Starting phenix.real_space_refine on Fri Feb 16 00:38:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/02_2024/7tc0_25803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/02_2024/7tc0_25803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/02_2024/7tc0_25803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/02_2024/7tc0_25803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/02_2024/7tc0_25803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/02_2024/7tc0_25803_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 84 5.16 5 C 8965 2.51 5 N 2289 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A ASP 807": "OD1" <-> "OD2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A PHE 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 986": "OD1" <-> "OD2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A ASP 1064": "OD1" <-> "OD2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ASP 1095": "OD1" <-> "OD2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A ASP 1179": "OD1" <-> "OD2" Residue "A TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1245": "OE1" <-> "OE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1386": "OE1" <-> "OE2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "A ASP 1426": "OD1" <-> "OD2" Residue "A PHE 1449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1503": "NH1" <-> "NH2" Residue "A ASP 1553": "OD1" <-> "OD2" Residue "A ASP 1567": "OD1" <-> "OD2" Residue "A PHE 1605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1654": "OD1" <-> "OD2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A TYR 1710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1801": "OD1" <-> "OD2" Residue "A ASP 1821": "OD1" <-> "OD2" Residue "A GLU 1833": "OE1" <-> "OE2" Residue "A TYR 1872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1999": "OE1" <-> "OE2" Residue "A ARG 2004": "NH1" <-> "NH2" Residue "A GLU 2005": "OE1" <-> "OE2" Residue "A GLU 2018": "OE1" <-> "OE2" Residue "A TYR 2041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2051": "NH1" <-> "NH2" Residue "A ASP 2069": "OD1" <-> "OD2" Residue "A GLU 2070": "OE1" <-> "OE2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2095": "NH1" <-> "NH2" Residue "A ARG 2113": "NH1" <-> "NH2" Residue "A ASP 2137": "OD1" <-> "OD2" Residue "A TYR 2178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2204": "OE1" <-> "OE2" Residue "A ASP 2223": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13809 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1781, 13636 Classifications: {'peptide': 1781} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 85, 'TRANS': 1693} Chain breaks: 13 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 285 Chain: "B" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.76, per 1000 atoms: 0.56 Number of scatterers: 13809 At special positions: 0 Unit cell: (82.516, 98.514, 218.078, 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 84 16.00 O 2471 8.00 N 2289 7.00 C 8965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A1465 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2502 " - " ASN A1637 " " NAG A2503 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 2.7 seconds 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 8 sheets defined 53.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Proline residue: A 32 - end of helix removed outlier: 3.638A pdb=" N SER A 45 " --> pdb=" O SER A 41 " (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 66 through 74 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.777A pdb=" N GLN A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.784A pdb=" N GLN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 4.013A pdb=" N TYR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 372 through 379 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 390 through 409 removed outlier: 4.762A pdb=" N LEU A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 484 through 504 removed outlier: 4.632A pdb=" N CYS A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 Processing helix chain 'A' and resid 587 through 590 No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 640 through 664 removed outlier: 4.605A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'A' and resid 678 through 706 Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 715 through 739 removed outlier: 4.088A pdb=" N THR A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 766 removed outlier: 4.349A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Proline residue: A 760 - end of helix removed outlier: 3.608A pdb=" N ALA A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 773 through 779 Processing helix chain 'A' and resid 783 through 799 Processing helix chain 'A' and resid 821 through 845 removed outlier: 3.627A pdb=" N ALA A 844 " --> pdb=" O TRP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 Processing helix chain 'A' and resid 969 through 974 removed outlier: 3.584A pdb=" N GLN A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN A 974 " --> pdb=" O THR A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 969 through 974' Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1024 through 1027 No H-bonds generated for 'chain 'A' and resid 1024 through 1027' Processing helix chain 'A' and resid 1035 through 1050 removed outlier: 3.860A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1077 Processing helix chain 'A' and resid 1091 through 1097 Processing helix chain 'A' and resid 1115 through 1121 Processing helix chain 'A' and resid 1181 through 1190 Processing helix chain 'A' and resid 1217 through 1227 Processing helix chain 'A' and resid 1244 through 1251 Processing helix chain 'A' and resid 1322 through 1341 removed outlier: 4.199A pdb=" N GLN A1326 " --> pdb=" O TRP A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1364 Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1381 through 1383 No H-bonds generated for 'chain 'A' and resid 1381 through 1383' Processing helix chain 'A' and resid 1399 through 1409 Processing helix chain 'A' and resid 1443 through 1451 Processing helix chain 'A' and resid 1505 through 1521 Processing helix chain 'A' and resid 1550 through 1561 Processing helix chain 'A' and resid 1569 through 1584 removed outlier: 3.998A pdb=" N LEU A1584 " --> pdb=" O PHE A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1617 Processing helix chain 'A' and resid 1624 through 1626 No H-bonds generated for 'chain 'A' and resid 1624 through 1626' Processing helix chain 'A' and resid 1640 through 1680 removed outlier: 4.064A pdb=" N THR A1650 " --> pdb=" O VAL A1646 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N THR A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER A1652 " --> pdb=" O LEU A1648 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL A1653 " --> pdb=" O MET A1649 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU A1656 " --> pdb=" O SER A1652 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1657 " --> pdb=" O VAL A1653 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1667 " --> pdb=" O PHE A1663 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL A1668 " --> pdb=" O ALA A1664 " (cutoff:3.500A) Proline residue: A1669 - end of helix removed outlier: 3.768A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1690 Processing helix chain 'A' and resid 1695 through 1723 removed outlier: 3.563A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1727 through 1730 No H-bonds generated for 'chain 'A' and resid 1727 through 1730' Processing helix chain 'A' and resid 1735 through 1752 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1755 through 1757 No H-bonds generated for 'chain 'A' and resid 1755 through 1757' Processing helix chain 'A' and resid 1766 through 1786 Processing helix chain 'A' and resid 1801 through 1809 removed outlier: 3.916A pdb=" N LEU A1808 " --> pdb=" O LYS A1804 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A1809 " --> pdb=" O SER A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1835 Processing helix chain 'A' and resid 1851 through 1872 removed outlier: 3.710A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A1872 " --> pdb=" O VAL A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2013 removed outlier: 3.714A pdb=" N VAL A2007 " --> pdb=" O GLY A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2031 Processing helix chain 'A' and resid 2035 through 2037 No H-bonds generated for 'chain 'A' and resid 2035 through 2037' Processing helix chain 'A' and resid 2042 through 2044 No H-bonds generated for 'chain 'A' and resid 2042 through 2044' Processing helix chain 'A' and resid 2047 through 2059 removed outlier: 3.567A pdb=" N LEU A2059 " --> pdb=" O THR A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2093 removed outlier: 3.737A pdb=" N GLU A2093 " --> pdb=" O SER A2089 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2110 Processing helix chain 'A' and resid 2129 through 2134 Processing helix chain 'A' and resid 2153 through 2162 Processing helix chain 'A' and resid 2187 through 2200 removed outlier: 4.388A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2213 through 2222 Processing sheet with id= A, first strand: chain 'A' and resid 384 through 386 removed outlier: 4.360A pdb=" N LYS A 553 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY A1628 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR A 554 " --> pdb=" O GLY A1628 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A1630 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 556 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE A1632 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 615 through 621 removed outlier: 7.185A pdb=" N ASN A1588 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N TYR A 618 " --> pdb=" O ASN A1588 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLN A 620 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A1592 " --> pdb=" O GLN A 620 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY A1533 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A1390 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A1496 " --> pdb=" O THR A1389 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A1391 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A1498 " --> pdb=" O VAL A1391 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASN A1393 " --> pdb=" O GLN A1498 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 956 through 959 removed outlier: 6.784A pdb=" N PHE A 923 " --> pdb=" O GLY A 898 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A 900 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 921 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 975 through 978 removed outlier: 6.821A pdb=" N VAL A1053 " --> pdb=" O GLY A 976 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N CYS A 978 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1055 " --> pdb=" O CYS A 978 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1236 through 1240 removed outlier: 6.356A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1988 through 1991 removed outlier: 6.931A pdb=" N VAL A2065 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N CYS A1991 " --> pdb=" O VAL A2065 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A2067 " --> pdb=" O CYS A1991 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2203 through 2209 removed outlier: 6.954A pdb=" N ARG A2144 " --> pdb=" O GLU A2204 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR A2206 " --> pdb=" O VAL A2142 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A2142 " --> pdb=" O TYR A2206 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A2208 " --> pdb=" O THR A2140 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A2140 " --> pdb=" O VAL A2208 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A2175 " --> pdb=" O HIS A2172 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1101 through 1105 removed outlier: 6.035A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 5.90 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: 4331 1.34 - 1.46: 3159 1.46 - 1.58: 6503 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14129 Sorted by residual: bond pdb=" C VAL A1737 " pdb=" N LEU A1738 " ideal model delta sigma weight residual 1.335 1.555 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" C LEU A1738 " pdb=" N ALA A1739 " ideal model delta sigma weight residual 1.334 1.413 -0.079 1.33e-02 5.65e+03 3.52e+01 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.82e+00 ... (remaining 14124 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.73: 444 106.73 - 113.55: 7805 113.55 - 120.36: 5221 120.36 - 127.18: 5590 127.18 - 134.00: 159 Bond angle restraints: 19219 Sorted by residual: angle pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" CD PRO A1713 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" C SER A2127 " pdb=" CA SER A2127 " pdb=" CB SER A2127 " ideal model delta sigma weight residual 116.63 108.52 8.11 1.16e+00 7.43e-01 4.89e+01 angle pdb=" C VAL A1712 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " ideal model delta sigma weight residual 119.05 111.77 7.28 1.11e+00 8.12e-01 4.30e+01 angle pdb=" C VAL A1737 " pdb=" N LEU A1738 " pdb=" CA LEU A1738 " ideal model delta sigma weight residual 120.82 129.27 -8.45 1.50e+00 4.44e-01 3.18e+01 angle pdb=" CA VAL A1712 " pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 120.83 117.41 3.42 6.10e-01 2.69e+00 3.15e+01 ... (remaining 19214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 8047 23.45 - 46.90: 412 46.90 - 70.35: 64 70.35 - 93.80: 30 93.80 - 117.25: 18 Dihedral angle restraints: 8571 sinusoidal: 3421 harmonic: 5150 Sorted by residual: dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1429 " pdb=" CB CYS A1429 " ideal model delta sinusoidal sigma weight residual -86.00 0.95 -86.95 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1463 " pdb=" SG CYS A1463 " pdb=" SG CYS A1477 " pdb=" CB CYS A1477 " ideal model delta sinusoidal sigma weight residual -86.00 -8.54 -77.46 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C PRO A1713 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " pdb=" CB PRO A1713 " ideal model delta harmonic sigma weight residual -120.70 -131.27 10.57 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 8568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2191 0.106 - 0.212: 40 0.212 - 0.318: 8 0.318 - 0.423: 2 0.423 - 0.529: 1 Chirality restraints: 2242 Sorted by residual: chirality pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" C PRO A1713 " pdb=" CB PRO A1713 " both_signs ideal model delta sigma weight residual False 2.72 2.19 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C14 CLR A2504 " pdb=" C13 CLR A2504 " pdb=" C15 CLR A2504 " pdb=" C8 CLR A2504 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C14 CLR A2501 " pdb=" C13 CLR A2501 " pdb=" C15 CLR A2501 " pdb=" C8 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2239 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1712 " 0.149 5.00e-02 4.00e+02 2.25e-01 8.09e+01 pdb=" N PRO A1713 " -0.389 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.124 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.117 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1738 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C LEU A1738 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A1738 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A1739 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1710 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TYR A1710 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR A1710 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A1711 " 0.014 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 35 2.43 - 3.05: 8514 3.05 - 3.67: 20326 3.67 - 4.28: 29306 4.28 - 4.90: 48682 Nonbonded interactions: 106863 Sorted by model distance: nonbonded pdb=" CE1 PHE A2158 " pdb=" NH2 ARG A2200 " model vdw 1.817 3.420 nonbonded pdb=" CD1 PHE A2158 " pdb=" NH2 ARG A2200 " model vdw 1.992 3.420 nonbonded pdb=" OE2 GLU A2070 " pdb=" ND1 HIS A2102 " model vdw 2.141 2.520 nonbonded pdb=" CZ PHE A2158 " pdb=" NH2 ARG A2200 " model vdw 2.217 3.420 nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.231 2.440 ... (remaining 106858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.430 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 39.390 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 0.221 14129 Z= 0.187 Angle : 0.594 16.477 19219 Z= 0.334 Chirality : 0.044 0.529 2242 Planarity : 0.006 0.225 2400 Dihedral : 15.733 117.246 5227 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 9.87 % Favored : 87.64 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1753 helix: 0.11 (0.16), residues: 966 sheet: -1.33 (0.39), residues: 174 loop : -3.26 (0.21), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP A1705 HIS 0.001 0.000 HIS A 894 PHE 0.006 0.000 PHE A1449 TYR 0.007 0.000 TYR A1698 ARG 0.001 0.000 ARG A2173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8219 (m-80) cc_final: 0.7997 (t80) REVERT: A 99 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6198 (tmmt) REVERT: A 662 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 982 ASN cc_start: 0.7514 (p0) cc_final: 0.7311 (p0) REVERT: A 1128 LEU cc_start: 0.8084 (pt) cc_final: 0.7794 (pt) REVERT: A 1180 VAL cc_start: 0.9163 (m) cc_final: 0.8934 (t) REVERT: A 1245 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8209 (tt0) REVERT: A 1363 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 1656 LEU cc_start: 0.8922 (tt) cc_final: 0.8570 (mm) outliers start: 35 outliers final: 22 residues processed: 302 average time/residue: 0.2798 time to fit residues: 120.9155 Evaluate side-chains 212 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1537 LEU Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1713 PRO Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2073 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 0.0870 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 24 GLN A 51 GLN A 52 HIS A 283 GLN A 302 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 470 HIS A 820 ASN A 894 HIS A 934 HIS A1491 GLN A1600 HIS A1688 GLN A2179 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14129 Z= 0.196 Angle : 0.562 10.710 19219 Z= 0.269 Chirality : 0.041 0.199 2242 Planarity : 0.004 0.070 2400 Dihedral : 10.012 91.860 2238 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.34 % Allowed : 13.21 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1753 helix: 0.97 (0.17), residues: 983 sheet: -0.70 (0.41), residues: 174 loop : -2.90 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1705 HIS 0.007 0.001 HIS A 470 PHE 0.022 0.002 PHE A 287 TYR 0.022 0.001 TYR A1210 ARG 0.007 0.001 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7635 (mmtt) cc_final: 0.6559 (tmmt) REVERT: A 601 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7276 (mt-10) REVERT: A 662 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 982 ASN cc_start: 0.7746 (p0) cc_final: 0.7427 (p0) REVERT: A 1180 VAL cc_start: 0.9131 (m) cc_final: 0.8901 (t) REVERT: A 1245 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: A 1357 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.5894 (t80) REVERT: A 1363 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8555 (m) outliers start: 47 outliers final: 31 residues processed: 232 average time/residue: 0.2369 time to fit residues: 83.3637 Evaluate side-chains 208 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 ASP Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1537 LEU Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1720 ILE Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 0.0570 chunk 161 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14129 Z= 0.142 Angle : 0.523 10.787 19219 Z= 0.252 Chirality : 0.040 0.231 2242 Planarity : 0.004 0.068 2400 Dihedral : 7.886 80.800 2227 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.12 % Allowed : 14.63 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1753 helix: 1.42 (0.17), residues: 977 sheet: -0.50 (0.42), residues: 173 loop : -2.62 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 278 HIS 0.005 0.001 HIS A 470 PHE 0.019 0.001 PHE A1530 TYR 0.015 0.001 TYR A1210 ARG 0.006 0.000 ARG A 965 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 175 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7689 (mmtt) cc_final: 0.6623 (tmmt) REVERT: A 601 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7183 (mt-10) REVERT: A 662 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 1180 VAL cc_start: 0.9124 (m) cc_final: 0.8892 (t) REVERT: A 1245 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8190 (tt0) REVERT: A 1357 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.5995 (t80) outliers start: 44 outliers final: 31 residues processed: 211 average time/residue: 0.2525 time to fit residues: 82.6765 Evaluate side-chains 202 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1426 ASP Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1558 MET Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1491 GLN A1552 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14129 Z= 0.365 Angle : 0.673 11.255 19219 Z= 0.339 Chirality : 0.047 0.201 2242 Planarity : 0.005 0.055 2400 Dihedral : 6.980 59.357 2222 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.62 % Allowed : 15.41 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1753 helix: 1.39 (0.17), residues: 983 sheet: -0.44 (0.40), residues: 189 loop : -2.44 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1747 HIS 0.009 0.002 HIS A1634 PHE 0.023 0.002 PHE A 287 TYR 0.018 0.002 TYR A 924 ARG 0.005 0.001 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 176 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7205 (tmmt) REVERT: A 842 ILE cc_start: 0.8584 (mm) cc_final: 0.8359 (mt) REVERT: A 1180 VAL cc_start: 0.9106 (m) cc_final: 0.8899 (t) REVERT: A 1245 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: A 1721 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.5914 (t80) REVERT: A 2131 LEU cc_start: 0.8902 (mt) cc_final: 0.8636 (mt) outliers start: 65 outliers final: 40 residues processed: 227 average time/residue: 0.2412 time to fit residues: 82.8246 Evaluate side-chains 204 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 934 HIS Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1426 ASP Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1558 MET Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1552 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14129 Z= 0.160 Angle : 0.537 8.902 19219 Z= 0.267 Chirality : 0.041 0.168 2242 Planarity : 0.004 0.049 2400 Dihedral : 6.088 54.848 2220 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.62 % Allowed : 17.33 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1753 helix: 1.66 (0.17), residues: 981 sheet: -0.30 (0.42), residues: 178 loop : -2.24 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.020 0.001 PHE A2158 TYR 0.010 0.001 TYR A1698 ARG 0.004 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 171 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7336 (ptmm) REVERT: A 644 MET cc_start: 0.8513 (tpp) cc_final: 0.8198 (tpt) REVERT: A 1180 VAL cc_start: 0.9130 (m) cc_final: 0.8882 (t) REVERT: A 1245 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 2059 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8201 (pp) outliers start: 51 outliers final: 37 residues processed: 210 average time/residue: 0.2512 time to fit residues: 79.0540 Evaluate side-chains 200 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 0.0050 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1552 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14129 Z= 0.285 Angle : 0.589 9.242 19219 Z= 0.296 Chirality : 0.043 0.196 2242 Planarity : 0.004 0.050 2400 Dihedral : 6.238 59.594 2220 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.76 % Allowed : 18.04 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1753 helix: 1.67 (0.17), residues: 983 sheet: -0.30 (0.40), residues: 188 loop : -2.20 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1705 HIS 0.006 0.001 HIS A1634 PHE 0.026 0.002 PHE A 287 TYR 0.013 0.001 TYR A1729 ARG 0.004 0.000 ARG A2189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 160 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 1180 VAL cc_start: 0.9131 (m) cc_final: 0.8895 (t) REVERT: A 1245 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8092 (tt0) REVERT: A 1380 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: A 2059 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8265 (pp) REVERT: A 2204 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8183 (mt-10) REVERT: A 2205 ASP cc_start: 0.8178 (m-30) cc_final: 0.7622 (m-30) outliers start: 53 outliers final: 39 residues processed: 201 average time/residue: 0.2482 time to fit residues: 75.6192 Evaluate side-chains 191 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 934 HIS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1210 TYR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1426 ASP Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14129 Z= 0.273 Angle : 0.601 12.788 19219 Z= 0.301 Chirality : 0.043 0.187 2242 Planarity : 0.004 0.051 2400 Dihedral : 6.298 59.225 2220 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.98 % Allowed : 18.68 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1753 helix: 1.74 (0.17), residues: 974 sheet: -0.31 (0.40), residues: 188 loop : -2.16 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.006 0.001 HIS A 551 PHE 0.024 0.002 PHE A 287 TYR 0.012 0.001 TYR A 924 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 159 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 1180 VAL cc_start: 0.9115 (m) cc_final: 0.8903 (t) REVERT: A 1245 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8087 (tt0) REVERT: A 1357 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7659 (t80) REVERT: A 1380 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8382 (pt0) REVERT: A 2059 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8235 (pp) REVERT: A 2204 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8105 (mt-10) outliers start: 56 outliers final: 40 residues processed: 202 average time/residue: 0.2398 time to fit residues: 73.6179 Evaluate side-chains 195 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 934 HIS Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1210 TYR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1426 ASP Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14129 Z= 0.167 Angle : 0.559 12.914 19219 Z= 0.275 Chirality : 0.041 0.176 2242 Planarity : 0.004 0.052 2400 Dihedral : 6.011 57.731 2220 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.34 % Allowed : 19.67 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1753 helix: 1.90 (0.17), residues: 974 sheet: -0.18 (0.40), residues: 188 loop : -2.07 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 278 HIS 0.004 0.001 HIS A 470 PHE 0.021 0.001 PHE A2135 TYR 0.012 0.001 TYR A 754 ARG 0.005 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 156 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1245 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8061 (tt0) REVERT: A 1357 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7626 (t80) REVERT: A 1380 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: A 2059 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8230 (pp) outliers start: 47 outliers final: 33 residues processed: 193 average time/residue: 0.2418 time to fit residues: 71.0618 Evaluate side-chains 185 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1828 MET Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 7.9990 chunk 159 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14129 Z= 0.171 Angle : 0.556 12.344 19219 Z= 0.276 Chirality : 0.040 0.177 2242 Planarity : 0.004 0.053 2400 Dihedral : 5.854 56.139 2219 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.20 % Allowed : 20.17 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1753 helix: 1.97 (0.17), residues: 980 sheet: -0.11 (0.41), residues: 178 loop : -2.09 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.004 0.001 HIS A 470 PHE 0.030 0.001 PHE A1835 TYR 0.011 0.001 TYR A2206 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8205 (mm-40) REVERT: A 1245 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8068 (tt0) REVERT: A 1357 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7602 (t80) REVERT: A 1380 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: A 2059 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8211 (pp) REVERT: A 2204 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7941 (mt-10) outliers start: 45 outliers final: 38 residues processed: 189 average time/residue: 0.2377 time to fit residues: 68.9715 Evaluate side-chains 192 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1828 MET Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 177 optimal weight: 0.4980 chunk 163 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1422 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14129 Z= 0.370 Angle : 0.680 12.654 19219 Z= 0.341 Chirality : 0.046 0.203 2242 Planarity : 0.004 0.053 2400 Dihedral : 6.399 59.822 2219 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.27 % Allowed : 20.24 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1753 helix: 1.71 (0.17), residues: 986 sheet: -0.21 (0.40), residues: 179 loop : -2.14 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1747 HIS 0.010 0.002 HIS A1634 PHE 0.031 0.002 PHE A1835 TYR 0.015 0.002 TYR A 924 ARG 0.003 0.001 ARG A 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 146 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 461 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8166 (mm-40) REVERT: A 548 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7443 (mt) REVERT: A 1245 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: A 1357 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 1380 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8412 (pt0) REVERT: A 2059 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8274 (pp) REVERT: A 2204 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 2205 ASP cc_start: 0.8316 (m-30) cc_final: 0.8072 (m-30) outliers start: 46 outliers final: 36 residues processed: 178 average time/residue: 0.2407 time to fit residues: 65.1328 Evaluate side-chains 183 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1477 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 20 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A1634 HIS ** 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 = 0.3591 r_free = 0.3591 target = 0.104339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072518 restraints weight = 26652.990| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.60 r_work: 0.2877 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14129 Z= 0.169 Angle : 0.584 13.927 19219 Z= 0.290 Chirality : 0.041 0.176 2242 Planarity : 0.004 0.052 2400 Dihedral : 6.139 59.176 2219 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.77 % Allowed : 21.09 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1753 helix: 1.90 (0.17), residues: 979 sheet: -0.11 (0.40), residues: 187 loop : -1.95 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.003 0.001 HIS A1634 PHE 0.030 0.001 PHE A1835 TYR 0.012 0.001 TYR A2206 ARG 0.002 0.000 ARG A 965 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.87 seconds wall clock time: 59 minutes 42.79 seconds (3582.79 seconds total)