Starting phenix.real_space_refine on Mon Mar 18 01:19:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjv_21701/03_2024/6wjv_21701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjv_21701/03_2024/6wjv_21701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjv_21701/03_2024/6wjv_21701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjv_21701/03_2024/6wjv_21701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjv_21701/03_2024/6wjv_21701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjv_21701/03_2024/6wjv_21701.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 88 5.16 5 C 12520 2.51 5 N 3274 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 802": "OD1" <-> "OD2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 928": "OD1" <-> "OD2" Residue "A TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 975": "OD1" <-> "OD2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "A GLU 1175": "OE1" <-> "OE2" Residue "A ARG 1285": "NH1" <-> "NH2" Residue "A ASP 1291": "OD1" <-> "OD2" Residue "A PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1428": "OE1" <-> "OE2" Residue "A ASP 1467": "OD1" <-> "OD2" Residue "A TYR 1548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1551": "OD1" <-> "OD2" Residue "A ASP 1555": "OD1" <-> "OD2" Residue "A PHE 1558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1572": "NH1" <-> "NH2" Residue "A ASP 1669": "OD1" <-> "OD2" Residue "A ASP 1704": "OD1" <-> "OD2" Residue "A ARG 1833": "NH1" <-> "NH2" Residue "A TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1932": "OD1" <-> "OD2" Residue "A TYR 1933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2105": "OD1" <-> "OD2" Residue "A PHE 2119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2151": "NH1" <-> "NH2" Residue "A ASP 2161": "OD1" <-> "OD2" Residue "A ARG 2163": "NH1" <-> "NH2" Residue "A ARG 2166": "NH1" <-> "NH2" Residue "A ARG 2172": "NH1" <-> "NH2" Residue "A ARG 2191": "NH1" <-> "NH2" Residue "A ASP 2211": "OD1" <-> "OD2" Residue "2 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 382": "OD1" <-> "OD2" Residue "2 PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 506": "OD1" <-> "OD2" Residue "2 PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 552": "NH1" <-> "NH2" Residue "2 ASP 627": "OD1" <-> "OD2" Residue "2 PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 650": "OD1" <-> "OD2" Residue "2 TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 26": "OE1" <-> "OE2" Residue "3 PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 52": "OE1" <-> "OE2" Residue "3 ARG 68": "NH1" <-> "NH2" Residue "3 ARG 81": "NH1" <-> "NH2" Residue "3 PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 43": "NH1" <-> "NH2" Residue "4 GLU 44": "OE1" <-> "OE2" Residue "4 ARG 65": "NH1" <-> "NH2" Residue "4 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 79": "NH1" <-> "NH2" Residue "4 ARG 112": "NH1" <-> "NH2" Residue "4 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19593 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 14886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1951, 14886 Classifications: {'peptide': 1951} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 250} Link IDs: {'PTRANS': 79, 'TRANS': 1871} Chain breaks: 10 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1052 Unresolved non-hydrogen angles: 1285 Unresolved non-hydrogen dihedrals: 910 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 25, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 10, 'GLU:plan': 32, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 597 Chain: "2" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3225 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 24, 'TRANS': 399} Chain breaks: 4 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "3" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 652 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "4" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14066 SG CYS A2111 59.017 83.609 140.895 1.00 59.99 S ATOM 14175 SG CYS A2130 57.816 79.614 144.181 1.00 48.53 S ATOM 14193 SG CYS A2133 56.013 82.706 143.462 1.00 61.49 S Time building chain proxies: 9.54, per 1000 atoms: 0.49 Number of scatterers: 19593 At special positions: 0 Unit cell: (120.393, 119.364, 195.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 88 16.00 O 3710 8.00 N 3274 7.00 C 12520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2167 " - pdb=" SG CYS A2179 " distance=2.02 Simple disulfide: pdb=" SG CYS A2167 " - pdb=" SG CYS A2181 " distance=2.04 Simple disulfide: pdb=" SG CYS A2179 " - pdb=" SG CYS A2181 " distance=2.07 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=0, symmetry=0 Time building additional restraints: 7.07 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2111 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2133 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2130 " 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 22 sheets defined 37.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 31 through 48 removed outlier: 3.788A pdb=" N GLN A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.916A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.598A pdb=" N LEU A 182 " --> pdb=" O ASN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 214 removed outlier: 3.523A pdb=" N LEU A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Proline residue: A 208 - end of helix removed outlier: 3.691A pdb=" N GLN A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 354 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.684A pdb=" N ILE A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.935A pdb=" N VAL A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.756A pdb=" N LEU A 458 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.989A pdb=" N PHE A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 498 removed outlier: 3.793A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 511 through 527 removed outlier: 3.551A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 585 removed outlier: 4.026A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 599 Processing helix chain 'A' and resid 609 through 627 removed outlier: 3.602A pdb=" N ILE A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 693 through 705 Processing helix chain 'A' and resid 728 through 746 Processing helix chain 'A' and resid 768 through 799 removed outlier: 3.945A pdb=" N ASP A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 834 Processing helix chain 'A' and resid 843 through 867 removed outlier: 3.900A pdb=" N ALA A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR A 850 " --> pdb=" O MET A 846 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 992 through 1007 removed outlier: 3.593A pdb=" N LYS A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1032 Processing helix chain 'A' and resid 1039 through 1047 removed outlier: 3.775A pdb=" N CYS A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 4.011A pdb=" N GLU A1060 " --> pdb=" O LYS A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1077 removed outlier: 3.702A pdb=" N ALA A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1104 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1115 through 1128 removed outlier: 3.826A pdb=" N ARG A1124 " --> pdb=" O ARG A1120 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A1125 " --> pdb=" O SER A1121 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP A1126 " --> pdb=" O PHE A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 3.718A pdb=" N ILE A1140 " --> pdb=" O ASP A1136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1136 through 1141' Processing helix chain 'A' and resid 1142 through 1158 removed outlier: 3.814A pdb=" N TYR A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1182 Processing helix chain 'A' and resid 1272 through 1294 Processing helix chain 'A' and resid 1298 through 1302 removed outlier: 4.098A pdb=" N GLU A1302 " --> pdb=" O SER A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1316 Processing helix chain 'A' and resid 1454 through 1462 Processing helix chain 'A' and resid 1525 through 1546 removed outlier: 3.676A pdb=" N TYR A1546 " --> pdb=" O LYS A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1584 removed outlier: 3.767A pdb=" N ARG A1584 " --> pdb=" O LEU A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1656 removed outlier: 3.659A pdb=" N VAL A1639 " --> pdb=" O LEU A1635 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A1656 " --> pdb=" O LEU A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1683 removed outlier: 3.903A pdb=" N GLU A1683 " --> pdb=" O LYS A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1709 removed outlier: 4.297A pdb=" N ASN A1708 " --> pdb=" O ASP A1704 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A1709 " --> pdb=" O PHE A1705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1704 through 1709' Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.771A pdb=" N ILE A1744 " --> pdb=" O THR A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1802 removed outlier: 3.780A pdb=" N ASP A1800 " --> pdb=" O LYS A1796 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A1802 " --> pdb=" O TRP A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1820 removed outlier: 4.116A pdb=" N ASN A1814 " --> pdb=" O ASP A1810 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A1820 " --> pdb=" O LEU A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1831 through 1847 Processing helix chain 'A' and resid 1878 through 1892 removed outlier: 4.113A pdb=" N ASN A1892 " --> pdb=" O ALA A1888 " (cutoff:3.500A) Processing helix chain 'A' and resid 1948 through 1975 removed outlier: 3.905A pdb=" N ILE A1960 " --> pdb=" O TRP A1956 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A1961 " --> pdb=" O MET A1957 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A1975 " --> pdb=" O TYR A1971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1995 through 2022 removed outlier: 3.513A pdb=" N SER A2000 " --> pdb=" O SER A1996 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A2001 " --> pdb=" O VAL A1997 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A2002 " --> pdb=" O GLU A1998 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A2003 " --> pdb=" O ASN A1999 " (cutoff:3.500A) Proline residue: A2011 - end of helix removed outlier: 3.883A pdb=" N ASN A2022 " --> pdb=" O LYS A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2033 Processing helix chain 'A' and resid 2048 through 2055 Processing helix chain 'A' and resid 2139 through 2158 Processing helix chain 'A' and resid 2190 through 2208 removed outlier: 4.033A pdb=" N ILE A2194 " --> pdb=" O PRO A2190 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A2208 " --> pdb=" O VAL A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2210 through 2220 Processing helix chain '2' and resid 210 through 224 Processing helix chain '2' and resid 225 through 229 removed outlier: 3.825A pdb=" N VAL 2 229 " --> pdb=" O ASN 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 351 through 356 removed outlier: 3.680A pdb=" N LEU 2 356 " --> pdb=" O ARG 2 352 " (cutoff:3.500A) Processing helix chain '2' and resid 385 through 394 removed outlier: 4.146A pdb=" N LEU 2 394 " --> pdb=" O LEU 2 390 " (cutoff:3.500A) Processing helix chain '2' and resid 410 through 426 removed outlier: 3.575A pdb=" N MET 2 414 " --> pdb=" O ASP 2 410 " (cutoff:3.500A) Processing helix chain '2' and resid 455 through 470 Processing helix chain '2' and resid 545 through 550 Processing helix chain '3' and resid 13 through 20 removed outlier: 3.721A pdb=" N VAL 3 17 " --> pdb=" O PRO 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 33 through 53 Processing helix chain '3' and resid 70 through 81 removed outlier: 3.684A pdb=" N ARG 3 81 " --> pdb=" O CYS 3 77 " (cutoff:3.500A) Processing helix chain '4' and resid 35 through 41 Processing helix chain '4' and resid 56 through 83 removed outlier: 3.504A pdb=" N LYS 4 83 " --> pdb=" O ARG 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 96 Processing helix chain '4' and resid 104 through 122 Proline residue: 4 110 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.690A pdb=" N ILE A 273 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 271 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 86 removed outlier: 3.594A pdb=" N GLY A 116 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 172 removed outlier: 3.875A pdb=" N SER A 166 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 187 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N CYS A 143 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 189 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP A 241 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 288 removed outlier: 6.313A pdb=" N MET A 287 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 374 " --> pdb=" O MET A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.645A pdb=" N MET A 309 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY A 319 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N PHE A 350 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 321 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU A 352 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR A 323 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 347 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AA7, first strand: chain 'A' and resid 552 through 553 removed outlier: 3.500A pdb=" N TRP A 683 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 756 " --> pdb=" O TRP A 685 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 687 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 754 " --> pdb=" O GLY A 687 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 689 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 761 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 560 removed outlier: 6.564A pdb=" N TRP A 880 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 564 through 567 removed outlier: 4.933A pdb=" N ALA A 952 " --> pdb=" O PHE A 972 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 972 " --> pdb=" O ALA A 952 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 982 " --> pdb=" O TYR A 969 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 572 through 573 removed outlier: 3.542A pdb=" N GLU A 632 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 709 through 710 removed outlier: 3.529A pdb=" N PHE A 709 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 890 through 894 Processing sheet with id=AB4, first strand: chain 'A' and resid 920 through 926 removed outlier: 5.676A pdb=" N HIS A 921 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU A 939 " --> pdb=" O HIS A 921 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 923 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1091 through 1093 Processing sheet with id=AB6, first strand: chain 'A' and resid 1445 through 1446 Processing sheet with id=AB7, first strand: chain 'A' and resid 1500 through 1503 Processing sheet with id=AB8, first strand: chain 'A' and resid 1512 through 1513 Processing sheet with id=AB9, first strand: chain '2' and resid 284 through 287 removed outlier: 3.781A pdb=" N SER 2 343 " --> pdb=" O GLU 2 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 296 through 300 removed outlier: 4.460A pdb=" N TRP 2 296 " --> pdb=" O ILE 2 307 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP 2 300 " --> pdb=" O GLY 2 303 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY 2 303 " --> pdb=" O ASP 2 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 399 through 400 removed outlier: 3.545A pdb=" N LYS 2 681 " --> pdb=" O VAL 2 676 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '2' and resid 481 through 483 Processing sheet with id=AC4, first strand: chain '2' and resid 541 through 543 removed outlier: 6.315A pdb=" N PHE 2 542 " --> pdb=" O CYS 2 642 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL 2 658 " --> pdb=" O LEU 2 651 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU 2 651 " --> pdb=" O VAL 2 658 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2121 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: 7.02 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5644 1.34 - 1.47: 5380 1.47 - 1.60: 8821 1.60 - 1.73: 4 1.73 - 1.86: 137 Bond restraints: 19986 Sorted by residual: bond pdb=" N PRO A1161 " pdb=" CD PRO A1161 " ideal model delta sigma weight residual 1.473 1.350 0.123 1.40e-02 5.10e+03 7.71e+01 bond pdb=" C LYS A1515 " pdb=" N PRO A1516 " ideal model delta sigma weight residual 1.335 1.407 -0.072 8.70e-03 1.32e+04 6.80e+01 bond pdb=" N PRO 4 110 " pdb=" CD PRO 4 110 " ideal model delta sigma weight residual 1.473 1.370 0.103 1.40e-02 5.10e+03 5.36e+01 bond pdb=" C HIS A 490 " pdb=" N PRO A 491 " ideal model delta sigma weight residual 1.337 1.419 -0.082 1.24e-02 6.50e+03 4.39e+01 bond pdb=" CA LYS A1540 " pdb=" C LYS A1540 " ideal model delta sigma weight residual 1.523 1.460 0.062 1.37e-02 5.33e+03 2.08e+01 ... (remaining 19981 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.82: 519 105.82 - 113.85: 10759 113.85 - 121.88: 11641 121.88 - 129.91: 4086 129.91 - 137.94: 148 Bond angle restraints: 27153 Sorted by residual: angle pdb=" N ILE A1310 " pdb=" CA ILE A1310 " pdb=" C ILE A1310 " ideal model delta sigma weight residual 111.90 102.91 8.99 8.10e-01 1.52e+00 1.23e+02 angle pdb=" N ILE 4 28 " pdb=" CA ILE 4 28 " pdb=" C ILE 4 28 " ideal model delta sigma weight residual 111.90 103.08 8.82 8.10e-01 1.52e+00 1.18e+02 angle pdb=" N ILE A1552 " pdb=" CA ILE A1552 " pdb=" C ILE A1552 " ideal model delta sigma weight residual 112.90 102.97 9.93 9.60e-01 1.09e+00 1.07e+02 angle pdb=" N ILE A1721 " pdb=" CA ILE A1721 " pdb=" C ILE A1721 " ideal model delta sigma weight residual 112.90 103.29 9.61 9.60e-01 1.09e+00 1.00e+02 angle pdb=" N ILE 2 385 " pdb=" CA ILE 2 385 " pdb=" C ILE 2 385 " ideal model delta sigma weight residual 112.83 103.32 9.51 9.90e-01 1.02e+00 9.23e+01 ... (remaining 27148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10595 17.96 - 35.92: 1127 35.92 - 53.88: 271 53.88 - 71.85: 43 71.85 - 89.81: 9 Dihedral angle restraints: 12045 sinusoidal: 4506 harmonic: 7539 Sorted by residual: dihedral pdb=" CB CYS A2179 " pdb=" SG CYS A2179 " pdb=" SG CYS A2181 " pdb=" CB CYS A2181 " ideal model delta sinusoidal sigma weight residual -86.00 -4.39 -81.61 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS A2167 " pdb=" SG CYS A2167 " pdb=" SG CYS A2181 " pdb=" CB CYS A2181 " ideal model delta sinusoidal sigma weight residual -86.00 -151.88 65.88 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CA GLY 2 403 " pdb=" C GLY 2 403 " pdb=" N ALA 2 404 " pdb=" CA ALA 2 404 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 12042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2260 0.079 - 0.157: 674 0.157 - 0.236: 150 0.236 - 0.315: 36 0.315 - 0.393: 15 Chirality restraints: 3135 Sorted by residual: chirality pdb=" CA ASN A1386 " pdb=" N ASN A1386 " pdb=" C ASN A1386 " pdb=" CB ASN A1386 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CB ILE 2 508 " pdb=" CA ILE 2 508 " pdb=" CG1 ILE 2 508 " pdb=" CG2 ILE 2 508 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA GLU A1876 " pdb=" N GLU A1876 " pdb=" C GLU A1876 " pdb=" CB GLU A1876 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 3132 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 2 321 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO 2 322 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO 2 322 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO 2 322 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1096 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A1097 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A1097 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1097 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1693 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A1694 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO A1694 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1694 " -0.062 5.00e-02 4.00e+02 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 3 2.15 - 2.84: 6017 2.84 - 3.53: 25330 3.53 - 4.21: 43960 4.21 - 4.90: 74486 Nonbonded interactions: 149796 Sorted by model distance: nonbonded pdb=" CB ALA A1114 " pdb=" NH2 ARG A1289 " model vdw 1.466 3.540 nonbonded pdb=" OD1 ASP A 306 " pdb=" NH1 ARG A1301 " model vdw 1.927 2.520 nonbonded pdb=" OD1 ASP A1115 " pdb=" CG1 ILE A1118 " model vdw 1.993 3.440 nonbonded pdb=" CA ALA A1114 " pdb=" NH2 ARG A1289 " model vdw 2.190 3.550 nonbonded pdb=" OD1 ASP A1115 " pdb=" CB ILE A1118 " model vdw 2.192 3.470 ... (remaining 149791 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.200 Check model and map are aligned: 0.230 Set scattering table: 0.190 Process input model: 52.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 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 : 0.009 0.123 19986 Z= 0.586 Angle : 1.665 19.895 27153 Z= 1.056 Chirality : 0.083 0.393 3135 Planarity : 0.011 0.129 3496 Dihedral : 15.508 89.806 7130 Min Nonbonded Distance : 1.466 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 0.05 % Allowed : 14.10 % Favored : 85.85 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -5.50 (0.11), residues: 2531 helix: -4.06 (0.09), residues: 895 sheet: -2.49 (0.30), residues: 248 loop : -3.70 (0.12), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 683 HIS 0.014 0.002 HIS A1489 PHE 0.048 0.004 PHE 2 462 TYR 0.037 0.003 TYR A1933 ARG 0.018 0.001 ARG 2 669 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 LYS cc_start: 0.6145 (pttm) cc_final: 0.5504 (tptt) REVERT: A 1005 VAL cc_start: 0.7124 (m) cc_final: 0.6436 (p) REVERT: A 1366 MET cc_start: 0.6600 (tpt) cc_final: 0.5477 (pmm) REVERT: A 1885 MET cc_start: 0.8029 (tpt) cc_final: 0.7591 (ptt) REVERT: 2 270 PRO cc_start: 0.5748 (Cg_exo) cc_final: 0.5520 (Cg_endo) REVERT: 2 348 PRO cc_start: 0.6107 (Cg_endo) cc_final: 0.5775 (Cg_exo) REVERT: 2 669 ARG cc_start: 0.5715 (pmt-80) cc_final: 0.5443 (mmt-90) REVERT: 2 681 LYS cc_start: 0.7873 (mppt) cc_final: 0.7357 (mtpp) outliers start: 1 outliers final: 1 residues processed: 340 average time/residue: 0.3288 time to fit residues: 167.9295 Evaluate side-chains 200 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 43 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 199 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 148 optimal weight: 0.0870 chunk 231 optimal weight: 0.8980 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 389 ASN A 437 GLN A 523 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 794 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 HIS A1176 HIS A1489 HIS ** A1519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1609 GLN A1618 ASN A1624 GLN ** A1789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1838 ASN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2145 HIS ** A2199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 537 GLN 4 72 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19986 Z= 0.189 Angle : 0.684 11.551 27153 Z= 0.360 Chirality : 0.044 0.198 3135 Planarity : 0.006 0.088 3496 Dihedral : 5.241 33.245 2718 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.60 % Allowed : 17.93 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.85 (0.14), residues: 2531 helix: -1.81 (0.14), residues: 923 sheet: -1.74 (0.31), residues: 253 loop : -3.38 (0.13), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 2 525 HIS 0.018 0.001 HIS 2 666 PHE 0.026 0.002 PHE A1563 TYR 0.029 0.002 TYR A1884 ARG 0.004 0.000 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7409 (mt) REVERT: A 177 MET cc_start: 0.5748 (mtp) cc_final: 0.5508 (mtp) REVERT: A 505 ASP cc_start: 0.6251 (t70) cc_final: 0.6023 (t70) REVERT: A 844 MET cc_start: 0.6466 (tmm) cc_final: 0.6234 (tmm) REVERT: A 987 LYS cc_start: 0.6478 (pttm) cc_final: 0.5871 (tptt) REVERT: A 1436 ARG cc_start: 0.5405 (ptt180) cc_final: 0.4776 (ptt90) REVERT: A 1662 ASN cc_start: 0.6446 (OUTLIER) cc_final: 0.5586 (p0) REVERT: A 1885 MET cc_start: 0.8039 (tpt) cc_final: 0.7504 (ptt) REVERT: 2 224 LEU cc_start: 0.8450 (mp) cc_final: 0.8084 (mt) REVERT: 2 348 PRO cc_start: 0.5560 (Cg_endo) cc_final: 0.5216 (Cg_exo) REVERT: 2 681 LYS cc_start: 0.7899 (mppt) cc_final: 0.7530 (mtpp) REVERT: 3 51 GLU cc_start: 0.7917 (tp30) cc_final: 0.7547 (tm-30) outliers start: 53 outliers final: 24 residues processed: 267 average time/residue: 0.2721 time to fit residues: 116.5491 Evaluate side-chains 215 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 PHE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1648 HIS Chi-restraints excluded: chain A residue 1662 ASN Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 626 LEU Chi-restraints excluded: chain 3 residue 82 ASP Chi-restraints excluded: chain 4 residue 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 63 optimal weight: 0.0670 chunk 231 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 230 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 GLN A1489 HIS A1618 ASN ** A1789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 553 HIS 4 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19986 Z= 0.259 Angle : 0.708 11.259 27153 Z= 0.369 Chirality : 0.045 0.189 3135 Planarity : 0.005 0.081 3496 Dihedral : 5.340 28.009 2715 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 4.08 % Allowed : 18.27 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.94 (0.15), residues: 2531 helix: -0.60 (0.16), residues: 919 sheet: -1.29 (0.34), residues: 239 loop : -3.19 (0.14), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1911 HIS 0.013 0.001 HIS 2 666 PHE 0.029 0.002 PHE 2 542 TYR 0.033 0.002 TYR A1884 ARG 0.006 0.001 ARG 2 671 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 202 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7605 (mm) REVERT: A 177 MET cc_start: 0.5558 (mtp) cc_final: 0.5341 (mtp) REVERT: A 259 ILE cc_start: 0.7139 (mm) cc_final: 0.6563 (mm) REVERT: A 953 MET cc_start: 0.7120 (mmm) cc_final: 0.6889 (tpp) REVERT: A 987 LYS cc_start: 0.6422 (pttm) cc_final: 0.5932 (tptt) REVERT: A 1551 ASP cc_start: 0.6925 (p0) cc_final: 0.6606 (p0) REVERT: A 1662 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6330 (p0) REVERT: A 1912 MET cc_start: 0.5427 (tmm) cc_final: 0.5216 (tmm) REVERT: A 1920 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.6092 (mm) REVERT: 2 218 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5532 (t80) REVERT: 2 222 TYR cc_start: 0.6970 (t80) cc_final: 0.6681 (t80) REVERT: 2 274 LEU cc_start: 0.3720 (OUTLIER) cc_final: 0.3120 (tt) REVERT: 2 348 PRO cc_start: 0.5844 (Cg_endo) cc_final: 0.5404 (Cg_exo) REVERT: 2 544 ASP cc_start: 0.6564 (p0) cc_final: 0.6309 (p0) REVERT: 2 681 LYS cc_start: 0.8054 (mppt) cc_final: 0.7731 (mtpt) REVERT: 3 51 GLU cc_start: 0.8080 (tp30) cc_final: 0.7731 (tm-30) outliers start: 83 outliers final: 42 residues processed: 271 average time/residue: 0.2827 time to fit residues: 123.7261 Evaluate side-chains 218 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1006 PHE Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 PHE Chi-restraints excluded: chain A residue 1445 VAL Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1626 ASN Chi-restraints excluded: chain A residue 1662 ASN Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1703 ASN Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 220 THR Chi-restraints excluded: chain 2 residue 274 LEU Chi-restraints excluded: chain 2 residue 432 LEU Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 626 LEU Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 2 residue 682 THR Chi-restraints excluded: chain 3 residue 43 GLU Chi-restraints excluded: chain 4 residue 56 ASN Chi-restraints excluded: chain 4 residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 155 optimal weight: 0.0670 chunk 232 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 220 optimal weight: 0.1980 chunk 66 optimal weight: 20.0000 overall best weight: 2.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 213 ASN A 523 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS A1413 ASN ** A1657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1837 HIS 2 226 ASN ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19986 Z= 0.300 Angle : 0.710 12.333 27153 Z= 0.368 Chirality : 0.046 0.189 3135 Planarity : 0.005 0.077 3496 Dihedral : 5.576 28.798 2715 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.52 % Allowed : 19.11 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.15), residues: 2531 helix: -0.31 (0.17), residues: 938 sheet: -1.49 (0.35), residues: 229 loop : -3.11 (0.14), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1627 HIS 0.011 0.001 HIS 2 666 PHE 0.037 0.002 PHE 2 542 TYR 0.029 0.002 TYR A1884 ARG 0.004 0.001 ARG 2 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 193 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6339 (ptt) cc_final: 0.6116 (ptt) REVERT: A 177 MET cc_start: 0.5433 (mtp) cc_final: 0.5191 (mtp) REVERT: A 213 ASN cc_start: 0.6073 (OUTLIER) cc_final: 0.5689 (m110) REVERT: A 259 ILE cc_start: 0.7223 (mm) cc_final: 0.6722 (mm) REVERT: A 844 MET cc_start: 0.6936 (tmm) cc_final: 0.6655 (tmm) REVERT: A 953 MET cc_start: 0.7071 (mmm) cc_final: 0.6590 (tpp) REVERT: A 987 LYS cc_start: 0.6578 (pttm) cc_final: 0.6034 (tptt) REVERT: A 1618 ASN cc_start: 0.7156 (OUTLIER) cc_final: 0.6754 (m110) REVERT: A 1912 MET cc_start: 0.5539 (tmm) cc_final: 0.5178 (tmm) REVERT: A 1920 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6310 (mm) REVERT: 2 218 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5592 (t80) REVERT: 2 274 LEU cc_start: 0.4367 (OUTLIER) cc_final: 0.3929 (tt) REVERT: 2 681 LYS cc_start: 0.8044 (mppt) cc_final: 0.7735 (mtpt) REVERT: 3 51 GLU cc_start: 0.8142 (tp30) cc_final: 0.7749 (tm-30) outliers start: 92 outliers final: 53 residues processed: 272 average time/residue: 0.2575 time to fit residues: 116.1786 Evaluate side-chains 231 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 173 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 PHE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1445 VAL Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1594 SER Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1618 ASN Chi-restraints excluded: chain A residue 1626 ASN Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 220 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 274 LEU Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 625 ASP Chi-restraints excluded: chain 2 residue 626 LEU Chi-restraints excluded: chain 2 residue 638 THR Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 2 residue 682 THR Chi-restraints excluded: chain 3 residue 89 ASP Chi-restraints excluded: chain 4 residue 56 ASN Chi-restraints excluded: chain 4 residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.0020 chunk 139 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 170 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 0.0570 chunk 221 optimal weight: 0.0020 chunk 62 optimal weight: 3.9990 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN A 652 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1276 GLN A1296 ASN A1657 ASN 4 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19986 Z= 0.164 Angle : 0.627 9.146 27153 Z= 0.319 Chirality : 0.043 0.210 3135 Planarity : 0.004 0.075 3496 Dihedral : 5.117 25.147 2715 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.09 % Allowed : 20.87 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.29 (0.16), residues: 2531 helix: 0.24 (0.17), residues: 927 sheet: -1.65 (0.34), residues: 240 loop : -2.91 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1627 HIS 0.009 0.001 HIS 2 666 PHE 0.029 0.001 PHE 2 542 TYR 0.028 0.001 TYR A1884 ARG 0.004 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 213 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7536 (mm) REVERT: A 177 MET cc_start: 0.5233 (mtp) cc_final: 0.4997 (mtp) REVERT: A 259 ILE cc_start: 0.7079 (mm) cc_final: 0.6489 (mm) REVERT: A 830 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6054 (t80) REVERT: A 844 MET cc_start: 0.6740 (tmm) cc_final: 0.6400 (tmm) REVERT: A 987 LYS cc_start: 0.6450 (pttm) cc_final: 0.5941 (tptt) REVERT: A 1618 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6645 (m110) REVERT: A 1912 MET cc_start: 0.5347 (tmm) cc_final: 0.5017 (tmm) REVERT: 2 218 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5642 (t80) REVERT: 2 274 LEU cc_start: 0.4223 (OUTLIER) cc_final: 0.3837 (tt) REVERT: 2 481 MET cc_start: 0.6621 (mmm) cc_final: 0.6418 (mmm) REVERT: 2 544 ASP cc_start: 0.6497 (p0) cc_final: 0.5737 (p0) REVERT: 2 681 LYS cc_start: 0.8062 (mppt) cc_final: 0.7746 (mtpt) REVERT: 3 51 GLU cc_start: 0.8020 (tp30) cc_final: 0.7599 (tm-30) outliers start: 63 outliers final: 38 residues processed: 268 average time/residue: 0.2596 time to fit residues: 114.3089 Evaluate side-chains 230 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 PHE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1594 SER Chi-restraints excluded: chain A residue 1618 ASN Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 274 LEU Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 625 ASP Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 4 residue 56 ASN Chi-restraints excluded: chain 4 residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1703 ASN ** A1789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19986 Z= 0.327 Angle : 0.726 11.398 27153 Z= 0.376 Chirality : 0.047 0.321 3135 Planarity : 0.005 0.070 3496 Dihedral : 5.610 27.460 2715 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 4.27 % Allowed : 20.87 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.38 (0.16), residues: 2531 helix: 0.15 (0.17), residues: 942 sheet: -1.48 (0.35), residues: 231 loop : -3.03 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 2 296 HIS 0.012 0.001 HIS 2 666 PHE 0.032 0.002 PHE 2 542 TYR 0.029 0.002 TYR A1884 ARG 0.005 0.001 ARG A1436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 183 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 CYS cc_start: 0.5072 (OUTLIER) cc_final: 0.4450 (p) REVERT: A 259 ILE cc_start: 0.7258 (mm) cc_final: 0.6784 (mm) REVERT: A 386 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 459 MET cc_start: 0.6756 (tmm) cc_final: 0.6106 (tmm) REVERT: A 844 MET cc_start: 0.6876 (tmm) cc_final: 0.6485 (tmm) REVERT: A 945 GLU cc_start: 0.7684 (pp20) cc_final: 0.7354 (pp20) REVERT: A 1618 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6785 (m110) REVERT: A 1829 ASP cc_start: 0.5662 (OUTLIER) cc_final: 0.5257 (p0) REVERT: A 1912 MET cc_start: 0.5768 (tmm) cc_final: 0.5561 (tmm) REVERT: 2 218 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.5755 (t80) REVERT: 2 222 TYR cc_start: 0.7328 (t80) cc_final: 0.7066 (t80) REVERT: 2 274 LEU cc_start: 0.3845 (OUTLIER) cc_final: 0.3590 (tt) REVERT: 2 681 LYS cc_start: 0.8245 (mppt) cc_final: 0.7805 (mtpt) REVERT: 3 51 GLU cc_start: 0.8177 (tp30) cc_final: 0.7727 (tm-30) outliers start: 87 outliers final: 62 residues processed: 255 average time/residue: 0.2799 time to fit residues: 115.9698 Evaluate side-chains 244 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 176 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 738 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 PHE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1594 SER Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1618 ASN Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1703 ASN Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 1829 ASP Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1884 TYR Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 220 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 274 LEU Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 328 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 431 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 625 ASP Chi-restraints excluded: chain 2 residue 659 ILE Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 2 residue 682 THR Chi-restraints excluded: chain 3 residue 70 SER Chi-restraints excluded: chain 4 residue 56 ASN Chi-restraints excluded: chain 4 residue 61 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 245 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 149 optimal weight: 0.0010 chunk 113 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19986 Z= 0.165 Angle : 0.624 9.521 27153 Z= 0.317 Chirality : 0.043 0.192 3135 Planarity : 0.004 0.073 3496 Dihedral : 5.109 24.586 2715 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.34 % Allowed : 22.64 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.03 (0.16), residues: 2531 helix: 0.51 (0.18), residues: 938 sheet: -1.44 (0.35), residues: 226 loop : -2.84 (0.15), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1627 HIS 0.007 0.001 HIS 2 666 PHE 0.021 0.001 PHE 2 542 TYR 0.028 0.001 TYR A1884 ARG 0.003 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 202 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7604 (mm) REVERT: A 259 ILE cc_start: 0.7075 (mm) cc_final: 0.6461 (mm) REVERT: A 457 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7057 (pt0) REVERT: A 459 MET cc_start: 0.6819 (tmm) cc_final: 0.6132 (tmm) REVERT: A 830 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6179 (t80) REVERT: A 987 LYS cc_start: 0.6280 (pttm) cc_final: 0.5423 (tptt) REVERT: A 1482 MET cc_start: 0.8060 (ptm) cc_final: 0.7736 (ptt) REVERT: A 1618 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6544 (m110) REVERT: A 1638 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6547 (m170) REVERT: 2 222 TYR cc_start: 0.7103 (t80) cc_final: 0.6784 (t80) REVERT: 2 274 LEU cc_start: 0.3585 (OUTLIER) cc_final: 0.3355 (tt) REVERT: 2 681 LYS cc_start: 0.8102 (mppt) cc_final: 0.7788 (mtpt) REVERT: 3 51 GLU cc_start: 0.8024 (tp30) cc_final: 0.7588 (tm-30) outliers start: 68 outliers final: 49 residues processed: 260 average time/residue: 0.2777 time to fit residues: 116.4769 Evaluate side-chains 236 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 181 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 PHE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1594 SER Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1618 ASN Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1638 HIS Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1884 TYR Chi-restraints excluded: chain A residue 1917 PHE Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain A residue 2179 CYS Chi-restraints excluded: chain 2 residue 274 LEU Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 321 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 625 ASP Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 4 residue 56 ASN Chi-restraints excluded: chain 4 residue 61 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19986 Z= 0.192 Angle : 0.635 9.741 27153 Z= 0.323 Chirality : 0.044 0.258 3135 Planarity : 0.004 0.074 3496 Dihedral : 5.082 27.306 2715 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.63 % Allowed : 22.94 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.16), residues: 2531 helix: 0.60 (0.18), residues: 941 sheet: -1.37 (0.35), residues: 225 loop : -2.79 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1627 HIS 0.008 0.001 HIS 2 666 PHE 0.022 0.001 PHE 2 542 TYR 0.028 0.001 TYR A1884 ARG 0.012 0.000 ARG 3 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 180 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7611 (mm) REVERT: A 259 ILE cc_start: 0.7125 (mm) cc_final: 0.6561 (mm) REVERT: A 830 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6145 (t80) REVERT: A 947 ASP cc_start: 0.4993 (OUTLIER) cc_final: 0.3492 (t0) REVERT: A 953 MET cc_start: 0.6875 (tmm) cc_final: 0.6468 (tpp) REVERT: A 987 LYS cc_start: 0.6233 (pttm) cc_final: 0.5148 (tptt) REVERT: A 1618 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6714 (m110) REVERT: A 1638 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6606 (m170) REVERT: 2 222 TYR cc_start: 0.7173 (t80) cc_final: 0.6826 (t80) REVERT: 2 274 LEU cc_start: 0.3580 (OUTLIER) cc_final: 0.3340 (tt) REVERT: 2 681 LYS cc_start: 0.8089 (mppt) cc_final: 0.7782 (mtpt) REVERT: 3 51 GLU cc_start: 0.8081 (tp30) cc_final: 0.7644 (tm-30) outliers start: 74 outliers final: 55 residues processed: 246 average time/residue: 0.2687 time to fit residues: 109.1314 Evaluate side-chains 233 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 172 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 PHE Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1445 VAL Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1594 SER Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1618 ASN Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1638 HIS Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1815 SER Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1884 TYR Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 274 LEU Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 321 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 70 SER Chi-restraints excluded: chain 3 residue 89 ASP Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.5355 > 50: distance: 54 - 59: 26.468 distance: 59 - 60: 39.895 distance: 60 - 63: 39.881 distance: 61 - 62: 32.104 distance: 61 - 67: 39.787 distance: 63 - 64: 23.315 distance: 64 - 65: 42.808 distance: 64 - 66: 19.523 distance: 67 - 68: 53.052 distance: 67 - 73: 56.259 distance: 68 - 69: 8.789 distance: 68 - 71: 17.289 distance: 69 - 70: 13.020 distance: 69 - 74: 47.998 distance: 71 - 72: 29.523 distance: 72 - 73: 6.128 distance: 74 - 75: 21.769 distance: 75 - 76: 27.985 distance: 75 - 78: 16.084 distance: 76 - 77: 50.437 distance: 76 - 83: 46.451 distance: 78 - 79: 27.643 distance: 79 - 80: 43.472 distance: 80 - 81: 32.221 distance: 80 - 82: 20.618 distance: 83 - 84: 44.678 distance: 84 - 85: 34.685 distance: 84 - 87: 33.953 distance: 85 - 86: 21.852 distance: 85 - 91: 22.735 distance: 87 - 88: 42.992 distance: 88 - 89: 28.844 distance: 88 - 90: 33.015 distance: 91 - 92: 19.922 distance: 91 - 97: 44.680 distance: 92 - 93: 19.660 distance: 92 - 95: 42.459 distance: 93 - 94: 25.034 distance: 93 - 98: 14.271 distance: 95 - 96: 36.666 distance: 96 - 97: 46.520 distance: 98 - 99: 18.481 distance: 99 - 100: 17.816 distance: 99 - 102: 21.540 distance: 100 - 101: 27.182 distance: 100 - 106: 13.324 distance: 102 - 103: 27.748 distance: 102 - 104: 19.875 distance: 103 - 105: 30.910 distance: 106 - 107: 35.559 distance: 106 - 112: 23.232 distance: 107 - 108: 22.672 distance: 107 - 110: 37.626 distance: 108 - 109: 18.507 distance: 108 - 113: 29.195 distance: 110 - 111: 31.004 distance: 111 - 112: 32.145 distance: 113 - 114: 8.077 distance: 114 - 115: 24.045 distance: 114 - 117: 29.098 distance: 115 - 116: 19.041 distance: 115 - 119: 23.698 distance: 119 - 120: 28.620 distance: 120 - 121: 29.365 distance: 120 - 123: 42.152 distance: 121 - 122: 21.959 distance: 121 - 124: 10.802 distance: 124 - 125: 27.403 distance: 125 - 126: 3.368 distance: 125 - 128: 14.302 distance: 126 - 127: 31.160 distance: 126 - 135: 18.627 distance: 128 - 129: 28.505 distance: 129 - 130: 8.982 distance: 129 - 131: 17.662 distance: 130 - 132: 9.930 distance: 131 - 133: 7.644 distance: 132 - 134: 9.058 distance: 133 - 134: 15.920