1947 MET cc_start: 0.6713 (mmm) cc_final: 0.6169 (mmm) REVERT: B 2241 MET cc_start: 0.3442 (mpp) cc_final: 0.1845 (mmp) REVERT: B 2301 MET cc_start: 0.5335 (mmm) cc_final: 0.4994 (mmm) REVERT: B 2437 LEU cc_start: 0.8605 (pp) cc_final: 0.8378 (mm) REVERT: B 2459 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.4850 (pmm) outliers start: 37 outliers final: 23 residues processed: 160 average time/residue: 0.1556 time to fit residues: 42.5927 Evaluate side-chains 151 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1592 LEU 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 2416 THR 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 1288 MET Chi-restraints excluded: chain B residue 1340 VAL Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1827 LEU 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 2419 LEU Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2459 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 16 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A1999 ASN B 572 HIS B 678 GLN B2333 GLN ** B2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.121597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.087523 restraints weight = 83633.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.086953 restraints weight = 50800.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.087415 restraints weight = 37577.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.087774 restraints weight = 34345.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.087931 restraints weight = 32310.990| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25164 Z= 0.118 Angle : 0.543 6.728 34404 Z= 0.273 Chirality : 0.042 0.158 4282 Planarity : 0.004 0.035 4292 Dihedral : 5.051 55.395 3602 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 1.96 % Allowed : 18.43 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 3364 helix: 1.12 (0.17), residues: 1070 sheet: -1.25 (0.22), residues: 626 loop : -1.01 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1973 TYR 0.018 0.001 TYR B 846 PHE 0.013 0.001 PHE B1436 TRP 0.031 0.002 TRP B2104 HIS 0.008 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00263 (25164) covalent geometry : angle 0.54332 (34404) hydrogen bonds : bond 0.02929 ( 972) hydrogen bonds : angle 4.26407 ( 2649) *********************** 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 186 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 PHE cc_start: 0.8036 (m-80) cc_final: 0.7074 (m-10) REVERT: A 712 MET cc_start: 0.9056 (mmt) cc_final: 0.8388 (tpp) REVERT: A 1175 MET cc_start: 0.8499 (tpp) cc_final: 0.8109 (mmm) REVERT: A 1203 MET cc_start: 0.9230 (mmm) cc_final: 0.8521 (mmm) REVERT: A 1947 MET cc_start: 0.6301 (mmm) cc_final: 0.6024 (mmm) REVERT: A 2240 LYS cc_start: 0.8328 (tptt) cc_final: 0.8007 (tptt) REVERT: A 2241 MET cc_start: 0.5290 (mpp) cc_final: 0.4507 (ptp) REVERT: A 2470 MET cc_start: 0.7037 (mmm) cc_final: 0.5923 (mtp) REVERT: B 676 PHE cc_start: 0.7925 (m-80) cc_final: 0.6714 (m-10) REVERT: B 712 MET cc_start: 0.9065 (mmt) cc_final: 0.8323 (tpp) REVERT: B 724 MET cc_start: 0.8771 (ttt) cc_final: 0.8386 (ttt) REVERT: B 1088 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8033 (t80) REVERT: B 1162 MET cc_start: 0.9000 (mmm) cc_final: 0.8740 (mmm) REVERT: B 1203 MET cc_start: 0.8817 (mmm) cc_final: 0.8075 (mmm) REVERT: B 1485 TYR cc_start: 0.6443 (p90) cc_final: 0.6220 (p90) REVERT: B 1947 MET cc_start: 0.6849 (mmm) cc_final: 0.6409 (mmm) REVERT: B 2241 MET cc_start: 0.3299 (mpp) cc_final: 0.2086 (mmp) REVERT: B 2292 ASN cc_start: 0.8170 (m-40) cc_final: 0.7856 (p0) REVERT: B 2301 MET cc_start: 0.5334 (mmm) cc_final: 0.4924 (mmm) REVERT: B 2437 LEU cc_start: 0.8613 (pp) cc_final: 0.8337 (mm) REVERT: B 2459 MET cc_start: 0.5407 (pmm) cc_final: 0.4887 (pmm) outliers start: 47 outliers final: 30 residues processed: 175 average time/residue: 0.1399 time to fit residues: 43.1329 Evaluate side-chains 157 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2338 THR Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain B residue 572 HIS 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 1613 VAL Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1738 ILE 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 2419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 129 optimal weight: 3.9990 chunk 204 optimal weight: 0.0970 chunk 296 optimal weight: 2.9990 chunk 292 optimal weight: 0.5980 chunk 217 optimal weight: 8.9990 chunk 312 optimal weight: 10.0000 chunk 333 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 267 optimal weight: 0.0970 chunk 309 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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** A1251 HIS ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS ** B 678 GLN ** 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 = 0.4315 r_free = 0.4315 target = 0.116332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.085465 restraints weight = 84328.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.087226 restraints weight = 46317.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.087355 restraints weight = 33308.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.087719 restraints weight = 31909.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.087861 restraints weight = 28675.637| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25164 Z= 0.098 Angle : 0.529 13.413 34404 Z= 0.262 Chirality : 0.041 0.163 4282 Planarity : 0.003 0.035 4292 Dihedral : 4.984 55.269 3602 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 1.96 % Allowed : 19.26 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.15), residues: 3364 helix: 1.19 (0.17), residues: 1076 sheet: -1.33 (0.22), residues: 650 loop : -0.93 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1973 TYR 0.018 0.001 TYR B 846 PHE 0.018 0.001 PHE A1050 TRP 0.018 0.001 TRP B2104 HIS 0.013 0.001 HIS B 572 Details of bonding type rmsd covalent geometry : bond 0.00221 (25164) covalent geometry : angle 0.52865 (34404) hydrogen bonds : bond 0.02758 ( 972) hydrogen bonds : angle 4.19550 ( 2649) *********************** 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 183 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 PHE cc_start: 0.7864 (m-80) cc_final: 0.7201 (m-10) REVERT: A 712 MET cc_start: 0.8995 (mmt) cc_final: 0.8445 (tpp) REVERT: A 1175 MET cc_start: 0.8543 (tpp) cc_final: 0.8187 (mmm) REVERT: A 1203 MET cc_start: 0.9213 (mmm) cc_final: 0.8456 (mmm) REVERT: A 1277 TYR cc_start: 0.8882 (m-80) cc_final: 0.8679 (m-10) REVERT: A 1523 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9104 (tp) REVERT: A 2240 LYS cc_start: 0.8355 (tptt) cc_final: 0.8007 (tptt) REVERT: A 2241 MET cc_start: 0.5200 (mpp) cc_final: 0.4545 (ptp) REVERT: A 2470 MET cc_start: 0.7280 (mmm) cc_final: 0.6451 (mtp) REVERT: B 572 HIS cc_start: 0.6004 (OUTLIER) cc_final: 0.5799 (p90) REVERT: B 676 PHE cc_start: 0.7820 (m-80) cc_final: 0.6488 (m-10) REVERT: B 712 MET cc_start: 0.9023 (mmt) cc_final: 0.8309 (tpp) REVERT: B 724 MET cc_start: 0.8724 (ttt) cc_final: 0.8277 (ttt) REVERT: B 1175 MET cc_start: 0.7927 (tpp) cc_final: 0.7658 (tpp) REVERT: B 1203 MET cc_start: 0.8846 (mmm) cc_final: 0.8037 (mmm) REVERT: B 2241 MET cc_start: 0.3714 (mpp) cc_final: 0.2785 (mmp) REVERT: B 2292 ASN cc_start: 0.8107 (m-40) cc_final: 0.7791 (p0) REVERT: B 2301 MET cc_start: 0.5187 (mmm) cc_final: 0.4796 (mmm) REVERT: B 2437 LEU cc_start: 0.8545 (pp) cc_final: 0.8219 (mt) REVERT: B 2459 MET cc_start: 0.5448 (pmm) cc_final: 0.4925 (pmm) outliers start: 47 outliers final: 34 residues processed: 170 average time/residue: 0.1307 time to fit residues: 39.1102 Evaluate side-chains 163 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1523 ILE Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1738 ILE 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 2437 LEU Chi-restraints excluded: chain B residue 572 HIS 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 1180 LEU Chi-restraints excluded: chain B residue 1488 VAL Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1548 ILE 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 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 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 339 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 280 optimal weight: 0.0970 chunk 193 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 333 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 321 optimal weight: 20.0000 chunk 183 optimal weight: 0.0070 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 572 HIS B 678 GLN ** B1333 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 = 0.4252 r_free = 0.4252 target = 0.112160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.081444 restraints weight = 83147.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.081798 restraints weight = 52970.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.081793 restraints weight = 38159.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.082136 restraints weight = 36988.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.082698 restraints weight = 35837.628| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3284 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= 0.113 Angle : 0.532 10.635 34404 Z= 0.264 Chirality : 0.042 0.302 4282 Planarity : 0.003 0.036 4292 Dihedral : 4.953 55.468 3602 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 2.04 % Allowed : 19.68 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 3364 helix: 1.26 (0.17), residues: 1068 sheet: -1.21 (0.22), residues: 646 loop : -0.92 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2235 TYR 0.016 0.001 TYR B 846 PHE 0.016 0.001 PHE A1050 TRP 0.014 0.001 TRP A1734 HIS 0.033 0.001 HIS B 572 Details of bonding type rmsd covalent geometry : bond 0.00257 (25164) covalent geometry : angle 0.53207 (34404) hydrogen bonds : bond 0.02723 ( 972) hydrogen bonds : angle 4.14133 ( 2649) *********************** 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 180 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 676 PHE cc_start: 0.7925 (m-80) cc_final: 0.7303 (m-10) REVERT: A 712 MET cc_start: 0.9050 (mmt) cc_final: 0.8495 (tpp) REVERT: A 1088 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8174 (t80) REVERT: A 1175 MET cc_start: 0.8522 (tpp) cc_final: 0.8109 (mmm) REVERT: A 1203 MET cc_start: 0.9201 (mmm) cc_final: 0.8454 (mmm) REVERT: A 1277 TYR cc_start: 0.8942 (m-80) cc_final: 0.8737 (m-10) REVERT: A 1523 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9095 (tp) REVERT: A 2240 LYS cc_start: 0.8355 (tptt) cc_final: 0.7996 (tptt) REVERT: A 2241 MET cc_start: 0.5134 (mpp) cc_final: 0.4901 (ptp) REVERT: A 2425 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6694 (mt) REVERT: A 2470 MET cc_start: 0.7345 (mmm) cc_final: 0.6367 (mtp) REVERT: B 724 MET cc_start: 0.8779 (ttt) cc_final: 0.8505 (ttm) REVERT: B 1088 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 1175 MET cc_start: 0.7980 (tpp) cc_final: 0.7641 (tpp) REVERT: B 1203 MET cc_start: 0.8898 (mmm) cc_final: 0.8104 (mmm) REVERT: B 1947 MET cc_start: 0.6373 (mmm) cc_final: 0.6097 (mmt) REVERT: B 2241 MET cc_start: 0.3716 (mpp) cc_final: 0.2833 (mmp) REVERT: B 2292 ASN cc_start: 0.8226 (m-40) cc_final: 0.7913 (p0) REVERT: B 2301 MET cc_start: 0.5210 (mmm) cc_final: 0.4861 (mmm) REVERT: B 2437 LEU cc_start: 0.8620 (pp) cc_final: 0.8268 (mt) REVERT: B 2459 MET cc_start: 0.5472 (pmm) cc_final: 0.4937 (pmm) outliers start: 49 outliers final: 33 residues processed: 172 average time/residue: 0.1240 time to fit residues: 37.5224 Evaluate side-chains 164 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 813 VAL 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 1485 TYR Chi-restraints excluded: chain A residue 1523 ILE Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1738 ILE 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 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 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 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 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2338 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 246 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 119 optimal weight: 0.0670 chunk 300 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 238 optimal weight: 0.1980 chunk 166 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 A2353 ASN ** B1333 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 = 0.4255 r_free = 0.4255 target = 0.112336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.081408 restraints weight = 82873.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.082149 restraints weight = 54743.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.082097 restraints weight = 38857.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.082392 restraints weight = 38266.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.082733 restraints weight = 34773.429| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25164 Z= 0.097 Angle : 0.517 9.973 34404 Z= 0.257 Chirality : 0.041 0.254 4282 Planarity : 0.003 0.037 4292 Dihedral : 4.888 55.631 3602 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 1.96 % Allowed : 20.22 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 3364 helix: 1.40 (0.17), residues: 1060 sheet: -1.22 (0.22), residues: 654 loop : -0.85 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2235 TYR 0.015 0.001 TYR B 846 PHE 0.014 0.001 PHE A1050 TRP 0.014 0.001 TRP B2104 HIS 0.004 0.001 HIS B 572 Details of bonding type rmsd covalent geometry : bond 0.00219 (25164) covalent geometry : angle 0.51744 (34404) hydrogen bonds : bond 0.02618 ( 972) hydrogen bonds : angle 4.05393 ( 2649) *********************** 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 179 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1088 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8035 (t80) REVERT: A 1175 MET cc_start: 0.8595 (tpp) cc_final: 0.8332 (mmm) REVERT: A 1523 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9024 (tp) REVERT: A 2240 LYS cc_start: 0.8352 (tptt) cc_final: 0.7959 (tptt) REVERT: A 2241 MET cc_start: 0.5000 (mpp) cc_final: 0.4751 (ptp) REVERT: A 2425 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6929 (mt) REVERT: A 2470 MET cc_start: 0.7263 (mmm) cc_final: 0.6542 (mtp) REVERT: B 712 MET cc_start: 0.9177 (mmt) cc_final: 0.8406 (tpp) REVERT: B 724 MET cc_start: 0.8730 (ttt) cc_final: 0.8465 (ttm) REVERT: B 1088 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 1115 GLU cc_start: 0.8299 (tt0) cc_final: 0.8042 (tm-30) REVERT: B 1175 MET cc_start: 0.8115 (tpp) cc_final: 0.7767 (tpp) REVERT: B 1203 MET cc_start: 0.8971 (mmm) cc_final: 0.8190 (mmm) REVERT: B 1702 MET cc_start: 0.8197 (mmm) cc_final: 0.7961 (tpt) REVERT: B 1947 MET cc_start: 0.6429 (mmm) cc_final: 0.5898 (mmt) REVERT: B 2155 MET cc_start: 0.6872 (tpp) cc_final: 0.6669 (tpp) REVERT: B 2241 MET cc_start: 0.3688 (mpp) cc_final: 0.2831 (mmp) REVERT: B 2292 ASN cc_start: 0.8201 (m-40) cc_final: 0.7898 (p0) REVERT: B 2301 MET cc_start: 0.5016 (mmm) cc_final: 0.4732 (mmm) REVERT: B 2437 LEU cc_start: 0.8607 (pp) cc_final: 0.8260 (mt) REVERT: B 2459 MET cc_start: 0.5643 (pmm) cc_final: 0.5104 (pmm) outliers start: 47 outliers final: 33 residues processed: 172 average time/residue: 0.1263 time to fit residues: 38.6421 Evaluate side-chains 162 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1523 ILE Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 2169 LEU 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 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 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 1890 PHE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1905 VAL Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2338 THR Chi-restraints excluded: chain B residue 2419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 245 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 259 optimal weight: 0.2980 chunk 76 optimal weight: 0.0570 chunk 109 optimal weight: 0.2980 chunk 246 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 232 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 A1972 HIS ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 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 = 0.4255 r_free = 0.4255 target = 0.115175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.078949 restraints weight = 82237.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.080425 restraints weight = 49561.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081301 restraints weight = 33217.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.082006 restraints weight = 28732.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.082006 restraints weight = 25370.604| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25164 Z= 0.091 Angle : 0.510 8.868 34404 Z= 0.253 Chirality : 0.041 0.254 4282 Planarity : 0.003 0.038 4292 Dihedral : 4.777 54.864 3602 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.10 % Rotamer: Outliers : 2.16 % Allowed : 20.05 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3364 helix: 1.48 (0.17), residues: 1060 sheet: -1.14 (0.22), residues: 654 loop : -0.82 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2235 TYR 0.015 0.001 TYR B 846 PHE 0.017 0.001 PHE A1050 TRP 0.013 0.001 TRP A2104 HIS 0.004 0.001 HIS B 572 Details of bonding type rmsd covalent geometry : bond 0.00201 (25164) covalent geometry : angle 0.50951 (34404) hydrogen bonds : bond 0.02490 ( 972) hydrogen bonds : angle 3.97681 ( 2649) *********************** 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 178 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1088 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7877 (t80) REVERT: A 1175 MET cc_start: 0.8541 (tpp) cc_final: 0.8087 (tpp) REVERT: A 1203 MET cc_start: 0.9216 (mmm) cc_final: 0.8634 (mmm) REVERT: A 1523 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8993 (tp) REVERT: A 1531 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: A 2240 LYS cc_start: 0.8507 (tptt) cc_final: 0.8151 (tptt) REVERT: A 2241 MET cc_start: 0.4837 (mpp) cc_final: 0.4518 (ptp) REVERT: A 2425 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 2470 MET cc_start: 0.7036 (mmm) cc_final: 0.6226 (mtp) REVERT: B 712 MET cc_start: 0.9210 (mmt) cc_final: 0.8437 (tpp) REVERT: B 724 MET cc_start: 0.8787 (ttt) cc_final: 0.8519 (ttm) REVERT: B 1088 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8150 (t80) REVERT: B 1115 GLU cc_start: 0.8472 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 1175 MET cc_start: 0.8121 (tpp) cc_final: 0.7846 (tpp) REVERT: B 1203 MET cc_start: 0.8997 (mmm) cc_final: 0.8216 (mmm) REVERT: B 2241 MET cc_start: 0.3796 (mpp) cc_final: 0.2954 (mmp) REVERT: B 2292 ASN cc_start: 0.8275 (m-40) cc_final: 0.7999 (p0) REVERT: B 2301 MET cc_start: 0.5075 (mmm) cc_final: 0.4829 (mmm) REVERT: B 2437 LEU cc_start: 0.8702 (pp) cc_final: 0.8335 (mt) outliers start: 52 outliers final: 34 residues processed: 172 average time/residue: 0.1213 time to fit residues: 37.3999 Evaluate side-chains 163 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1149 LEU 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 1523 ILE Chi-restraints excluded: chain A residue 1531 GLU Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1890 PHE Chi-restraints excluded: chain A residue 2169 LEU 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 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 1613 VAL 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 1905 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 27 optimal weight: 10.0000 chunk 315 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 236 optimal weight: 0.3980 chunk 214 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 206 optimal weight: 0.0030 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1999 ASN ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 GLN B1324 GLN ** B1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1986 HIS ** B2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.113534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.078459 restraints weight = 84013.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.077769 restraints weight = 58336.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.077746 restraints weight = 44635.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.078329 restraints weight = 40143.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.078412 restraints weight = 36091.301| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25164 Z= 0.168 Angle : 0.610 10.880 34404 Z= 0.301 Chirality : 0.043 0.254 4282 Planarity : 0.004 0.043 4292 Dihedral : 5.165 57.611 3602 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.12 % Allowed : 20.05 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3364 helix: 1.26 (0.17), residues: 1064 sheet: -1.10 (0.22), residues: 634 loop : -0.90 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2514 TYR 0.023 0.001 TYR B1402 PHE 0.024 0.002 PHE B1816 TRP 0.017 0.002 TRP A1734 HIS 0.005 0.001 HIS A1929 Details of bonding type rmsd covalent geometry : bond 0.00380 (25164) covalent geometry : angle 0.61028 (34404) hydrogen bonds : bond 0.03253 ( 972) hydrogen bonds : angle 4.26820 ( 2649) *********************** 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 177 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 712 MET cc_start: 0.9030 (mmt) cc_final: 0.8645 (tpp) REVERT: A 1088 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8044 (t80) REVERT: A 1175 MET cc_start: 0.8640 (tpp) cc_final: 0.8192 (tpp) REVERT: A 1338 MET cc_start: 0.8489 (mpp) cc_final: 0.7230 (mpp) REVERT: A 1719 MET cc_start: 0.7183 (ptp) cc_final: 0.6948 (ptt) REVERT: A 2240 LYS cc_start: 0.8253 (tptt) cc_final: 0.7879 (tptt) REVERT: A 2241 MET cc_start: 0.4895 (mpp) cc_final: 0.4580 (ptp) REVERT: A 2425 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6872 (mt) REVERT: A 2470 MET cc_start: 0.7328 (mmm) cc_final: 0.6462 (mtp) REVERT: B 712 MET cc_start: 0.9193 (mmt) cc_final: 0.8445 (tpp) REVERT: B 724 MET cc_start: 0.8785 (ttt) cc_final: 0.8503 (ttm) REVERT: B 1057 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6808 (mpp) REVERT: B 1088 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8238 (t80) REVERT: B 1175 MET cc_start: 0.8221 (tpp) cc_final: 0.7999 (tpp) REVERT: B 1203 MET cc_start: 0.9092 (mmm) cc_final: 0.8317 (mmm) REVERT: B 1431 MET cc_start: 0.7739 (ptm) cc_final: 0.7521 (ttp) REVERT: B 2224 LEU cc_start: 0.8052 (mp) cc_final: 0.7716 (tt) REVERT: B 2241 MET cc_start: 0.3832 (mpp) cc_final: 0.2892 (mmp) REVERT: B 2292 ASN cc_start: 0.8235 (m-40) cc_final: 0.7989 (p0) REVERT: B 2301 MET cc_start: 0.5109 (mmm) cc_final: 0.4797 (mmm) REVERT: B 2437 LEU cc_start: 0.8667 (pp) cc_final: 0.8268 (mp) outliers start: 51 outliers final: 35 residues processed: 171 average time/residue: 0.1310 time to fit residues: 39.7755 Evaluate side-chains 162 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 1738 ILE 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 2338 THR Chi-restraints excluded: chain A residue 2396 VAL 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 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1057 MET 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 82 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 302 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 242 optimal weight: 5.9990 chunk 320 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A1928 HIS ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1574 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.114498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.080110 restraints weight = 83804.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.079040 restraints weight = 58165.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.079441 restraints weight = 42760.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.079927 restraints weight = 37112.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.080033 restraints weight = 32992.346| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4278 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= 0.111 Angle : 0.563 15.432 34404 Z= 0.275 Chirality : 0.042 0.250 4282 Planarity : 0.003 0.037 4292 Dihedral : 5.037 58.311 3602 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.79 % Allowed : 20.51 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.15), residues: 3364 helix: 1.36 (0.17), residues: 1062 sheet: -1.07 (0.22), residues: 646 loop : -0.87 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1973 TYR 0.015 0.001 TYR B 846 PHE 0.015 0.001 PHE B1816 TRP 0.014 0.001 TRP A1734 HIS 0.003 0.001 HIS A1929 Details of bonding type rmsd covalent geometry : bond 0.00254 (25164) covalent geometry : angle 0.56257 (34404) hydrogen bonds : bond 0.02719 ( 972) hydrogen bonds : angle 4.16530 ( 2649) ********************** 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 168 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 712 MET cc_start: 0.9013 (mmt) cc_final: 0.8571 (tpp) REVERT: A 1088 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8041 (t80) REVERT: A 1175 MET cc_start: 0.8679 (tpp) cc_final: 0.8215 (tpp) REVERT: A 1203 MET cc_start: 0.9207 (mmm) cc_final: 0.8561 (mmm) REVERT: A 1338 MET cc_start: 0.8481 (mpp) cc_final: 0.7376 (mpp) REVERT: A 1719 MET cc_start: 0.7086 (ptp) cc_final: 0.6834 (ptt) REVERT: A 2240 LYS cc_start: 0.8405 (tptt) cc_final: 0.8085 (tptt) REVERT: A 2241 MET cc_start: 0.4739 (mpp) cc_final: 0.4461 (ptp) REVERT: A 2425 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7080 (mt) REVERT: A 2470 MET cc_start: 0.6911 (mmm) cc_final: 0.6397 (mtp) REVERT: B 676 PHE cc_start: 0.7962 (m-80) cc_final: 0.6448 (m-10) REVERT: B 712 MET cc_start: 0.9194 (mmt) cc_final: 0.8293 (tpp) REVERT: B 724 MET cc_start: 0.8722 (ttt) cc_final: 0.8486 (ttt) REVERT: B 1057 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6797 (mpp) REVERT: B 1088 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8273 (t80) REVERT: B 1175 MET cc_start: 0.8201 (tpp) cc_final: 0.7896 (tpp) REVERT: B 1203 MET cc_start: 0.9039 (mmm) cc_final: 0.8298 (mmm) REVERT: B 1702 MET cc_start: 0.8222 (mmm) cc_final: 0.7962 (tpt) REVERT: B 2224 LEU cc_start: 0.8143 (mp) cc_final: 0.7836 (tt) REVERT: B 2241 MET cc_start: 0.3784 (mpp) cc_final: 0.2906 (mmp) REVERT: B 2292 ASN cc_start: 0.8232 (m-40) cc_final: 0.7964 (p0) REVERT: B 2301 MET cc_start: 0.4951 (mmm) cc_final: 0.4688 (mmm) REVERT: B 2437 LEU cc_start: 0.8661 (pp) cc_final: 0.8257 (mp) REVERT: B 2521 MET cc_start: 0.8517 (ptt) cc_final: 0.8057 (ptm) outliers start: 43 outliers final: 34 residues processed: 161 average time/residue: 0.1345 time to fit residues: 38.6714 Evaluate side-chains 161 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 CYS 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 1149 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 1738 ILE 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 2338 THR Chi-restraints excluded: chain A residue 2396 VAL 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 842 MET Chi-restraints excluded: chain B residue 1043 HIS Chi-restraints excluded: chain B residue 1057 MET 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 1652 LEU Chi-restraints excluded: chain B residue 1738 ILE 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 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 308 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 200 optimal weight: 6.9990 chunk 246 optimal weight: 0.3980 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 323 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.110038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.078712 restraints weight = 82128.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.078885 restraints weight = 53281.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078775 restraints weight = 40661.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.079081 restraints weight = 42929.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.079216 restraints weight = 37681.954| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25164 Z= 0.140 Angle : 0.583 13.546 34404 Z= 0.286 Chirality : 0.042 0.244 4282 Planarity : 0.004 0.038 4292 Dihedral : 5.041 58.253 3602 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.71 % Allowed : 20.72 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3364 helix: 1.35 (0.17), residues: 1062 sheet: -1.08 (0.22), residues: 648 loop : -0.87 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1483 TYR 0.014 0.001 TYR B 846 PHE 0.016 0.001 PHE B1816 TRP 0.016 0.001 TRP A1734 HIS 0.009 0.001 HIS A1043 Details of bonding type rmsd covalent geometry : bond 0.00323 (25164) covalent geometry : angle 0.58304 (34404) hydrogen bonds : bond 0.02833 ( 972) hydrogen bonds : angle 4.19483 ( 2649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3924.86 seconds wall clock time: 68 minutes 37.59 seconds (4117.59 seconds total)