Starting phenix.real_space_refine on Tue May 27 04:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8l_44349/05_2025/9b8l_44349.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8l_44349/05_2025/9b8l_44349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8l_44349/05_2025/9b8l_44349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8l_44349/05_2025/9b8l_44349.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8l_44349/05_2025/9b8l_44349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8l_44349/05_2025/9b8l_44349.cif" } resolution = 4.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 18168 2.51 5 N 4852 2.21 5 O 5292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28456 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1762, 14228 Classifications: {'peptide': 1762} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 114, 'TRANS': 1646} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 14228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1762, 14228 Classifications: {'peptide': 1762} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 114, 'TRANS': 1646} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 16.93, per 1000 atoms: 0.59 Number of scatterers: 28456 At special positions: 0 Unit cell: (106.92, 202.257, 166.617, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5292 8.00 N 4852 7.00 C 18168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.20 Conformation dependent library (CDL) restraints added in 3.9 seconds 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6620 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 38 sheets defined 16.5% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 404 through 407 Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.829A pdb=" N ARG A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 587 removed outlier: 4.003A pdb=" N LEU A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 698 removed outlier: 3.995A pdb=" N THR A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 720 Processing helix chain 'A' and resid 734 through 761 removed outlier: 5.028A pdb=" N LEU A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 782 Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'A' and resid 862 through 871 removed outlier: 4.730A pdb=" N LYS A 865 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 871 " --> pdb=" O ASN A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.792A pdb=" N ILE A 986 " --> pdb=" O LYS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1058 Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1107 through 1113 Processing helix chain 'A' and resid 1115 through 1119 Processing helix chain 'A' and resid 1213 through 1218 Processing helix chain 'A' and resid 1394 through 1398 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1469 through 1474 Processing helix chain 'A' and resid 1476 through 1486 Processing helix chain 'A' and resid 1493 through 1498 removed outlier: 3.935A pdb=" N ASP A1498 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 removed outlier: 6.109A pdb=" N GLU A1513 " --> pdb=" O GLU A1510 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA A1514 " --> pdb=" O ASN A1511 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A1517 " --> pdb=" O ALA A1514 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A1519 " --> pdb=" O GLU A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1671 removed outlier: 3.510A pdb=" N LEU A1671 " --> pdb=" O GLU A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1709 removed outlier: 3.528A pdb=" N HIS A1703 " --> pdb=" O SER A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1735 Processing helix chain 'A' and resid 1745 through 1756 Processing helix chain 'A' and resid 1847 through 1851 Processing helix chain 'A' and resid 1938 through 1942 Processing helix chain 'A' and resid 1943 through 1947 Processing helix chain 'A' and resid 1999 through 2004 Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 397 through 403 removed outlier: 3.926A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 407 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 576 through 585 removed outlier: 3.632A pdb=" N ILE B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 697 removed outlier: 4.860A pdb=" N THR B 674 " --> pdb=" O HIS B 670 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 688 " --> pdb=" O ARG B 684 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 689 " --> pdb=" O LEU B 685 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 719 Processing helix chain 'B' and resid 720 through 722 No H-bonds generated for 'chain 'B' and resid 720 through 722' Processing helix chain 'B' and resid 734 through 761 removed outlier: 4.935A pdb=" N LEU B 756 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 757 " --> pdb=" O GLU B 753 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 782 Processing helix chain 'B' and resid 820 through 824 Processing helix chain 'B' and resid 863 through 868 removed outlier: 4.222A pdb=" N ASN B 868 " --> pdb=" O GLU B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 871 No H-bonds generated for 'chain 'B' and resid 869 through 871' Processing helix chain 'B' and resid 982 through 986 removed outlier: 3.674A pdb=" N ILE B 986 " --> pdb=" O LYS B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1059 removed outlier: 4.021A pdb=" N LYS B1057 " --> pdb=" O MET B1053 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS B1059 " --> pdb=" O ALA B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1111 removed outlier: 3.906A pdb=" N ALA B1107 " --> pdb=" O THR B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1119 Processing helix chain 'B' and resid 1213 through 1218 Processing helix chain 'B' and resid 1394 through 1398 Processing helix chain 'B' and resid 1409 through 1413 Processing helix chain 'B' and resid 1424 through 1429 Processing helix chain 'B' and resid 1470 through 1474 Processing helix chain 'B' and resid 1476 through 1486 Processing helix chain 'B' and resid 1493 through 1498 removed outlier: 4.044A pdb=" N ASP B1498 " --> pdb=" O LEU B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1508 through 1519 removed outlier: 6.400A pdb=" N GLU B1513 " --> pdb=" O GLU B1510 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA B1514 " --> pdb=" O ASN B1511 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B1517 " --> pdb=" O ALA B1514 " (cutoff:3.500A) Processing helix chain 'B' and resid 1666 through 1671 Processing helix chain 'B' and resid 1697 through 1709 removed outlier: 3.552A pdb=" N LEU B1702 " --> pdb=" O PRO B1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1735 Processing helix chain 'B' and resid 1745 through 1757 Processing helix chain 'B' and resid 1847 through 1851 Processing helix chain 'B' and resid 1938 through 1942 Processing helix chain 'B' and resid 1943 through 1947 Processing helix chain 'B' and resid 2000 through 2004 Processing sheet with id=AA1, first strand: chain 'A' and resid 218 through 226 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 218 through 226 current: chain 'A' and resid 336 through 344 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 288 removed outlier: 5.086A pdb=" N VAL A 286 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 378 through 389 removed outlier: 7.568A pdb=" N ARG A 387 " --> pdb=" O TRP A 442 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP A 442 " --> pdb=" O ARG A 387 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 441 through 447 current: chain 'A' and resid 551 through 564 Processing sheet with id=AA4, first strand: chain 'A' and resid 419 through 424 removed outlier: 5.063A pdb=" N VAL A 420 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 458 through 461 Processing sheet with id=AA6, first strand: chain 'A' and resid 590 through 602 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 657 through 661 current: chain 'A' and resid 850 through 860 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 850 through 860 current: chain 'A' and resid 894 through 895 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 894 through 895 current: chain 'A' and resid 1089 through 1100 Processing sheet with id=AA7, first strand: chain 'A' and resid 611 through 617 removed outlier: 6.262A pdb=" N GLN A 799 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG A 803 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 641 through 642 Processing sheet with id=AA9, first strand: chain 'A' and resid 948 through 958 removed outlier: 12.064A pdb=" N GLU A 952 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N TYR A 972 " --> pdb=" O GLU A 952 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N PHE A 954 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASP A 970 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN A 956 " --> pdb=" O MET A 968 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N MET A 968 " --> pdb=" O ASN A 956 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 966 through 973 current: chain 'A' and resid 1035 through 1048 Processing sheet with id=AB1, first strand: chain 'A' and resid 1198 through 1211 removed outlier: 6.832A pdb=" N TRP A1199 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN A1160 " --> pdb=" O TRP A1199 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A1207 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR A1152 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU A1209 " --> pdb=" O ASN A1150 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A1150 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A1271 " --> pdb=" O TYR A1159 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA A1161 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU A1269 " --> pdb=" O ALA A1161 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A1268 " --> pdb=" O LEU A1260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1185 through 1187 removed outlier: 5.962A pdb=" N ASP A1230 " --> pdb=" O PHE A1239 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A1239 " --> pdb=" O ASP A1230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1313 through 1315 removed outlier: 3.582A pdb=" N GLU A1315 " --> pdb=" O ILE A1318 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1384 through 1392 removed outlier: 3.765A pdb=" N ARG A1331 " --> pdb=" O LEU A1554 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS A1546 " --> pdb=" O TRP A1339 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU A1341 " --> pdb=" O GLU A1544 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU A1544 " --> pdb=" O LEU A1341 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A1543 " --> pdb=" O LEU A1527 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1356 through 1361 removed outlier: 4.466A pdb=" N LEU A1357 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1401 through 1406 removed outlier: 6.028A pdb=" N ILE A1401 " --> pdb=" O THR A1421 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A1421 " --> pdb=" O ILE A1401 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A1403 " --> pdb=" O GLN A1419 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN A1419 " --> pdb=" O VAL A1403 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A1405 " --> pdb=" O VAL A1417 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1626 through 1629 removed outlier: 6.584A pdb=" N VAL A1585 " --> pdb=" O PHE A1627 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS A1629 " --> pdb=" O TYR A1583 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A1583 " --> pdb=" O LYS A1629 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A1580 " --> pdb=" O PHE A1790 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE A1790 " --> pdb=" O VAL A1580 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE A1582 " --> pdb=" O ASP A1788 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP A1788 " --> pdb=" O ILE A1582 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE A1584 " --> pdb=" O TRP A1786 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TRP A1786 " --> pdb=" O ILE A1584 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A1770 " --> pdb=" O GLN A1780 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A1782 " --> pdb=" O ARG A1768 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG A1768 " --> pdb=" O LYS A1782 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN A1784 " --> pdb=" O GLU A1766 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU A1766 " --> pdb=" O GLN A1784 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1610 through 1613 removed outlier: 6.866A pdb=" N LEU A1643 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL A1663 " --> pdb=" O LEU A1643 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A1645 " --> pdb=" O GLU A1661 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU A1661 " --> pdb=" O ILE A1645 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A1647 " --> pdb=" O ILE A1659 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1721 through 1723 removed outlier: 3.513A pdb=" N VAL A1721 " --> pdb=" O TYR A1728 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1870 through 1872 removed outlier: 7.588A pdb=" N GLU A1986 " --> pdb=" O TRP A1818 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1841 through 1842 removed outlier: 3.515A pdb=" N GLN A1852 " --> pdb=" O GLY A1842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 261 through 272 removed outlier: 6.285A pdb=" N ILE B 227 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU B 264 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN B 225 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 266 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG B 223 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE B 268 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN B 221 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU B 270 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP B 219 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE B 222 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 344 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL B 224 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N CYS B 342 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL B 226 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER B 340 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 228 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU B 341 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 317 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 343 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA B 315 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU B 368 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP B 320 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 239 through 240 removed outlier: 7.255A pdb=" N ILE B 284 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU B 300 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 286 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 518 through 527 removed outlier: 5.254A pdb=" N GLY B 519 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU B 560 " --> pdb=" O GLY B 519 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 554 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY B 527 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TYR B 552 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG B 555 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA B 388 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU B 557 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY B 378 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 450 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N HIS B 380 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 448 " --> pdb=" O HIS B 380 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N CYS B 382 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B 446 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS B 384 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN B 444 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE B 386 " --> pdb=" O TRP B 442 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 571 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 419 through 424 removed outlier: 5.680A pdb=" N VAL B 420 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 458 through 465 removed outlier: 4.489A pdb=" N ILE B 463 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA B 476 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP B 465 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE B 474 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 590 through 602 removed outlier: 6.793A pdb=" N SER B 600 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 10.986A pdb=" N VAL B 655 " --> pdb=" O SER B 600 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 655 through 661 current: chain 'B' and resid 851 through 860 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 851 through 860 current: chain 'B' and resid 894 through 895 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 894 through 895 current: chain 'B' and resid 1089 through 1100 Processing sheet with id=AC9, first strand: chain 'B' and resid 611 through 617 removed outlier: 3.526A pdb=" N ALA B 805 " --> pdb=" O MET B 797 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN B 799 " --> pdb=" O ARG B 803 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG B 803 " --> pdb=" O GLN B 799 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 641 through 642 Processing sheet with id=AD2, first strand: chain 'B' and resid 948 through 958 removed outlier: 12.650A pdb=" N GLU B 952 " --> pdb=" O TYR B 972 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N TYR B 972 " --> pdb=" O GLU B 952 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N PHE B 954 " --> pdb=" O ASP B 970 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP B 970 " --> pdb=" O PHE B 954 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN B 956 " --> pdb=" O MET B 968 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N MET B 968 " --> pdb=" O ASN B 956 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 966 through 973 current: chain 'B' and resid 1035 through 1048 Processing sheet with id=AD3, first strand: chain 'B' and resid 1148 through 1162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1148 through 1162 current: chain 'B' and resid 1185 through 1187 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1185 through 1187 current: chain 'B' and resid 1238 through 1245 removed outlier: 4.127A pdb=" N ILE B1244 " --> pdb=" O PRO B1259 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA B1256 " --> pdb=" O LEU B1271 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B1271 " --> pdb=" O ALA B1256 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE B1258 " --> pdb=" O GLU B1269 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B1269 " --> pdb=" O PHE B1258 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B1260 " --> pdb=" O SER B1267 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1265 through 1278 current: chain 'B' and resid 1318 through 1320 Processing sheet with id=AD4, first strand: chain 'B' and resid 1384 through 1392 removed outlier: 5.585A pdb=" N THR B1332 " --> pdb=" O LEU B1554 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B1554 " --> pdb=" O THR B1332 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE B1334 " --> pdb=" O TYR B1552 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR B1552 " --> pdb=" O ILE B1334 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE B1336 " --> pdb=" O LYS B1550 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS B1550 " --> pdb=" O ILE B1336 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA B1338 " --> pdb=" O LEU B1548 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B1548 " --> pdb=" O ALA B1338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B1527 " --> pdb=" O ILE B1542 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU B1544 " --> pdb=" O PHE B1525 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE B1525 " --> pdb=" O GLU B1544 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYS B1546 " --> pdb=" O ASN B1523 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN B1523 " --> pdb=" O LYS B1546 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1359 through 1361 Processing sheet with id=AD6, first strand: chain 'B' and resid 1401 through 1402 Processing sheet with id=AD7, first strand: chain 'B' and resid 1626 through 1633 removed outlier: 6.347A pdb=" N PHE B1627 " --> pdb=" O ARG B1586 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG B1586 " --> pdb=" O PHE B1627 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN B1784 " --> pdb=" O VAL B1585 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA B1587 " --> pdb=" O LYS B1782 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS B1782 " --> pdb=" O ALA B1587 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B1770 " --> pdb=" O GLN B1780 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS B1782 " --> pdb=" O ARG B1768 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B1768 " --> pdb=" O LYS B1782 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN B1784 " --> pdb=" O GLU B1766 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1766 " --> pdb=" O GLN B1784 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1610 through 1613 removed outlier: 6.863A pdb=" N ASP B1649 " --> pdb=" O LYS B1658 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS B1658 " --> pdb=" O ASP B1649 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1721 through 1723 removed outlier: 3.650A pdb=" N VAL B1721 " --> pdb=" O TYR B1728 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1869 through 1875 removed outlier: 4.307A pdb=" N TRP B1869 " --> pdb=" O ILE B1817 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1877 through 1878 565 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.41 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5201 1.32 - 1.44: 7370 1.44 - 1.57: 16409 1.57 - 1.69: 0 1.69 - 1.82: 216 Bond restraints: 29196 Sorted by residual: bond pdb=" CG ASP A1600 " pdb=" OD1 ASP A1600 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.60e+00 bond pdb=" CG ASP B1147 " pdb=" OD2 ASP B1147 " ideal model delta sigma weight residual 1.249 1.194 0.055 1.90e-02 2.77e+03 8.47e+00 bond pdb=" N PRO B1327 " pdb=" CA PRO B1327 " ideal model delta sigma weight residual 1.466 1.432 0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" NE ARG A 230 " pdb=" CZ ARG A 230 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.10e-02 8.26e+03 7.85e+00 bond pdb=" NE ARG B1151 " pdb=" CZ ARG B1151 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.10e-02 8.26e+03 7.72e+00 ... (remaining 29191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 34854 1.68 - 3.37: 3840 3.37 - 5.05: 427 5.05 - 6.73: 309 6.73 - 8.41: 158 Bond angle restraints: 39588 Sorted by residual: angle pdb=" C PRO B1310 " pdb=" N PRO B1311 " pdb=" CA PRO B1311 " ideal model delta sigma weight residual 119.66 126.77 -7.11 7.20e-01 1.93e+00 9.76e+01 angle pdb=" C MET B1562 " pdb=" N PRO B1563 " pdb=" CA PRO B1563 " ideal model delta sigma weight residual 119.66 126.74 -7.08 7.30e-01 1.88e+00 9.39e+01 angle pdb=" C TYR B1309 " pdb=" N PRO B1310 " pdb=" CA PRO B1310 " ideal model delta sigma weight residual 119.66 126.09 -6.43 7.20e-01 1.93e+00 7.97e+01 angle pdb=" C GLN B1220 " pdb=" N PRO B1221 " pdb=" CA PRO B1221 " ideal model delta sigma weight residual 119.66 125.82 -6.16 7.20e-01 1.93e+00 7.32e+01 angle pdb=" C ASN A1377 " pdb=" N PRO A1378 " pdb=" CA PRO A1378 " ideal model delta sigma weight residual 119.82 128.17 -8.35 9.80e-01 1.04e+00 7.25e+01 ... (remaining 39583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16817 17.85 - 35.70: 584 35.70 - 53.55: 108 53.55 - 71.40: 68 71.40 - 89.25: 47 Dihedral angle restraints: 17624 sinusoidal: 7362 harmonic: 10262 Sorted by residual: dihedral pdb=" CA ILE B1902 " pdb=" C ILE B1902 " pdb=" N PRO B1903 " pdb=" CA PRO B1903 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ARG B 370 " pdb=" C ARG B 370 " pdb=" N PRO B 371 " pdb=" CA PRO B 371 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE B 452 " pdb=" C PHE B 452 " pdb=" N PRO B 453 " pdb=" CA PRO B 453 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 17621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2612 0.045 - 0.090: 1054 0.090 - 0.135: 436 0.135 - 0.180: 98 0.180 - 0.225: 6 Chirality restraints: 4206 Sorted by residual: chirality pdb=" CA ILE A1142 " pdb=" N ILE A1142 " pdb=" C ILE A1142 " pdb=" CB ILE A1142 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU A1752 " pdb=" CB LEU A1752 " pdb=" CD1 LEU A1752 " pdb=" CD2 LEU A1752 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA ALA A1338 " pdb=" N ALA A1338 " pdb=" C ALA A1338 " pdb=" CB ALA A1338 " both_signs ideal model delta sigma weight residual False 2.48 2.67 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 4203 not shown) Planarity restraints: 5176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1583 " -0.028 2.00e-02 2.50e+03 1.51e-02 4.56e+00 pdb=" CG TYR A1583 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A1583 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A1583 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A1583 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A1583 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A1583 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1583 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1477 " -0.027 2.00e-02 2.50e+03 1.33e-02 4.42e+00 pdb=" CG TRP A1477 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A1477 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1477 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A1477 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A1477 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A1477 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1477 " -0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1477 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1477 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1650 " 0.026 2.00e-02 2.50e+03 1.42e-02 4.05e+00 pdb=" CG TYR B1650 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B1650 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B1650 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B1650 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B1650 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B1650 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B1650 " 0.023 2.00e-02 2.50e+03 ... (remaining 5173 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4382 2.76 - 3.29: 27417 3.29 - 3.83: 49398 3.83 - 4.36: 61286 4.36 - 4.90: 98055 Nonbonded interactions: 240538 Sorted by model distance: nonbonded pdb=" OG SER B 431 " pdb=" OE1 GLN B 444 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLN B1508 " pdb=" OG1 THR B1662 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU B 491 " pdb=" CD1 PHE B 514 " model vdw 2.287 3.340 nonbonded pdb=" OE1 GLU B1227 " pdb=" OH TYR B1229 " model vdw 2.303 3.040 nonbonded pdb=" O ASP B1876 " pdb=" OG1 THR B1885 " model vdw 2.317 3.040 ... (remaining 240533 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 11.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 66.090 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 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 : 0.012 0.070 29196 Z= 0.632 Angle : 1.266 8.413 39588 Z= 0.892 Chirality : 0.057 0.225 4206 Planarity : 0.004 0.019 5176 Dihedral : 11.852 89.251 11004 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.64 % Rotamer: Outliers : 0.13 % Allowed : 1.29 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3516 helix: -2.18 (0.19), residues: 441 sheet: 0.49 (0.17), residues: 844 loop : 0.74 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1477 HIS 0.004 0.001 HIS A 380 PHE 0.016 0.002 PHE B 419 TYR 0.028 0.003 TYR A1583 ARG 0.003 0.000 ARG A1093 Details of bonding type rmsd hydrogen bonds : bond 0.22643 ( 565) hydrogen bonds : angle 9.19858 ( 1356) covalent geometry : bond 0.01156 (29196) covalent geometry : angle 1.26625 (39588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: -0.2814 (mmm) cc_final: -0.3018 (ttt) REVERT: A 557 LEU cc_start: 0.8610 (tp) cc_final: 0.8390 (tp) REVERT: A 626 MET cc_start: 0.7959 (mtp) cc_final: 0.7736 (mtp) REVERT: A 1390 MET cc_start: 0.4845 (mmm) cc_final: 0.4614 (mmp) REVERT: A 1987 MET cc_start: -0.1868 (OUTLIER) cc_final: -0.3160 (ptm) outliers start: 4 outliers final: 0 residues processed: 66 average time/residue: 0.2990 time to fit residues: 29.8738 Evaluate side-chains 49 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 3.9990 chunk 266 optimal weight: 0.0870 chunk 148 optimal weight: 20.0000 chunk 91 optimal weight: 0.4980 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN A1183 HIS A1724 GLN A1753 HIS A1758 GLN A1930 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.061834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.043363 restraints weight = 208046.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.042908 restraints weight = 218842.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.042625 restraints weight = 214789.495| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 1.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29196 Z= 0.141 Angle : 0.649 8.103 39588 Z= 0.361 Chirality : 0.045 0.214 4206 Planarity : 0.005 0.081 5176 Dihedral : 5.216 23.929 3856 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % Rotamer: Outliers : 0.13 % Allowed : 1.10 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3516 helix: -0.71 (0.24), residues: 428 sheet: 0.51 (0.17), residues: 874 loop : 0.24 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 442 HIS 0.005 0.001 HIS A 380 PHE 0.024 0.002 PHE B 835 TYR 0.037 0.002 TYR A1014 ARG 0.008 0.001 ARG B1581 Details of bonding type rmsd hydrogen bonds : bond 0.07010 ( 565) hydrogen bonds : angle 7.38483 ( 1356) covalent geometry : bond 0.00286 (29196) covalent geometry : angle 0.64933 (39588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.6828 (tmm) cc_final: 0.5956 (ptm) REVERT: A 482 MET cc_start: 0.6506 (mpp) cc_final: 0.6209 (mpp) REVERT: A 848 MET cc_start: 0.8245 (mpp) cc_final: 0.8034 (mpp) REVERT: A 1053 MET cc_start: 0.7486 (mtt) cc_final: 0.6971 (mtm) REVERT: A 1158 MET cc_start: 0.9655 (mpp) cc_final: 0.9404 (mpp) REVERT: A 1390 MET cc_start: 0.5263 (mmm) cc_final: 0.4948 (mmp) REVERT: A 1722 MET cc_start: 0.2667 (mmp) cc_final: 0.1145 (ttm) REVERT: A 1987 MET cc_start: -0.1995 (pmm) cc_final: -0.2536 (ptt) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.3207 time to fit residues: 29.3298 Evaluate side-chains 50 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 39 optimal weight: 7.9990 chunk 289 optimal weight: 0.0060 chunk 115 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 149 optimal weight: 0.2980 chunk 193 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 129 optimal weight: 3.9990 chunk 282 optimal weight: 0.2980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 HIS A1913 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.061829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.040639 restraints weight = 208468.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.040726 restraints weight = 202367.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.040771 restraints weight = 188267.517| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 1.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29196 Z= 0.114 Angle : 0.558 7.203 39588 Z= 0.311 Chirality : 0.042 0.196 4206 Planarity : 0.004 0.053 5176 Dihedral : 4.727 27.038 3856 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.06 % Allowed : 1.03 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3516 helix: -0.48 (0.24), residues: 444 sheet: 0.50 (0.18), residues: 862 loop : 0.10 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 442 HIS 0.004 0.001 HIS B 746 PHE 0.017 0.001 PHE B1873 TYR 0.029 0.001 TYR A1014 ARG 0.005 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05906 ( 565) hydrogen bonds : angle 6.81169 ( 1356) covalent geometry : bond 0.00229 (29196) covalent geometry : angle 0.55813 (39588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.6455 (tmm) cc_final: 0.5729 (ptm) REVERT: A 626 MET cc_start: 0.6593 (mtt) cc_final: 0.6335 (mtp) REVERT: A 1053 MET cc_start: 0.7707 (mtt) cc_final: 0.7210 (mtm) REVERT: A 1158 MET cc_start: 0.9682 (mpp) cc_final: 0.9428 (mpp) REVERT: A 1390 MET cc_start: 0.4978 (mmm) cc_final: 0.4687 (mmp) REVERT: A 1630 MET cc_start: 0.5698 (tpt) cc_final: 0.5370 (mtt) REVERT: A 1722 MET cc_start: 0.2287 (mmp) cc_final: 0.0847 (ttm) REVERT: A 1987 MET cc_start: -0.1974 (pmm) cc_final: -0.2435 (ptt) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2932 time to fit residues: 26.2412 Evaluate side-chains 45 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 259 optimal weight: 7.9990 chunk 266 optimal weight: 0.0270 chunk 80 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 269 optimal weight: 0.7980 chunk 323 optimal weight: 10.0000 chunk 267 optimal weight: 0.0010 chunk 98 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 300 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 overall best weight: 0.9648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.061741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.040225 restraints weight = 207832.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.040225 restraints weight = 198093.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.040225 restraints weight = 198093.917| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 1.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29196 Z= 0.107 Angle : 0.542 9.469 39588 Z= 0.298 Chirality : 0.042 0.176 4206 Planarity : 0.004 0.047 5176 Dihedral : 4.518 24.387 3856 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.06 % Allowed : 1.23 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3516 helix: -0.29 (0.24), residues: 448 sheet: 0.43 (0.18), residues: 856 loop : 0.06 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1786 HIS 0.004 0.001 HIS B 746 PHE 0.019 0.001 PHE B1812 TYR 0.031 0.001 TYR A1014 ARG 0.005 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 565) hydrogen bonds : angle 6.65003 ( 1356) covalent geometry : bond 0.00216 (29196) covalent geometry : angle 0.54249 (39588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.6419 (mtt) cc_final: 0.6199 (mtp) REVERT: A 1053 MET cc_start: 0.7759 (mtt) cc_final: 0.7311 (mtm) REVERT: A 1098 MET cc_start: 0.6051 (mpp) cc_final: 0.5805 (mpp) REVERT: A 1158 MET cc_start: 0.9705 (mpp) cc_final: 0.9445 (mpp) REVERT: A 1390 MET cc_start: 0.5085 (mmm) cc_final: 0.4795 (mmp) REVERT: A 1722 MET cc_start: 0.2269 (mmp) cc_final: 0.0723 (ttm) REVERT: A 1987 MET cc_start: -0.1500 (pmm) cc_final: -0.2179 (ptt) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.2745 time to fit residues: 22.8862 Evaluate side-chains 46 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 203 optimal weight: 0.0060 chunk 324 optimal weight: 10.0000 chunk 275 optimal weight: 0.0370 chunk 39 optimal weight: 0.6980 chunk 168 optimal weight: 0.0020 chunk 318 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 130 optimal weight: 0.3980 chunk 210 optimal weight: 0.9980 overall best weight: 0.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.062005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.041324 restraints weight = 207436.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.041440 restraints weight = 190962.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.041440 restraints weight = 175442.041| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 1.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29196 Z= 0.103 Angle : 0.528 8.463 39588 Z= 0.289 Chirality : 0.042 0.196 4206 Planarity : 0.004 0.063 5176 Dihedral : 4.358 23.490 3856 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3516 helix: -0.27 (0.24), residues: 458 sheet: 0.48 (0.18), residues: 834 loop : 0.07 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1786 HIS 0.004 0.001 HIS B 746 PHE 0.018 0.001 PHE B1812 TYR 0.019 0.001 TYR B1014 ARG 0.014 0.000 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 565) hydrogen bonds : angle 6.42427 ( 1356) covalent geometry : bond 0.00205 (29196) covalent geometry : angle 0.52761 (39588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: -0.1886 (ttt) cc_final: -0.2299 (tpt) REVERT: A 557 LEU cc_start: 0.8250 (tp) cc_final: 0.8046 (tp) REVERT: A 603 MET cc_start: 0.9554 (ptm) cc_final: 0.9241 (ptm) REVERT: A 626 MET cc_start: 0.6761 (mtt) cc_final: 0.6522 (mtp) REVERT: A 848 MET cc_start: 0.8499 (mpp) cc_final: 0.8190 (mpp) REVERT: A 1053 MET cc_start: 0.7143 (mtt) cc_final: 0.6682 (mtm) REVERT: A 1098 MET cc_start: 0.5988 (mpp) cc_final: 0.5749 (mpp) REVERT: A 1158 MET cc_start: 0.9690 (mpp) cc_final: 0.9429 (mpp) REVERT: A 1344 MET cc_start: 0.7178 (mpp) cc_final: 0.6955 (mmm) REVERT: A 1390 MET cc_start: 0.4989 (mmm) cc_final: 0.4698 (mmp) REVERT: A 1722 MET cc_start: 0.2174 (mmp) cc_final: 0.0769 (ttm) REVERT: A 1987 MET cc_start: -0.0516 (pmm) cc_final: -0.1227 (ptt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2813 time to fit residues: 23.7044 Evaluate side-chains 47 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 218 optimal weight: 0.0980 chunk 348 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 284 optimal weight: 0.5980 chunk 142 optimal weight: 0.0050 chunk 88 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 0.3980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN A1962 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.062102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.043576 restraints weight = 207709.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.043043 restraints weight = 218595.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.042712 restraints weight = 215939.569| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 1.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29196 Z= 0.098 Angle : 0.512 7.662 39588 Z= 0.281 Chirality : 0.041 0.170 4206 Planarity : 0.004 0.047 5176 Dihedral : 4.216 21.085 3856 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3516 helix: -0.01 (0.25), residues: 446 sheet: 0.48 (0.18), residues: 832 loop : 0.04 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1478 HIS 0.004 0.001 HIS B 746 PHE 0.020 0.001 PHE B1812 TYR 0.011 0.001 TYR B1014 ARG 0.006 0.000 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 565) hydrogen bonds : angle 6.22533 ( 1356) covalent geometry : bond 0.00196 (29196) covalent geometry : angle 0.51227 (39588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.6169 (mmp) cc_final: 0.5897 (ttp) REVERT: A 428 MET cc_start: 0.7166 (tpt) cc_final: 0.6701 (tpp) REVERT: A 557 LEU cc_start: 0.7964 (tp) cc_final: 0.7597 (tp) REVERT: A 1053 MET cc_start: -0.2656 (mtt) cc_final: -0.2856 (mtm) REVERT: A 1098 MET cc_start: 0.7356 (mpp) cc_final: 0.6889 (mpp) REVERT: A 1344 MET cc_start: 0.5225 (mpp) cc_final: 0.4761 (mmm) REVERT: A 1722 MET cc_start: 0.3590 (mmp) cc_final: 0.1240 (ttp) REVERT: A 1987 MET cc_start: -0.0774 (pmm) cc_final: -0.1276 (ptt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2718 time to fit residues: 23.6888 Evaluate side-chains 48 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 330 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 252 optimal weight: 0.0170 chunk 339 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 315 optimal weight: 9.9990 chunk 4 optimal weight: 0.0170 chunk 283 optimal weight: 3.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.061855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.040632 restraints weight = 208458.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.040632 restraints weight = 191439.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.040632 restraints weight = 191439.769| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 1.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29196 Z= 0.097 Angle : 0.503 8.089 39588 Z= 0.276 Chirality : 0.041 0.186 4206 Planarity : 0.004 0.045 5176 Dihedral : 4.129 19.900 3856 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3516 helix: 0.07 (0.25), residues: 446 sheet: 0.40 (0.18), residues: 828 loop : 0.10 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1478 HIS 0.004 0.001 HIS B 746 PHE 0.018 0.001 PHE A1812 TYR 0.012 0.001 TYR B1014 ARG 0.005 0.000 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 565) hydrogen bonds : angle 6.15343 ( 1356) covalent geometry : bond 0.00197 (29196) covalent geometry : angle 0.50285 (39588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 LEU cc_start: 0.8294 (tp) cc_final: 0.8068 (tp) REVERT: A 1053 MET cc_start: 0.7462 (mtt) cc_final: 0.7079 (mtt) REVERT: A 1098 MET cc_start: 0.6144 (mpp) cc_final: 0.5891 (mpp) REVERT: A 1158 MET cc_start: 0.9727 (mpp) cc_final: 0.9447 (mpp) REVERT: A 1344 MET cc_start: 0.7249 (mpp) cc_final: 0.6954 (mmm) REVERT: A 1390 MET cc_start: 0.4680 (mmp) cc_final: 0.4406 (mmm) REVERT: A 1630 MET cc_start: 0.3479 (tpt) cc_final: 0.3108 (mtt) REVERT: A 1722 MET cc_start: 0.2176 (mmp) cc_final: 0.0852 (ttp) REVERT: A 1987 MET cc_start: -0.1064 (pmm) cc_final: -0.1536 (ptt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2817 time to fit residues: 24.9326 Evaluate side-chains 47 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 135 optimal weight: 0.0010 chunk 273 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 313 optimal weight: 0.1980 chunk 324 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 307 optimal weight: 0.0370 chunk 344 optimal weight: 0.0000 chunk 272 optimal weight: 0.7980 overall best weight: 0.0566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.056138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.052695 restraints weight = 267519.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.052032 restraints weight = 731762.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.051642 restraints weight = 869056.945| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4460 moved from start: 1.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29196 Z= 0.097 Angle : 0.510 10.596 39588 Z= 0.278 Chirality : 0.041 0.192 4206 Planarity : 0.004 0.082 5176 Dihedral : 4.108 19.329 3856 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3516 helix: 0.14 (0.25), residues: 446 sheet: 0.42 (0.18), residues: 830 loop : 0.09 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1478 HIS 0.004 0.000 HIS B 746 PHE 0.021 0.001 PHE A1812 TYR 0.013 0.001 TYR B 806 ARG 0.004 0.000 ARG B1814 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 565) hydrogen bonds : angle 6.08216 ( 1356) covalent geometry : bond 0.00194 (29196) covalent geometry : angle 0.51011 (39588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.4766 (ppp) cc_final: 0.4240 (ppp) REVERT: A 428 MET cc_start: 0.6385 (tpt) cc_final: 0.5743 (tpp) REVERT: A 557 LEU cc_start: 0.8337 (tp) cc_final: 0.7957 (tp) REVERT: A 848 MET cc_start: 0.7818 (mpp) cc_final: 0.7525 (mpp) REVERT: A 1053 MET cc_start: -0.2001 (mtt) cc_final: -0.2289 (mtm) REVERT: A 1098 MET cc_start: 0.7494 (mpp) cc_final: 0.7008 (mpp) REVERT: A 1158 MET cc_start: 0.9042 (mpp) cc_final: 0.8716 (mpp) REVERT: A 1240 MET cc_start: 0.9592 (mmp) cc_final: 0.9380 (mmm) REVERT: A 1344 MET cc_start: 0.4200 (mpp) cc_final: 0.3703 (mmm) REVERT: A 1390 MET cc_start: 0.4589 (mmp) cc_final: 0.4056 (mmm) REVERT: A 1630 MET cc_start: 0.2637 (tpt) cc_final: -0.0670 (mtt) REVERT: A 1722 MET cc_start: 0.4540 (mmp) cc_final: 0.0314 (ttm) REVERT: A 1835 MET cc_start: 0.0005 (ptm) cc_final: -0.0304 (ptm) REVERT: A 1987 MET cc_start: -0.0169 (pmm) cc_final: -0.1207 (ptt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2836 time to fit residues: 24.9285 Evaluate side-chains 48 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 220 optimal weight: 8.9990 chunk 299 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 323 optimal weight: 0.9980 chunk 351 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 266 optimal weight: 0.0020 chunk 142 optimal weight: 0.0470 chunk 207 optimal weight: 6.9990 overall best weight: 1.8090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.061645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.040218 restraints weight = 207914.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.040218 restraints weight = 192530.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.040218 restraints weight = 192530.295| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 1.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29196 Z= 0.105 Angle : 0.513 8.863 39588 Z= 0.280 Chirality : 0.041 0.193 4206 Planarity : 0.004 0.073 5176 Dihedral : 4.091 18.760 3856 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3516 helix: 0.20 (0.26), residues: 446 sheet: 0.37 (0.18), residues: 834 loop : 0.09 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1012 HIS 0.005 0.001 HIS A 471 PHE 0.018 0.001 PHE A1812 TYR 0.023 0.001 TYR A1583 ARG 0.007 0.000 ARG B1041 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 565) hydrogen bonds : angle 6.04513 ( 1356) covalent geometry : bond 0.00217 (29196) covalent geometry : angle 0.51259 (39588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.5710 (ppp) cc_final: 0.5059 (ppp) REVERT: A 848 MET cc_start: 0.8680 (mpp) cc_final: 0.8222 (mpp) REVERT: A 1053 MET cc_start: 0.7492 (mtt) cc_final: 0.6607 (mtm) REVERT: A 1098 MET cc_start: 0.6318 (mpp) cc_final: 0.6088 (mpp) REVERT: A 1158 MET cc_start: 0.9740 (mpp) cc_final: 0.9460 (mpp) REVERT: A 1344 MET cc_start: 0.7200 (mpp) cc_final: 0.6916 (mmm) REVERT: A 1630 MET cc_start: 0.2903 (tpt) cc_final: 0.2582 (mtt) REVERT: A 1722 MET cc_start: 0.2037 (mmp) cc_final: 0.0554 (ttm) REVERT: A 1987 MET cc_start: -0.1031 (pmm) cc_final: -0.1503 (ptt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2938 time to fit residues: 26.1648 Evaluate side-chains 49 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 217 optimal weight: 3.9990 chunk 339 optimal weight: 0.4980 chunk 95 optimal weight: 0.4980 chunk 2 optimal weight: 0.0970 chunk 322 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 309 optimal weight: 0.0170 chunk 218 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.056649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.043711 restraints weight = 256963.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.042877 restraints weight = 257188.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.042912 restraints weight = 232951.247| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5140 moved from start: 1.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29196 Z= 0.094 Angle : 0.509 10.505 39588 Z= 0.276 Chirality : 0.041 0.197 4206 Planarity : 0.004 0.069 5176 Dihedral : 4.046 19.265 3856 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3516 helix: 0.21 (0.25), residues: 456 sheet: 0.42 (0.18), residues: 832 loop : 0.01 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 442 HIS 0.004 0.001 HIS B 746 PHE 0.020 0.001 PHE B1812 TYR 0.012 0.001 TYR A 838 ARG 0.004 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 565) hydrogen bonds : angle 5.96627 ( 1356) covalent geometry : bond 0.00186 (29196) covalent geometry : angle 0.50928 (39588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.6519 (mmp) cc_final: 0.5841 (mpp) REVERT: A 394 MET cc_start: 0.3610 (ppp) cc_final: 0.3337 (ppp) REVERT: A 428 MET cc_start: 0.4814 (tpt) cc_final: 0.4424 (tpp) REVERT: A 1098 MET cc_start: 0.7796 (mpp) cc_final: 0.7339 (mpp) REVERT: A 1344 MET cc_start: 0.4179 (mpp) cc_final: 0.3645 (mmm) REVERT: A 1390 MET cc_start: 0.4057 (mmp) cc_final: 0.3711 (mmm) REVERT: A 1630 MET cc_start: 0.3048 (tpt) cc_final: 0.1445 (mtt) REVERT: A 1722 MET cc_start: 0.4849 (mmp) cc_final: 0.0428 (ttm) REVERT: A 1987 MET cc_start: -0.0514 (pmm) cc_final: -0.1014 (ptt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3014 time to fit residues: 27.1821 Evaluate side-chains 47 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 223 optimal weight: 9.9990 chunk 330 optimal weight: 0.0980 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 254 optimal weight: 7.9990 chunk 184 optimal weight: 0.0770 chunk 52 optimal weight: 0.0570 chunk 45 optimal weight: 8.9990 chunk 181 optimal weight: 0.0670 chunk 318 optimal weight: 8.9990 chunk 322 optimal weight: 9.9990 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.062376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.041631 restraints weight = 206226.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.041109 restraints weight = 191260.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.041320 restraints weight = 180932.294| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 1.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29196 Z= 0.092 Angle : 0.501 7.962 39588 Z= 0.272 Chirality : 0.041 0.195 4206 Planarity : 0.004 0.066 5176 Dihedral : 3.930 19.065 3856 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3516 helix: 0.47 (0.26), residues: 448 sheet: 0.47 (0.18), residues: 818 loop : -0.01 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1786 HIS 0.005 0.001 HIS A 471 PHE 0.020 0.001 PHE A1812 TYR 0.010 0.001 TYR A1583 ARG 0.007 0.000 ARG B1048 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 565) hydrogen bonds : angle 5.85124 ( 1356) covalent geometry : bond 0.00181 (29196) covalent geometry : angle 0.50121 (39588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8115.89 seconds wall clock time: 143 minutes 23.38 seconds (8603.38 seconds total)