Starting phenix.real_space_refine on Mon Aug 25 15:33:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8l_44349/08_2025/9b8l_44349.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8l_44349/08_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_44349/08_2025/9b8l_44349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8l_44349/08_2025/9b8l_44349.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8l_44349/08_2025/9b8l_44349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8l_44349/08_2025/9b8l_44349.cif" } resolution = 4.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'GLN:plan1': 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: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.49, per 1000 atoms: 0.19 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: 1.72 Conformation dependent library (CDL) restraints added in 869.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.07 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: 5.78 Time building geometry restraints manager: 2.24 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: 0.03 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: 12.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.570 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.030 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (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 ARG 0.003 0.000 ARG A1093 TYR 0.028 0.003 TYR A1583 PHE 0.016 0.002 PHE B 419 TRP 0.027 0.003 TRP A1477 HIS 0.004 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.01156 (29196) covalent geometry : angle 1.26625 (39588) hydrogen bonds : bond 0.22643 ( 565) hydrogen bonds : angle 9.19858 ( 1356) *********************** 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 : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: -0.2814 (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: 0.1110 time to fit residues: 10.9839 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 9.9990 overall best weight: 0.1276 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.061944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.041541 restraints weight = 208378.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.040545 restraints weight = 197432.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.040730 restraints weight = 183984.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.040829 restraints weight = 175045.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.040829 restraints weight = 165738.734| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 1.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29196 Z= 0.142 Angle : 0.645 7.060 39588 Z= 0.360 Chirality : 0.045 0.201 4206 Planarity : 0.005 0.072 5176 Dihedral : 5.175 24.937 3856 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 0.06 % Allowed : 1.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.14), residues: 3516 helix: -0.69 (0.24), residues: 426 sheet: 0.51 (0.17), residues: 878 loop : 0.25 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1581 TYR 0.032 0.002 TYR A1014 PHE 0.022 0.002 PHE B 835 TRP 0.020 0.002 TRP B 442 HIS 0.005 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00288 (29196) covalent geometry : angle 0.64536 (39588) hydrogen bonds : bond 0.07270 ( 565) hydrogen bonds : angle 7.38613 ( 1356) *********************** 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: 1 poor density : 60 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.6728 (tmm) cc_final: 0.5876 (ptm) REVERT: A 482 MET cc_start: 0.6429 (mpp) cc_final: 0.6114 (mpp) REVERT: A 1053 MET cc_start: 0.7683 (mtt) cc_final: 0.7376 (mtm) REVERT: A 1158 MET cc_start: 0.9649 (mpp) cc_final: 0.9390 (mpp) REVERT: A 1390 MET cc_start: 0.5108 (mmm) cc_final: 0.4789 (mmp) REVERT: A 1722 MET cc_start: 0.2634 (mmp) cc_final: 0.0948 (ttm) REVERT: A 1987 MET cc_start: -0.1992 (pmm) cc_final: -0.2543 (ptt) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.1307 time to fit residues: 11.5154 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 193 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 344 optimal weight: 0.0370 chunk 200 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 166 optimal weight: 0.1980 chunk 136 optimal weight: 0.0470 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.057646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.051901 restraints weight = 242758.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.043982 restraints weight = 766140.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.042712 restraints weight = 900342.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.042260 restraints weight = 945929.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.042209 restraints weight = 1002170.952| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 1.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29196 Z= 0.114 Angle : 0.560 7.245 39588 Z= 0.311 Chirality : 0.042 0.199 4206 Planarity : 0.004 0.052 5176 Dihedral : 4.696 26.530 3856 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3516 helix: -0.47 (0.24), residues: 444 sheet: 0.48 (0.18), residues: 852 loop : 0.13 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1048 TYR 0.030 0.001 TYR B1014 PHE 0.021 0.001 PHE A 835 TRP 0.016 0.001 TRP A 442 HIS 0.004 0.001 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00227 (29196) covalent geometry : angle 0.55955 (39588) hydrogen bonds : bond 0.05869 ( 565) hydrogen bonds : angle 6.78937 ( 1356) *********************** 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 : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.6989 (tmm) cc_final: 0.6401 (ptm) REVERT: A 428 MET cc_start: 0.8038 (tpt) cc_final: 0.7106 (tpp) REVERT: A 455 MET cc_start: 0.7751 (mmm) cc_final: 0.6634 (ttt) REVERT: A 557 LEU cc_start: 0.8123 (tp) cc_final: 0.7839 (tp) REVERT: A 603 MET cc_start: 0.9342 (ptm) cc_final: 0.9036 (ptp) REVERT: A 848 MET cc_start: 0.8402 (mpp) cc_final: 0.8075 (mpp) REVERT: A 1053 MET cc_start: 0.3918 (mtt) cc_final: 0.3029 (mtm) REVERT: A 1128 MET cc_start: 0.3756 (mtm) cc_final: 0.3419 (ptp) REVERT: A 1158 MET cc_start: 0.9408 (mpp) cc_final: 0.9086 (mpp) REVERT: A 1390 MET cc_start: 0.5073 (mmm) cc_final: 0.4633 (mmp) REVERT: A 1630 MET cc_start: 0.4867 (tpt) cc_final: 0.3021 (mtt) REVERT: A 1722 MET cc_start: 0.3835 (mmp) cc_final: 0.0942 (ttm) REVERT: A 1987 MET cc_start: -0.1775 (pmm) cc_final: -0.2208 (ptt) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1251 time to fit residues: 10.7486 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 : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 306 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 296 optimal weight: 0.0980 chunk 26 optimal weight: 0.0060 chunk 235 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 310 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.056111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.052354 restraints weight = 277196.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.051441 restraints weight = 639844.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.051058 restraints weight = 845258.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.050909 restraints weight = 819830.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.050728 restraints weight = 730629.414| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4823 moved from start: 1.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29196 Z= 0.105 Angle : 0.538 8.101 39588 Z= 0.297 Chirality : 0.042 0.175 4206 Planarity : 0.004 0.048 5176 Dihedral : 4.500 24.448 3856 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.14), residues: 3516 helix: -0.30 (0.24), residues: 448 sheet: 0.53 (0.18), residues: 836 loop : 0.11 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1048 TYR 0.026 0.001 TYR A1014 PHE 0.020 0.001 PHE B1812 TRP 0.013 0.001 TRP B 442 HIS 0.004 0.001 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00212 (29196) covalent geometry : angle 0.53837 (39588) hydrogen bonds : bond 0.05185 ( 565) hydrogen bonds : angle 6.59633 ( 1356) *********************** 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 54 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.7698 (tpt) cc_final: 0.6715 (tpp) REVERT: A 603 MET cc_start: 0.9423 (ptm) cc_final: 0.9155 (ptp) REVERT: A 848 MET cc_start: 0.8316 (mpp) cc_final: 0.7985 (mpp) REVERT: A 1053 MET cc_start: -0.0208 (mtt) cc_final: -0.0772 (mtm) REVERT: A 1158 MET cc_start: 0.9311 (mpp) cc_final: 0.9005 (mpp) REVERT: A 1240 MET cc_start: 0.9711 (mmp) cc_final: 0.9438 (mmm) REVERT: A 1722 MET cc_start: 0.4244 (mmp) cc_final: 0.0556 (ttm) REVERT: A 1987 MET cc_start: -0.0670 (pmm) cc_final: -0.1794 (ptt) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1151 time to fit residues: 9.5808 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 : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 304 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 230 optimal weight: 0.0010 chunk 288 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 290 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 235 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.056143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.055244 restraints weight = 272000.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.055047 restraints weight = 543153.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.054899 restraints weight = 635435.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.054723 restraints weight = 676585.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.046481 restraints weight = 801987.633| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 1.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29196 Z= 0.100 Angle : 0.519 7.840 39588 Z= 0.285 Chirality : 0.042 0.183 4206 Planarity : 0.004 0.044 5176 Dihedral : 4.282 20.859 3856 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.14), residues: 3516 helix: -0.16 (0.25), residues: 448 sheet: 0.46 (0.18), residues: 834 loop : 0.11 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B1038 TYR 0.012 0.001 TYR B1014 PHE 0.018 0.001 PHE A1812 TRP 0.020 0.001 TRP A1786 HIS 0.004 0.001 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00199 (29196) covalent geometry : angle 0.51890 (39588) hydrogen bonds : bond 0.04669 ( 565) hydrogen bonds : angle 6.38065 ( 1356) *********************** 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 54 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7472 (mmm) cc_final: 0.7149 (mmm) REVERT: A 394 MET cc_start: 0.6504 (tmm) cc_final: 0.5634 (ptm) REVERT: A 428 MET cc_start: 0.7683 (tpp) cc_final: 0.7051 (tpp) REVERT: A 557 LEU cc_start: 0.7941 (tp) cc_final: 0.7611 (tp) REVERT: A 603 MET cc_start: 0.9095 (ptm) cc_final: 0.8808 (ptp) REVERT: A 848 MET cc_start: 0.8400 (mpp) cc_final: 0.8122 (mpp) REVERT: A 1053 MET cc_start: -0.0057 (mtt) cc_final: -0.0478 (mtm) REVERT: A 1098 MET cc_start: 0.7267 (mpp) cc_final: 0.6831 (mpp) REVERT: A 1128 MET cc_start: 0.2634 (mpp) cc_final: 0.2283 (mpp) REVERT: A 1158 MET cc_start: 0.9283 (mpp) cc_final: 0.9009 (mpp) REVERT: A 1344 MET cc_start: 0.3944 (mpp) cc_final: 0.3317 (mmm) REVERT: A 1390 MET cc_start: 0.4532 (mmp) cc_final: 0.3839 (mmm) REVERT: A 1722 MET cc_start: 0.3955 (mmp) cc_final: 0.0637 (ttm) REVERT: A 1932 MET cc_start: 0.5089 (ptp) cc_final: 0.4817 (mtm) REVERT: A 1987 MET cc_start: 0.1595 (pmm) cc_final: 0.1098 (ptt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1036 time to fit residues: 8.6842 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 : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 11 optimal weight: 0.2980 chunk 246 optimal weight: 0.0870 chunk 347 optimal weight: 0.0470 chunk 280 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 261 optimal weight: 0.0870 chunk 338 optimal weight: 20.0000 chunk 287 optimal weight: 6.9990 chunk 265 optimal weight: 0.3980 chunk 164 optimal weight: 7.9990 chunk 268 optimal weight: 0.1980 overall best weight: 0.1434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1913 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.062293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.043639 restraints weight = 206089.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.043091 restraints weight = 214342.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.042889 restraints weight = 212831.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.042933 restraints weight = 199246.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.043005 restraints weight = 185128.978| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 1.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29196 Z= 0.097 Angle : 0.508 7.933 39588 Z= 0.279 Chirality : 0.041 0.177 4206 Planarity : 0.004 0.043 5176 Dihedral : 4.140 18.869 3856 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3516 helix: 0.02 (0.25), residues: 446 sheet: 0.42 (0.18), residues: 824 loop : 0.10 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1038 TYR 0.011 0.001 TYR A1014 PHE 0.019 0.001 PHE A1812 TRP 0.019 0.001 TRP A1786 HIS 0.004 0.000 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00194 (29196) covalent geometry : angle 0.50760 (39588) hydrogen bonds : bond 0.04500 ( 565) hydrogen bonds : angle 6.20832 ( 1356) *********************** 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 54 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 LEU cc_start: 0.8206 (tp) cc_final: 0.7987 (tp) REVERT: A 603 MET cc_start: 0.9503 (ptm) cc_final: 0.9299 (ptp) REVERT: A 1053 MET cc_start: 0.7385 (mtt) cc_final: 0.6986 (mtm) REVERT: A 1098 MET cc_start: 0.5978 (mpp) cc_final: 0.5720 (mpp) REVERT: A 1128 MET cc_start: 0.6463 (mpp) cc_final: 0.6034 (mpp) REVERT: A 1158 MET cc_start: 0.9680 (mpp) cc_final: 0.9410 (mpp) REVERT: A 1344 MET cc_start: 0.7270 (mpp) cc_final: 0.7024 (mmm) REVERT: A 1390 MET cc_start: 0.4861 (mmp) cc_final: 0.4519 (mmm) REVERT: A 1722 MET cc_start: 0.2230 (mmp) cc_final: 0.0859 (ttp) REVERT: A 1987 MET cc_start: -0.1051 (pmm) cc_final: -0.1574 (ptt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1065 time to fit residues: 8.9598 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 : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 350 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 310 optimal weight: 0.0020 chunk 59 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 262 optimal weight: 0.0010 chunk 121 optimal weight: 10.0000 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.056252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.055333 restraints weight = 270833.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.055148 restraints weight = 537077.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.054994 restraints weight = 611562.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.054895 restraints weight = 661992.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.054811 restraints weight = 680326.101| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3766 moved from start: 1.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29196 Z= 0.095 Angle : 0.504 7.999 39588 Z= 0.276 Chirality : 0.041 0.173 4206 Planarity : 0.004 0.041 5176 Dihedral : 4.068 18.627 3856 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.14), residues: 3516 helix: 0.14 (0.26), residues: 446 sheet: 0.36 (0.18), residues: 856 loop : 0.15 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 370 TYR 0.016 0.001 TYR B1014 PHE 0.019 0.001 PHE A1812 TRP 0.019 0.001 TRP B1786 HIS 0.004 0.000 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00189 (29196) covalent geometry : angle 0.50432 (39588) hydrogen bonds : bond 0.04264 ( 565) hydrogen bonds : angle 6.11357 ( 1356) *********************** 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 56 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.5914 (tpt) cc_final: 0.4186 (tmm) REVERT: A 557 LEU cc_start: 0.7701 (tp) cc_final: 0.7301 (tp) REVERT: A 603 MET cc_start: 0.9010 (ptm) cc_final: 0.8724 (ptp) REVERT: A 1053 MET cc_start: -0.1795 (mtt) cc_final: -0.2326 (mtm) REVERT: A 1098 MET cc_start: 0.7448 (mpp) cc_final: 0.6917 (mpp) REVERT: A 1344 MET cc_start: 0.4074 (mpp) cc_final: 0.3527 (mmm) REVERT: A 1390 MET cc_start: 0.4751 (mmp) cc_final: 0.4396 (mmp) REVERT: A 1630 MET cc_start: 0.2166 (tpt) cc_final: -0.1259 (mtt) REVERT: A 1722 MET cc_start: 0.4295 (mmp) cc_final: -0.0045 (ttp) REVERT: A 1987 MET cc_start: 0.0040 (pmm) cc_final: -0.1388 (ptt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1101 time to fit residues: 9.3487 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 65 optimal weight: 0.6980 chunk 186 optimal weight: 0.3980 chunk 328 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 chunk 98 optimal weight: 0.0570 chunk 64 optimal weight: 0.0970 chunk 35 optimal weight: 0.1980 chunk 265 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 212 optimal weight: 0.8980 overall best weight: 0.1696 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.062471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.041442 restraints weight = 205127.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.041394 restraints weight = 193763.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.041502 restraints weight = 183530.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.041795 restraints weight = 172108.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.042141 restraints weight = 158950.143| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 1.2485 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= 0.096 Angle : 0.506 8.315 39588 Z= 0.276 Chirality : 0.042 0.169 4206 Planarity : 0.004 0.082 5176 Dihedral : 4.056 23.221 3856 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3516 helix: 0.19 (0.26), residues: 444 sheet: 0.43 (0.18), residues: 838 loop : 0.07 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1038 TYR 0.015 0.001 TYR B1583 PHE 0.021 0.001 PHE B1812 TRP 0.014 0.001 TRP B 442 HIS 0.004 0.001 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00191 (29196) covalent geometry : angle 0.50582 (39588) hydrogen bonds : bond 0.04281 ( 565) hydrogen bonds : angle 6.03217 ( 1356) *********************** 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 54 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1053 MET cc_start: 0.6587 (mtt) cc_final: 0.5475 (mtm) REVERT: A 1128 MET cc_start: 0.6061 (mpp) cc_final: 0.5549 (mpp) REVERT: A 1158 MET cc_start: 0.9645 (mpp) cc_final: 0.9322 (mpp) REVERT: A 1344 MET cc_start: 0.6875 (mpp) cc_final: 0.6547 (mmm) REVERT: A 1390 MET cc_start: 0.4612 (mmp) cc_final: 0.4402 (mmp) REVERT: A 1630 MET cc_start: 0.3378 (tpt) cc_final: 0.2912 (mtt) REVERT: A 1722 MET cc_start: 0.2231 (mmp) cc_final: 0.0619 (ttm) REVERT: A 1987 MET cc_start: -0.0820 (pmm) cc_final: -0.1432 (ptt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1020 time to fit residues: 8.5427 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 : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 101 optimal weight: 6.9990 chunk 246 optimal weight: 0.0980 chunk 111 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 178 optimal weight: 0.0970 chunk 171 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 210 optimal weight: 0.0870 chunk 214 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.062434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.044193 restraints weight = 205373.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.043228 restraints weight = 213103.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.042842 restraints weight = 243923.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.042693 restraints weight = 243038.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.042702 restraints weight = 222416.671| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 1.2550 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= 0.093 Angle : 0.502 10.404 39588 Z= 0.273 Chirality : 0.041 0.202 4206 Planarity : 0.004 0.072 5176 Dihedral : 3.988 20.858 3856 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3516 helix: 0.27 (0.25), residues: 450 sheet: 0.35 (0.17), residues: 864 loop : 0.09 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1038 TYR 0.011 0.001 TYR B1583 PHE 0.017 0.001 PHE A1812 TRP 0.013 0.001 TRP A 442 HIS 0.003 0.000 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00186 (29196) covalent geometry : angle 0.50244 (39588) hydrogen bonds : bond 0.04094 ( 565) hydrogen bonds : angle 5.93426 ( 1356) *********************** 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 54 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.6587 (tmm) cc_final: 0.6385 (tmm) REVERT: A 848 MET cc_start: 0.8649 (mpp) cc_final: 0.8167 (mpp) REVERT: A 1053 MET cc_start: 0.7373 (mtt) cc_final: 0.6630 (mtm) REVERT: A 1098 MET cc_start: 0.6036 (mpp) cc_final: 0.5822 (mpp) REVERT: A 1128 MET cc_start: 0.6144 (mpp) cc_final: 0.5688 (mpp) REVERT: A 1158 MET cc_start: 0.9703 (mpp) cc_final: 0.9390 (mpp) REVERT: A 1344 MET cc_start: 0.7365 (mpp) cc_final: 0.7071 (mmm) REVERT: A 1390 MET cc_start: 0.4591 (mmp) cc_final: 0.4384 (mmp) REVERT: A 1630 MET cc_start: 0.3256 (tpt) cc_final: 0.2736 (mtt) REVERT: A 1722 MET cc_start: 0.2247 (mmp) cc_final: 0.0737 (ttm) REVERT: A 1987 MET cc_start: -0.0961 (pmm) cc_final: -0.1423 (ptt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1215 time to fit residues: 10.1822 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 122 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 113 optimal weight: 0.0070 chunk 247 optimal weight: 0.0770 chunk 184 optimal weight: 1.9990 chunk 348 optimal weight: 0.0870 chunk 212 optimal weight: 6.9990 chunk 130 optimal weight: 0.1980 chunk 246 optimal weight: 0.0060 chunk 61 optimal weight: 8.9990 chunk 248 optimal weight: 0.0170 overall best weight: 0.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.056781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.054344 restraints weight = 303900.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.054067 restraints weight = 807436.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.053964 restraints weight = 932609.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.048286 restraints weight = 804875.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.046882 restraints weight = 1348731.142| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 1.2696 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= 0.092 Angle : 0.506 9.058 39588 Z= 0.273 Chirality : 0.041 0.199 4206 Planarity : 0.004 0.067 5176 Dihedral : 3.913 19.337 3856 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.14), residues: 3516 helix: 0.41 (0.26), residues: 448 sheet: 0.35 (0.18), residues: 866 loop : 0.08 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1038 TYR 0.010 0.001 TYR B1014 PHE 0.018 0.001 PHE A1812 TRP 0.016 0.001 TRP A 442 HIS 0.003 0.001 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00181 (29196) covalent geometry : angle 0.50569 (39588) hydrogen bonds : bond 0.03982 ( 565) hydrogen bonds : angle 5.82134 ( 1356) ********************** 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 54 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.6906 (mmm) cc_final: 0.6493 (mmm) REVERT: A 428 MET cc_start: 0.6640 (tpt) cc_final: 0.4867 (tmm) REVERT: A 848 MET cc_start: 0.8130 (mpp) cc_final: 0.7851 (mpp) REVERT: A 1053 MET cc_start: -0.0952 (mtt) cc_final: -0.1454 (mtm) REVERT: A 1128 MET cc_start: 0.1562 (mpp) cc_final: 0.1312 (mpp) REVERT: A 1344 MET cc_start: 0.4545 (mpp) cc_final: 0.4023 (mmm) REVERT: A 1390 MET cc_start: 0.4416 (mmp) cc_final: 0.4106 (mmp) REVERT: A 1630 MET cc_start: 0.2467 (tpt) cc_final: 0.1036 (mtt) REVERT: A 1722 MET cc_start: 0.4393 (mmp) cc_final: 0.0513 (ttm) REVERT: A 1987 MET cc_start: 0.0118 (pmm) cc_final: -0.0351 (ptt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0964 time to fit residues: 8.4507 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 : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 125 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 343 optimal weight: 3.9990 chunk 339 optimal weight: 0.7980 chunk 312 optimal weight: 0.0770 chunk 117 optimal weight: 3.9990 chunk 181 optimal weight: 0.0870 chunk 276 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 336 optimal weight: 0.9980 chunk 334 optimal weight: 20.0000 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.056593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.054667 restraints weight = 307239.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.053948 restraints weight = 571314.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.053797 restraints weight = 897430.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.053684 restraints weight = 959366.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.053583 restraints weight = 901007.299| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3727 moved from start: 1.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29196 Z= 0.089 Angle : 0.493 7.932 39588 Z= 0.267 Chirality : 0.041 0.191 4206 Planarity : 0.004 0.074 5176 Dihedral : 3.819 18.727 3856 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.14), residues: 3516 helix: 0.49 (0.26), residues: 448 sheet: 0.35 (0.18), residues: 848 loop : 0.09 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1038 TYR 0.009 0.001 TYR A 967 PHE 0.018 0.001 PHE B1812 TRP 0.013 0.001 TRP A 442 HIS 0.003 0.000 HIS B 746 Details of bonding type rmsd covalent geometry : bond 0.00177 (29196) covalent geometry : angle 0.49316 (39588) hydrogen bonds : bond 0.03819 ( 565) hydrogen bonds : angle 5.73044 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3337.83 seconds wall clock time: 58 minutes 48.94 seconds (3528.94 seconds total)