Starting phenix.real_space_refine on Fri Jul 3 11:10:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m1p_23617/07_2026/7m1p_23617.cif" } resolution = 3.6 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= 0.984 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 51 5.16 5 C 8662 2.51 5 N 2322 2.21 5 O 2476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13511 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13340 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1938, 13331 Classifications: {'peptide': 1938} Incomplete info: {'truncation_to_alanine': 579} Link IDs: {'PTRANS': 100, 'TRANS': 1837} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2175 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1789 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 27, 'TRP:plan': 10, 'ARG:plan': 42, 'GLU:plan': 71, 'ASN:plan1': 25, 'HIS:plan': 14, 'PHE:plan': 27, 'ASP:plan': 53, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 1246 Conformer: "B" Number of residues, atoms: 1938, 13331 Classifications: {'peptide': 1938} Incomplete info: {'truncation_to_alanine': 579} Link IDs: {'PTRANS': 100, 'TRANS': 1837} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2175 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1789 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 27, 'TRP:plan': 10, 'ARG:plan': 42, 'GLU:plan': 71, 'ASN:plan1': 25, 'HIS:plan': 14, 'PHE:plan': 27, 'ASP:plan': 53, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 1246 bond proxies already assigned to first conformer: 13615 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.64, per 1000 atoms: 0.42 Number of scatterers: 13511 At special positions: 0 Unit cell: (96.7808, 93.6921, 229.597, 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 51 16.00 O 2476 8.00 N 2322 7.00 C 8662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 504 " " NAG A2303 " - " ASN A1588 " " NAG B 1 " - " ASN A 415 " " NAG C 1 " - " ASN A1529 " " NAG D 1 " - " ASN A1662 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3642 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 10 sheets defined 51.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 removed outlier: 3.871A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 46 removed outlier: 3.539A pdb=" N VAL A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 3.531A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.711A pdb=" N TRP A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.226A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.751A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.179A pdb=" N LEU A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 324 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.599A pdb=" N ASN A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.555A pdb=" N GLU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 439 Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.551A pdb=" N ASP A 443 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 444' Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.637A pdb=" N ASN A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 531 through 542 removed outlier: 3.916A pdb=" N THR A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.787A pdb=" N VAL A 578 " --> pdb=" O ILE A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 654 through 680 removed outlier: 4.894A pdb=" N TYR A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 690 removed outlier: 3.759A pdb=" N THR A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 722 removed outlier: 3.903A pdb=" N ILE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'A' and resid 757 through 772 removed outlier: 3.762A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.779A pdb=" N ILE A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 removed outlier: 3.868A pdb=" N LEU A 796 " --> pdb=" O ALA A 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 797 through 814 Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.798A pdb=" N ILE A 824 " --> pdb=" O TRP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.827A pdb=" N GLY A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.571A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 977 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 997 removed outlier: 3.842A pdb=" N THR A 996 " --> pdb=" O ASP A 993 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 997 " --> pdb=" O ILE A 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 993 through 997' Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.750A pdb=" N LEU A1005 " --> pdb=" O ARG A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1030 removed outlier: 4.032A pdb=" N MET A1024 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU A1025 " --> pdb=" O ALA A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1050 removed outlier: 3.600A pdb=" N LEU A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 removed outlier: 3.995A pdb=" N ARG A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 Processing helix chain 'A' and resid 1119 through 1127 removed outlier: 3.609A pdb=" N ASP A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1149 removed outlier: 4.436A pdb=" N ASN A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1216 removed outlier: 3.556A pdb=" N VAL A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1253 Processing helix chain 'A' and resid 1268 through 1277 removed outlier: 3.613A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1277 " --> pdb=" O PHE A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.556A pdb=" N GLN A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1357 " --> pdb=" O GLN A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1378 Processing helix chain 'A' and resid 1378 through 1393 Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 3.890A pdb=" N TYR A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1436 Processing helix chain 'A' and resid 1470 through 1475 removed outlier: 3.876A pdb=" N GLN A1475 " --> pdb=" O THR A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.968A pdb=" N LYS A1536 " --> pdb=" O ASP A1532 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A1538 " --> pdb=" O LEU A1534 " (cutoff:3.500A) Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1575 through 1586 removed outlier: 3.512A pdb=" N PHE A1579 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A1586 " --> pdb=" O ASP A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1601 removed outlier: 4.529A pdb=" N GLU A1601 " --> pdb=" O GLU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1610 removed outlier: 3.846A pdb=" N PHE A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU A1610 " --> pdb=" O LEU A1606 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1643 removed outlier: 3.712A pdb=" N LEU A1643 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1652 Processing helix chain 'A' and resid 1664 through 1691 removed outlier: 3.839A pdb=" N GLU A1670 " --> pdb=" O GLU A1666 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A1671 " --> pdb=" O GLN A1667 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1678 " --> pdb=" O LEU A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1707 removed outlier: 3.563A pdb=" N ALA A1695 " --> pdb=" O SER A1691 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1716 Processing helix chain 'A' and resid 1719 through 1747 removed outlier: 3.682A pdb=" N TYR A1723 " --> pdb=" O SER A1719 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A1737 " --> pdb=" O MET A1733 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1754 Processing helix chain 'A' and resid 1759 through 1779 removed outlier: 3.909A pdb=" N GLY A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Proline residue: A1776 - end of helix Processing helix chain 'A' and resid 1780 through 1785 removed outlier: 3.791A pdb=" N LEU A1784 " --> pdb=" O PRO A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1789 through 1813 removed outlier: 4.117A pdb=" N VAL A1793 " --> pdb=" O SER A1789 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1798 " --> pdb=" O ALA A1794 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1813 " --> pdb=" O ILE A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1831 removed outlier: 4.195A pdb=" N ARG A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1835 removed outlier: 4.096A pdb=" N VAL A1835 " --> pdb=" O LEU A1832 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1832 through 1835' Processing helix chain 'A' and resid 1836 through 1861 removed outlier: 3.897A pdb=" N ARG A1860 " --> pdb=" O ASP A1856 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A1861 " --> pdb=" O VAL A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1875 through 1898 removed outlier: 3.565A pdb=" N VAL A1887 " --> pdb=" O VAL A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1986 removed outlier: 3.692A pdb=" N MET A1984 " --> pdb=" O THR A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2009 through 2014 Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2049 through 2056 removed outlier: 3.627A pdb=" N ILE A2055 " --> pdb=" O ALA A2051 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A2056 " --> pdb=" O ASN A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2071 removed outlier: 3.796A pdb=" N TYR A2071 " --> pdb=" O ALA A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2072 through 2084 removed outlier: 3.627A pdb=" N LYS A2076 " --> pdb=" O SER A2072 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG A2077 " --> pdb=" O GLY A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2120 removed outlier: 3.802A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A2119 " --> pdb=" O SER A2115 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A2120 " --> pdb=" O ILE A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.513A pdb=" N CYS A2133 " --> pdb=" O SER A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2161 removed outlier: 3.543A pdb=" N PHE A2161 " --> pdb=" O LEU A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2192 Processing helix chain 'A' and resid 2215 through 2219 Processing helix chain 'A' and resid 2240 through 2249 removed outlier: 3.623A pdb=" N VAL A2244 " --> pdb=" O THR A2240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.036A pdb=" N ILE A1615 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A1617 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1619 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ILE A1560 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE A1416 " --> pdb=" O ILE A1560 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A1562 " --> pdb=" O PHE A1416 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER A1418 " --> pdb=" O ILE A1562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 527 removed outlier: 6.235A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 399 " --> pdb=" O VAL A 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 566 through 571 Processing sheet with id=AA5, first strand: chain 'A' and resid 932 through 933 Processing sheet with id=AA6, first strand: chain 'A' and resid 961 through 962 removed outlier: 6.414A pdb=" N ALA A1131 " --> pdb=" O LEU A 962 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1007 through 1008 removed outlier: 6.996A pdb=" N CYS A1008 " --> pdb=" O ASP A1086 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1155 through 1158 removed outlier: 7.161A pdb=" N ILE A1230 " --> pdb=" O VAL A1222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2091 through 2094 removed outlier: 6.588A pdb=" N VAL A2092 " --> pdb=" O VAL A2124 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A2142 " --> pdb=" O ARG A2149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2205 through 2209 624 hydrogen bonds defined for protein. 1802 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: 3.05 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4424 1.34 - 1.47: 3330 1.47 - 1.59: 5977 1.59 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 13807 Sorted by residual: bond pdb=" C1 NAG A2301 " pdb=" O5 NAG A2301 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C1 NAG A2303 " pdb=" O5 NAG A2303 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 MAN C 4 " pdb=" C2 MAN C 4 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 13802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18506 1.79 - 3.58: 353 3.58 - 5.37: 71 5.37 - 7.16: 13 7.16 - 8.95: 3 Bond angle restraints: 18946 Sorted by residual: angle pdb=" N PRO A 458 " pdb=" CA PRO A 458 " pdb=" CB PRO A 458 " ideal model delta sigma weight residual 103.33 110.51 -7.18 9.30e-01 1.16e+00 5.95e+01 angle pdb=" N PRO A 188 " pdb=" CA PRO A 188 " pdb=" CB PRO A 188 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.55e+01 angle pdb=" C CYS A 930 " pdb=" CA CYS A 930 " pdb=" CB CYS A 930 " ideal model delta sigma weight residual 115.89 110.34 5.55 1.32e+00 5.74e-01 1.77e+01 angle pdb=" CA LYS A2049 " pdb=" CB LYS A2049 " pdb=" CG LYS A2049 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" C ASN A1442 " pdb=" CA ASN A1442 " pdb=" CB ASN A1442 " ideal model delta sigma weight residual 109.80 115.02 -5.22 1.61e+00 3.86e-01 1.05e+01 ... (remaining 18941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7396 17.77 - 35.55: 495 35.55 - 53.32: 91 53.32 - 71.10: 16 71.10 - 88.87: 9 Dihedral angle restraints: 8007 sinusoidal: 2391 harmonic: 5616 Sorted by residual: dihedral pdb=" CB CYS A1488 " pdb=" SG CYS A1488 " pdb=" SG CYS A1502 " pdb=" CB CYS A1502 " ideal model delta sinusoidal sigma weight residual 93.00 7.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1490 " pdb=" CB CYS A1490 " ideal model delta sinusoidal sigma weight residual 93.00 161.90 -68.90 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CA MET A1587 " pdb=" C MET A1587 " pdb=" N ASN A1588 " pdb=" CA ASN A1588 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 8004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1911 0.055 - 0.111: 366 0.111 - 0.166: 30 0.166 - 0.222: 3 0.222 - 0.277: 3 Chirality restraints: 2313 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA PRO A 188 " pdb=" N PRO A 188 " pdb=" C PRO A 188 " pdb=" CB PRO A 188 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2310 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 774 " -0.052 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO A 775 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 775 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 775 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 435 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 436 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1588 " 0.026 2.00e-02 2.50e+03 2.36e-02 6.97e+00 pdb=" CG ASN A1588 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A1588 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A1588 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A2303 " 0.027 2.00e-02 2.50e+03 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2268 2.76 - 3.30: 13644 3.30 - 3.83: 21952 3.83 - 4.37: 23402 4.37 - 4.90: 41608 Nonbonded interactions: 102874 Sorted by model distance: nonbonded pdb=" O ASP A 295 " pdb=" OG1 THR A 300 " model vdw 2.226 3.040 nonbonded pdb=" O VAL A1160 " pdb=" OG SER A1261 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 56 " pdb=" NE2 GLN A 635 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 89 " pdb=" NE2 GLN A 635 " model vdw 2.255 3.120 nonbonded pdb=" O ARG A1241 " pdb=" OG SER A1245 " model vdw 2.261 3.040 ... (remaining 102869 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.003 0.049 13825 Z= 0.143 Angle : 0.637 13.115 18995 Z= 0.319 Chirality : 0.044 0.277 2313 Planarity : 0.005 0.077 2438 Dihedral : 13.096 88.869 4350 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.37 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.96 (0.20), residues: 1911 helix: 1.20 (0.19), residues: 869 sheet: -0.77 (0.49), residues: 139 loop : -2.61 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.013 0.001 TYR A 633 PHE 0.031 0.001 PHE A1076 TRP 0.033 0.001 TRP A 663 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13807) covalent geometry : angle 0.61298 / 0.31 (18946) SS BOND : bond 0.00369 / 0.18 ( 5) SS BOND : angle 1.32900 / 0.69 ( 10) hydrogen bonds : bond 0.15170 / 10.67 ( 624) hydrogen bonds : angle 5.51742 / 3.99 ( 1802) link_ALPHA1-3 : bond 0.00610 / 0.32 ( 1) link_ALPHA1-3 : angle 1.40585 / 0.70 ( 3) link_ALPHA1-6 : bond 0.00305 / 0.16 ( 1) link_ALPHA1-6 : angle 1.63438 / 0.88 ( 3) link_BETA1-4 : bond 0.01163 / 0.64 ( 5) link_BETA1-4 : angle 4.91467 / 2.39 ( 15) link_NAG-ASN : bond 0.00342 / 0.21 ( 6) link_NAG-ASN : angle 3.31986 / 2.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.525 Fit side-chains REVERT: A 697 TRP cc_start: 0.8520 (m100) cc_final: 0.8018 (m100) REVERT: A 2034 TYR cc_start: 0.6206 (t80) cc_final: 0.5948 (t80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.0927 time to fit residues: 30.5399 Evaluate side-chains 175 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.160537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.139229 restraints weight = 24831.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.140646 restraints weight = 16250.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.141462 restraints weight = 10974.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.141569 restraints weight = 9512.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.141622 restraints weight = 9196.844| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4002 r_free = 0.4002 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13825 Z= 0.209 Angle : 0.693 12.519 18995 Z= 0.344 Chirality : 0.047 0.291 2313 Planarity : 0.005 0.067 2438 Dihedral : 4.406 26.492 2022 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.58 % Favored : 89.32 % Rotamer: Outliers : 1.16 % Allowed : 8.64 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.26 (0.20), residues: 1911 helix: 0.86 (0.18), residues: 886 sheet: -1.07 (0.47), residues: 146 loop : -2.72 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1362 TYR 0.022 0.002 TYR A1700 PHE 0.034 0.002 PHE A1076 TRP 0.021 0.002 TRP A 31 HIS 0.018 0.002 HIS A1871 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (13807) covalent geometry : angle 0.66966 / 0.34 (18946) SS BOND : bond 0.00738 / 0.35 ( 5) SS BOND : angle 1.37822 / 0.71 ( 10) hydrogen bonds : bond 0.04008 / 2.67 ( 624) hydrogen bonds : angle 4.57999 / 3.28 ( 1802) link_ALPHA1-3 : bond 0.00970 / 0.51 ( 1) link_ALPHA1-3 : angle 1.51833 / 0.82 ( 3) link_ALPHA1-6 : bond 0.00486 / 0.26 ( 1) link_ALPHA1-6 : angle 1.94226 / 1.05 ( 3) link_BETA1-4 : bond 0.00907 / 0.48 ( 5) link_BETA1-4 : angle 4.85184 / 2.36 ( 15) link_NAG-ASN : bond 0.00512 / 0.31 ( 6) link_NAG-ASN : angle 3.54254 / 2.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.392 Fit side-chains REVERT: A 697 TRP cc_start: 0.8616 (m100) cc_final: 0.8242 (m100) REVERT: A 2034 TYR cc_start: 0.6559 (t80) cc_final: 0.6067 (t80) outliers start: 13 outliers final: 9 residues processed: 186 average time/residue: 0.0857 time to fit residues: 25.6247 Evaluate side-chains 175 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 164 optimal weight: 0.4980 chunk 182 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.162348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.143406 restraints weight = 33852.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.143171 restraints weight = 24875.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143957 restraints weight = 21145.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.145326 restraints weight = 15103.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.145430 restraints weight = 13311.522| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4054 r_free = 0.4054 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4054 r_free = 0.4054 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13825 Z= 0.131 Angle : 0.620 12.022 18995 Z= 0.305 Chirality : 0.044 0.272 2313 Planarity : 0.005 0.064 2438 Dihedral : 4.240 22.597 2022 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.63 % Favored : 90.21 % Rotamer: Outliers : 0.98 % Allowed : 12.02 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.23 (0.20), residues: 1911 helix: 0.90 (0.18), residues: 896 sheet: -1.07 (0.46), residues: 146 loop : -2.76 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2038 TYR 0.016 0.001 TYR A1700 PHE 0.027 0.001 PHE A1533 TRP 0.023 0.001 TRP A 31 HIS 0.006 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13807) covalent geometry : angle 0.59943 / 0.30 (18946) SS BOND : bond 0.00455 / 0.23 ( 5) SS BOND : angle 1.20819 / 0.61 ( 10) hydrogen bonds : bond 0.03423 / 2.29 ( 624) hydrogen bonds : angle 4.31770 / 3.10 ( 1802) link_ALPHA1-3 : bond 0.00958 / 0.50 ( 1) link_ALPHA1-3 : angle 1.19192 / 0.62 ( 3) link_ALPHA1-6 : bond 0.00561 / 0.30 ( 1) link_ALPHA1-6 : angle 1.85728 / 0.99 ( 3) link_BETA1-4 : bond 0.01131 / 0.61 ( 5) link_BETA1-4 : angle 4.65263 / 2.27 ( 15) link_NAG-ASN : bond 0.00257 / 0.12 ( 6) link_NAG-ASN : angle 2.90483 / 1.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.351 Fit side-chains REVERT: A 855 TRP cc_start: 0.6736 (t-100) cc_final: 0.6270 (t-100) REVERT: A 1874 LEU cc_start: 0.7700 (mm) cc_final: 0.7279 (mp) REVERT: A 2034 TYR cc_start: 0.6493 (t80) cc_final: 0.5983 (t80) outliers start: 11 outliers final: 8 residues processed: 188 average time/residue: 0.0887 time to fit residues: 26.4668 Evaluate side-chains 185 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 82 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 158 optimal weight: 0.5980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.139615 restraints weight = 30096.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.138553 restraints weight = 24099.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.139957 restraints weight = 21036.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.140237 restraints weight = 14530.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.140618 restraints weight = 14183.435| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13825 Z= 0.180 Angle : 0.665 12.561 18995 Z= 0.328 Chirality : 0.046 0.278 2313 Planarity : 0.005 0.063 2438 Dihedral : 4.471 23.366 2022 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.20 % Favored : 88.64 % Rotamer: Outliers : 1.96 % Allowed : 13.45 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.35 (0.20), residues: 1911 helix: 0.79 (0.18), residues: 890 sheet: -1.19 (0.46), residues: 144 loop : -2.77 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 452 TYR 0.012 0.001 TYR A2016 PHE 0.032 0.002 PHE A1076 TRP 0.028 0.002 TRP A 431 HIS 0.008 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (13807) covalent geometry : angle 0.64284 / 0.32 (18946) SS BOND : bond 0.00628 / 0.30 ( 5) SS BOND : angle 1.42124 / 0.72 ( 10) hydrogen bonds : bond 0.03574 / 2.36 ( 624) hydrogen bonds : angle 4.33784 / 3.13 ( 1802) link_ALPHA1-3 : bond 0.00873 / 0.46 ( 1) link_ALPHA1-3 : angle 1.27467 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00317 / 0.17 ( 1) link_ALPHA1-6 : angle 1.92137 / 1.01 ( 3) link_BETA1-4 : bond 0.01101 / 0.60 ( 5) link_BETA1-4 : angle 4.79365 / 2.35 ( 15) link_NAG-ASN : bond 0.00364 / 0.22 ( 6) link_NAG-ASN : angle 3.26744 / 1.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.420 Fit side-chains REVERT: A 450 MET cc_start: 0.8514 (mmm) cc_final: 0.8302 (mmm) REVERT: A 633 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: A 648 MET cc_start: 0.8288 (mmp) cc_final: 0.7878 (mmp) REVERT: A 842 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6703 (ppp) REVERT: A 855 TRP cc_start: 0.6758 (t-100) cc_final: 0.6348 (t-100) REVERT: A 1690 MET cc_start: 0.8604 (tpp) cc_final: 0.8372 (mmt) REVERT: A 1874 LEU cc_start: 0.7700 (mm) cc_final: 0.7345 (mp) REVERT: A 2095 ASP cc_start: 0.7881 (t0) cc_final: 0.7457 (p0) outliers start: 22 outliers final: 15 residues processed: 191 average time/residue: 0.0909 time to fit residues: 27.7584 Evaluate side-chains 193 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Chi-restraints excluded: chain A residue 2150 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 178 optimal weight: 0.1980 chunk 144 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.137757 restraints weight = 26774.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.139600 restraints weight = 18251.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.140280 restraints weight = 11331.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.140336 restraints weight = 9649.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.140391 restraints weight = 8880.287| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13825 Z= 0.159 Angle : 0.640 12.299 18995 Z= 0.316 Chirality : 0.045 0.275 2313 Planarity : 0.005 0.061 2438 Dihedral : 4.447 21.201 2022 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.26 % Favored : 89.63 % Rotamer: Outliers : 1.96 % Allowed : 14.78 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.36 (0.20), residues: 1911 helix: 0.82 (0.18), residues: 893 sheet: -1.34 (0.45), residues: 146 loop : -2.80 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1514 TYR 0.013 0.001 TYR A2016 PHE 0.027 0.001 PHE A1076 TRP 0.034 0.002 TRP A 431 HIS 0.006 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (13807) covalent geometry : angle 0.61910 / 0.31 (18946) SS BOND : bond 0.00558 / 0.27 ( 5) SS BOND : angle 1.38415 / 0.70 ( 10) hydrogen bonds : bond 0.03360 / 2.22 ( 624) hydrogen bonds : angle 4.27456 / 3.09 ( 1802) link_ALPHA1-3 : bond 0.00869 / 0.46 ( 1) link_ALPHA1-3 : angle 1.30304 / 0.66 ( 3) link_ALPHA1-6 : bond 0.00364 / 0.19 ( 1) link_ALPHA1-6 : angle 1.85010 / 0.98 ( 3) link_BETA1-4 : bond 0.01191 / 0.65 ( 5) link_BETA1-4 : angle 4.64266 / 2.28 ( 15) link_NAG-ASN : bond 0.00285 / 0.15 ( 6) link_NAG-ASN : angle 3.09584 / 1.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.510 Fit side-chains REVERT: A 450 MET cc_start: 0.8544 (mmm) cc_final: 0.8315 (mmm) REVERT: A 633 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 648 MET cc_start: 0.8436 (mmp) cc_final: 0.7890 (mmp) REVERT: A 842 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6655 (ppp) REVERT: A 855 TRP cc_start: 0.6750 (t-100) cc_final: 0.6342 (t-100) REVERT: A 1690 MET cc_start: 0.8586 (tpp) cc_final: 0.8377 (mmt) REVERT: A 1874 LEU cc_start: 0.7646 (mm) cc_final: 0.7343 (mp) outliers start: 22 outliers final: 14 residues processed: 189 average time/residue: 0.0918 time to fit residues: 28.1171 Evaluate side-chains 194 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 72 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 176 optimal weight: 0.0570 chunk 98 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.161888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.142689 restraints weight = 30074.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142089 restraints weight = 21600.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143548 restraints weight = 19348.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.143776 restraints weight = 13213.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143948 restraints weight = 13020.890| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13825 Z= 0.117 Angle : 0.602 11.423 18995 Z= 0.295 Chirality : 0.043 0.268 2313 Planarity : 0.005 0.061 2438 Dihedral : 4.219 19.958 2022 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.00 % Favored : 89.90 % Rotamer: Outliers : 1.87 % Allowed : 16.03 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.16 (0.20), residues: 1911 helix: 1.03 (0.18), residues: 892 sheet: -1.10 (0.46), residues: 141 loop : -2.77 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1514 TYR 0.015 0.001 TYR A2016 PHE 0.023 0.001 PHE A1533 TRP 0.037 0.001 TRP A 431 HIS 0.006 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13807) covalent geometry : angle 0.58299 / 0.29 (18946) SS BOND : bond 0.00402 / 0.20 ( 5) SS BOND : angle 1.12069 / 0.57 ( 10) hydrogen bonds : bond 0.03008 / 2.00 ( 624) hydrogen bonds : angle 4.09762 / 2.96 ( 1802) link_ALPHA1-3 : bond 0.00913 / 0.48 ( 1) link_ALPHA1-3 : angle 1.40344 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00438 / 0.23 ( 1) link_ALPHA1-6 : angle 1.67569 / 0.89 ( 3) link_BETA1-4 : bond 0.01239 / 0.67 ( 5) link_BETA1-4 : angle 4.31573 / 2.12 ( 15) link_NAG-ASN : bond 0.00257 / 0.12 ( 6) link_NAG-ASN : angle 2.77183 / 1.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.690 Fit side-chains REVERT: A 450 MET cc_start: 0.8525 (mmm) cc_final: 0.8315 (mmm) REVERT: A 633 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: A 648 MET cc_start: 0.8351 (mmp) cc_final: 0.7872 (mmp) REVERT: A 842 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6611 (ppp) REVERT: A 855 TRP cc_start: 0.6775 (t-100) cc_final: 0.6459 (t-100) REVERT: A 1874 LEU cc_start: 0.7451 (mm) cc_final: 0.7175 (mp) outliers start: 21 outliers final: 13 residues processed: 195 average time/residue: 0.0908 time to fit residues: 28.5984 Evaluate side-chains 194 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 108 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 189 optimal weight: 0.0040 chunk 109 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1483 ASN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.161677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.142533 restraints weight = 38588.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.143474 restraints weight = 27592.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.144494 restraints weight = 22995.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.145100 restraints weight = 14229.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.145604 restraints weight = 13002.673| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4025 r_free = 0.4025 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4025 r_free = 0.4025 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13825 Z= 0.121 Angle : 0.601 11.211 18995 Z= 0.295 Chirality : 0.043 0.267 2313 Planarity : 0.005 0.059 2438 Dihedral : 4.172 19.161 2022 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.84 % Favored : 90.05 % Rotamer: Outliers : 1.96 % Allowed : 16.12 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.12 (0.20), residues: 1911 helix: 1.06 (0.18), residues: 892 sheet: -1.06 (0.46), residues: 141 loop : -2.76 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1514 TYR 0.013 0.001 TYR A 633 PHE 0.021 0.001 PHE A1076 TRP 0.039 0.001 TRP A 431 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13807) covalent geometry : angle 0.58188 / 0.29 (18946) SS BOND : bond 0.00422 / 0.20 ( 5) SS BOND : angle 1.14478 / 0.58 ( 10) hydrogen bonds : bond 0.02989 / 1.98 ( 624) hydrogen bonds : angle 4.06234 / 2.94 ( 1802) link_ALPHA1-3 : bond 0.00845 / 0.44 ( 1) link_ALPHA1-3 : angle 1.46100 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00435 / 0.23 ( 1) link_ALPHA1-6 : angle 1.66475 / 0.88 ( 3) link_BETA1-4 : bond 0.01169 / 0.64 ( 5) link_BETA1-4 : angle 4.27027 / 2.09 ( 15) link_NAG-ASN : bond 0.00255 / 0.13 ( 6) link_NAG-ASN : angle 2.80536 / 1.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.500 Fit side-chains REVERT: A 450 MET cc_start: 0.8477 (mmm) cc_final: 0.8274 (mmm) REVERT: A 633 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: A 648 MET cc_start: 0.8199 (mmp) cc_final: 0.7795 (mmp) REVERT: A 842 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6494 (ppp) REVERT: A 855 TRP cc_start: 0.6776 (t-100) cc_final: 0.6470 (t-100) REVERT: A 1843 ARG cc_start: 0.7504 (mmm160) cc_final: 0.7069 (mmm160) REVERT: A 1874 LEU cc_start: 0.7271 (mm) cc_final: 0.7002 (mp) REVERT: A 2049 LYS cc_start: 0.7654 (tppt) cc_final: 0.7377 (tppt) outliers start: 22 outliers final: 16 residues processed: 194 average time/residue: 0.0830 time to fit residues: 26.2139 Evaluate side-chains 200 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Chi-restraints excluded: chain A residue 2150 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 78 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.158539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.137059 restraints weight = 27108.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.138895 restraints weight = 18131.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.140111 restraints weight = 11040.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.139856 restraints weight = 9206.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.139916 restraints weight = 9173.165| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13825 Z= 0.170 Angle : 0.648 11.755 18995 Z= 0.320 Chirality : 0.045 0.278 2313 Planarity : 0.005 0.060 2438 Dihedral : 4.415 21.256 2022 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.89 % Favored : 89.01 % Rotamer: Outliers : 1.87 % Allowed : 16.74 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.28 (0.20), residues: 1911 helix: 0.92 (0.18), residues: 890 sheet: -1.47 (0.45), residues: 139 loop : -2.75 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1514 TYR 0.013 0.001 TYR A 633 PHE 0.027 0.001 PHE A1076 TRP 0.043 0.002 TRP A 431 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (13807) covalent geometry : angle 0.62805 / 0.32 (18946) SS BOND : bond 0.00633 / 0.30 ( 5) SS BOND : angle 1.38736 / 0.71 ( 10) hydrogen bonds : bond 0.03355 / 2.21 ( 624) hydrogen bonds : angle 4.21421 / 3.06 ( 1802) link_ALPHA1-3 : bond 0.00798 / 0.42 ( 1) link_ALPHA1-3 : angle 1.45006 / 0.72 ( 3) link_ALPHA1-6 : bond 0.00339 / 0.18 ( 1) link_ALPHA1-6 : angle 1.80158 / 0.95 ( 3) link_BETA1-4 : bond 0.01154 / 0.63 ( 5) link_BETA1-4 : angle 4.39315 / 2.16 ( 15) link_NAG-ASN : bond 0.00355 / 0.21 ( 6) link_NAG-ASN : angle 3.21926 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.526 Fit side-chains REVERT: A 633 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: A 648 MET cc_start: 0.8450 (mmp) cc_final: 0.8040 (mmp) REVERT: A 842 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6660 (ppp) REVERT: A 855 TRP cc_start: 0.6844 (t-100) cc_final: 0.6534 (t-100) REVERT: A 1843 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7183 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7544 (mm) cc_final: 0.7296 (mp) outliers start: 21 outliers final: 14 residues processed: 188 average time/residue: 0.0905 time to fit residues: 27.4546 Evaluate side-chains 190 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Chi-restraints excluded: chain A residue 2150 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 89 optimal weight: 0.0060 chunk 186 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.161205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.140003 restraints weight = 27459.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.141505 restraints weight = 20434.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.142736 restraints weight = 12053.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.142590 restraints weight = 9691.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.142604 restraints weight = 9462.078| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13825 Z= 0.121 Angle : 0.607 11.206 18995 Z= 0.299 Chirality : 0.043 0.266 2313 Planarity : 0.005 0.060 2438 Dihedral : 4.251 19.184 2022 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.10 % Favored : 89.79 % Rotamer: Outliers : 1.34 % Allowed : 17.54 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1911 helix: 1.02 (0.18), residues: 890 sheet: -1.13 (0.47), residues: 134 loop : -2.75 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1514 TYR 0.015 0.001 TYR A 633 PHE 0.021 0.001 PHE A1076 TRP 0.048 0.001 TRP A 431 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13807) covalent geometry : angle 0.58848 / 0.29 (18946) SS BOND : bond 0.00424 / 0.20 ( 5) SS BOND : angle 1.16114 / 0.59 ( 10) hydrogen bonds : bond 0.03012 / 2.00 ( 624) hydrogen bonds : angle 4.08450 / 2.96 ( 1802) link_ALPHA1-3 : bond 0.00833 / 0.44 ( 1) link_ALPHA1-3 : angle 1.56549 / 0.78 ( 3) link_ALPHA1-6 : bond 0.00433 / 0.23 ( 1) link_ALPHA1-6 : angle 1.65899 / 0.88 ( 3) link_BETA1-4 : bond 0.01268 / 0.69 ( 5) link_BETA1-4 : angle 4.12897 / 2.04 ( 15) link_NAG-ASN : bond 0.00256 / 0.12 ( 6) link_NAG-ASN : angle 2.83713 / 1.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.509 Fit side-chains REVERT: A 450 MET cc_start: 0.8583 (mmm) cc_final: 0.8357 (mmm) REVERT: A 633 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: A 842 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6602 (ppp) REVERT: A 855 TRP cc_start: 0.6795 (t-100) cc_final: 0.6500 (t-100) REVERT: A 1843 ARG cc_start: 0.7594 (mmm160) cc_final: 0.7224 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7367 (mm) cc_final: 0.7103 (mp) outliers start: 15 outliers final: 11 residues processed: 189 average time/residue: 0.0885 time to fit residues: 26.9374 Evaluate side-chains 192 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 122 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.164705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.143930 restraints weight = 29077.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.143947 restraints weight = 24319.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.145097 restraints weight = 21069.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.145184 restraints weight = 14508.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.145360 restraints weight = 14165.698| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13825 Z= 0.129 Angle : 0.618 11.014 18995 Z= 0.303 Chirality : 0.044 0.264 2313 Planarity : 0.005 0.060 2438 Dihedral : 4.234 19.570 2022 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.05 % Favored : 89.84 % Rotamer: Outliers : 1.42 % Allowed : 17.72 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1911 helix: 1.03 (0.18), residues: 887 sheet: -1.14 (0.47), residues: 134 loop : -2.70 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1514 TYR 0.014 0.001 TYR A 633 PHE 0.022 0.001 PHE A1076 TRP 0.048 0.002 TRP A 431 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13807) covalent geometry : angle 0.59943 / 0.30 (18946) SS BOND : bond 0.00463 / 0.22 ( 5) SS BOND : angle 1.19737 / 0.61 ( 10) hydrogen bonds : bond 0.03025 / 2.01 ( 624) hydrogen bonds : angle 4.06976 / 2.95 ( 1802) link_ALPHA1-3 : bond 0.00808 / 0.43 ( 1) link_ALPHA1-3 : angle 1.54873 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00406 / 0.21 ( 1) link_ALPHA1-6 : angle 1.67121 / 0.88 ( 3) link_BETA1-4 : bond 0.01191 / 0.65 ( 5) link_BETA1-4 : angle 4.10507 / 2.02 ( 15) link_NAG-ASN : bond 0.00269 / 0.14 ( 6) link_NAG-ASN : angle 2.91600 / 1.63 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.550 Fit side-chains REVERT: A 450 MET cc_start: 0.8533 (mmm) cc_final: 0.8319 (mmm) REVERT: A 633 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 842 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6649 (ppp) REVERT: A 855 TRP cc_start: 0.6828 (t-100) cc_final: 0.6540 (t-100) REVERT: A 1843 ARG cc_start: 0.7562 (mmm160) cc_final: 0.7243 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7334 (mm) cc_final: 0.7091 (mp) outliers start: 16 outliers final: 11 residues processed: 185 average time/residue: 0.0913 time to fit residues: 27.3095 Evaluate side-chains 191 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 104 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 186 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.162532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.142144 restraints weight = 28710.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.142853 restraints weight = 20252.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.143561 restraints weight = 14477.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.143634 restraints weight = 11623.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145112 restraints weight = 10589.571| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13825 Z= 0.114 Angle : 0.602 10.622 18995 Z= 0.295 Chirality : 0.043 0.263 2313 Planarity : 0.004 0.060 2438 Dihedral : 4.112 18.504 2022 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.69 % Favored : 90.16 % Rotamer: Outliers : 1.42 % Allowed : 17.90 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.08 (0.20), residues: 1911 helix: 1.09 (0.18), residues: 892 sheet: -1.03 (0.47), residues: 134 loop : -2.71 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1514 TYR 0.017 0.001 TYR A1723 PHE 0.018 0.001 PHE A1076 TRP 0.050 0.002 TRP A 431 HIS 0.006 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (13807) covalent geometry : angle 0.58499 / 0.29 (18946) SS BOND : bond 0.00374 / 0.18 ( 5) SS BOND : angle 1.07345 / 0.55 ( 10) hydrogen bonds : bond 0.02849 / 1.89 ( 624) hydrogen bonds : angle 3.99316 / 2.88 ( 1802) link_ALPHA1-3 : bond 0.00819 / 0.43 ( 1) link_ALPHA1-3 : angle 1.62068 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00458 / 0.24 ( 1) link_ALPHA1-6 : angle 1.59684 / 0.84 ( 3) link_BETA1-4 : bond 0.01230 / 0.67 ( 5) link_BETA1-4 : angle 3.91658 / 1.93 ( 15) link_NAG-ASN : bond 0.00266 / 0.12 ( 6) link_NAG-ASN : angle 2.72007 / 1.52 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.65 seconds wall clock time: 41 minutes 15.70 seconds (2475.70 seconds total)