Starting phenix.real_space_refine on Thu Mar 5 05:35:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wjv_21701/03_2026/6wjv_21701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wjv_21701/03_2026/6wjv_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/cci-nas-00/data/ceres_data/6wjv_21701/03_2026/6wjv_21701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wjv_21701/03_2026/6wjv_21701.map" model { file = "/net/cci-nas-00/data/ceres_data/6wjv_21701/03_2026/6wjv_21701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wjv_21701/03_2026/6wjv_21701.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'TYR:plan': 10, 'ASN:plan1': 13, 'GLN:plan1': 19, 'GLU:plan': 32, 'ASP:plan': 13, 'HIS:plan': 5, 'ARG:plan': 25, 'PHE:plan': 10, 'TRP:plan': 4} 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: {'TYR:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'TRP:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 2} 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: 4.44, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 974.3 milliseconds 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: 0.88 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: 4.02 Time building geometry restraints manager: 2.01 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: 0.00 - 3.98: 26142 3.98 - 7.96: 874 7.96 - 11.94: 113 11.94 - 15.92: 22 15.92 - 19.89: 2 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: 1.93 - 2.52: 121 2.52 - 3.12: 11659 3.12 - 3.71: 30951 3.71 - 4.31: 40318 4.31 - 4.90: 66744 Nonbonded interactions: 149793 Sorted by model distance: nonbonded pdb=" OD1 ASP A 306 " pdb=" NH1 ARG A1301 " model vdw 1.927 3.120 nonbonded pdb=" OD1 ASP A1115 " pdb=" CG1 ILE A1118 " model vdw 1.993 3.440 nonbonded pdb=" OD1 ASP A1115 " pdb=" CB ILE A1118 " model vdw 2.192 3.470 nonbonded pdb=" OD2 ASP A1115 " pdb=" CG1 ILE A1118 " model vdw 2.210 3.440 nonbonded pdb=" N ASP A1115 " pdb=" NH2 ARG A1289 " model vdw 2.254 3.200 ... (remaining 149788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- 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 : 0.010 0.503 19993 Z= 0.497 Angle : 1.672 19.895 27159 Z= 1.058 Chirality : 0.083 0.393 3135 Planarity : 0.011 0.129 3496 Dihedral : 15.508 89.806 7130 Min Nonbonded Distance : 1.927 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.018 0.001 ARG 2 669 TYR 0.037 0.003 TYR A1933 PHE 0.048 0.004 PHE 2 462 TRP 0.026 0.003 TRP A 683 HIS 0.014 0.002 HIS A1489 Details of bonding type rmsd covalent geometry : bond 0.00909 (19986) covalent geometry : angle 1.66469 (27153) SS BOND : bond 0.02505 ( 3) SS BOND : angle 10.80799 ( 6) hydrogen bonds : bond 0.19532 ( 735) hydrogen bonds : angle 8.39049 ( 2121) metal coordination : bond 0.42569 ( 3) Misc. bond : bond 0.03594 ( 1) *********************** 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 to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 0.642 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: 0.1471 time to fit residues: 75.8763 Evaluate side-chains 200 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0070 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 523 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN A1033 HIS A1176 HIS A1276 GLN A1489 HIS A1609 GLN A1618 ASN A1624 GLN A1838 ASN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 189 GLN 2 537 GLN 4 72 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.141208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.124040 restraints weight = 59375.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.123936 restraints weight = 40550.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.124962 restraints weight = 30347.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.125262 restraints weight = 26743.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.125327 restraints weight = 24027.499| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19993 Z= 0.136 Angle : 0.701 11.046 27159 Z= 0.369 Chirality : 0.044 0.196 3135 Planarity : 0.006 0.088 3496 Dihedral : 5.191 33.022 2718 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 2.41 % Allowed : 16.75 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.14), residues: 2531 helix: -1.88 (0.14), residues: 923 sheet: -1.80 (0.31), residues: 245 loop : -3.33 (0.13), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 630 TYR 0.029 0.002 TYR A1884 PHE 0.021 0.001 PHE A1895 TRP 0.022 0.001 TRP 2 525 HIS 0.018 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00279 (19986) covalent geometry : angle 0.69652 (27153) SS BOND : bond 0.00997 ( 3) SS BOND : angle 5.45172 ( 6) hydrogen bonds : bond 0.05783 ( 735) hydrogen bonds : angle 6.03540 ( 2121) metal coordination : bond 0.00145 ( 3) Misc. bond : bond 0.00273 ( 1) *********************** 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 292 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.820 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: 0.7644 (OUTLIER) cc_final: 0.7405 (mt) REVERT: A 177 MET cc_start: 0.5749 (mtp) cc_final: 0.5528 (mtp) REVERT: A 505 ASP cc_start: 0.6206 (t70) cc_final: 0.5968 (t70) REVERT: A 844 MET cc_start: 0.6461 (tmm) cc_final: 0.6220 (tmm) REVERT: A 987 LYS cc_start: 0.6305 (pttm) cc_final: 0.5737 (tptt) REVERT: A 1096 LYS cc_start: 0.7596 (tptp) cc_final: 0.7060 (tptp) REVERT: A 1436 ARG cc_start: 0.5320 (ptt180) cc_final: 0.4766 (ptt90) REVERT: 2 224 LEU cc_start: 0.8584 (mp) cc_final: 0.8208 (mt) REVERT: 2 348 PRO cc_start: 0.5848 (Cg_endo) cc_final: 0.5469 (Cg_exo) REVERT: 2 681 LYS cc_start: 0.7831 (mppt) cc_final: 0.7444 (mtpp) REVERT: 3 43 GLU cc_start: 0.7645 (pt0) cc_final: 0.7281 (pm20) REVERT: 3 51 GLU cc_start: 0.7952 (tp30) cc_final: 0.7588 (tm-30) outliers start: 49 outliers final: 22 residues processed: 276 average time/residue: 0.1239 time to fit residues: 54.4384 Evaluate side-chains 214 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 542 PHE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 643 SER 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 1294 PHE Chi-restraints excluded: chain A residue 1648 HIS Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 540 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 91 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 104 optimal weight: 0.0970 chunk 253 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS A 647 ASN A 937 HIS A1155 GLN A1837 HIS ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2145 HIS 2 553 HIS 4 23 GLN ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.133022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.115837 restraints weight = 59899.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.114881 restraints weight = 47124.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.115572 restraints weight = 41738.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.115939 restraints weight = 33375.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.115988 restraints weight = 32109.416| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 19993 Z= 0.235 Angle : 0.787 11.371 27159 Z= 0.414 Chirality : 0.048 0.245 3135 Planarity : 0.006 0.086 3496 Dihedral : 5.615 29.736 2715 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 4.22 % Allowed : 17.19 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.15), residues: 2531 helix: -0.79 (0.16), residues: 931 sheet: -1.61 (0.34), residues: 245 loop : -3.24 (0.14), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1289 TYR 0.034 0.002 TYR A1884 PHE 0.032 0.003 PHE 2 664 TRP 0.014 0.002 TRP A1627 HIS 0.015 0.002 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00514 (19986) covalent geometry : angle 0.78246 (27153) SS BOND : bond 0.01107 ( 3) SS BOND : angle 5.54576 ( 6) hydrogen bonds : bond 0.06138 ( 735) hydrogen bonds : angle 5.69660 ( 2121) metal coordination : bond 0.00421 ( 3) Misc. bond : bond 0.00585 ( 1) *********************** 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 to be fit. rotamer outliers: 86 poor density : 199 time to evaluate : 0.618 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 49 MET cc_start: 0.5835 (ptp) cc_final: 0.5634 (ptp) REVERT: A 56 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7203 (p) REVERT: A 164 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7657 (mm) REVERT: A 177 MET cc_start: 0.5828 (mtp) cc_final: 0.5613 (mtp) REVERT: A 987 LYS cc_start: 0.6384 (pttm) cc_final: 0.5887 (tptt) REVERT: A 1436 ARG cc_start: 0.5458 (ptt180) cc_final: 0.5079 (ptt90) REVERT: A 1543 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7472 (mt) REVERT: A 1920 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6357 (mm) REVERT: 2 218 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.5524 (t80) REVERT: 2 222 TYR cc_start: 0.6920 (t80) cc_final: 0.6712 (t80) REVERT: 2 224 LEU cc_start: 0.8516 (mp) cc_final: 0.8156 (mt) REVERT: 2 274 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3114 (tt) REVERT: 2 348 PRO cc_start: 0.6048 (Cg_endo) cc_final: 0.5586 (Cg_exo) REVERT: 2 544 ASP cc_start: 0.6802 (p0) cc_final: 0.6597 (p0) REVERT: 2 669 ARG cc_start: 0.6501 (pmt-80) cc_final: 0.6024 (mpp-170) REVERT: 2 681 LYS cc_start: 0.8001 (mppt) cc_final: 0.7749 (mtpt) REVERT: 3 51 GLU cc_start: 0.8167 (tp30) cc_final: 0.7774 (tm-30) outliers start: 86 outliers final: 39 residues processed: 268 average time/residue: 0.1188 time to fit residues: 51.9745 Evaluate side-chains 211 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL 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 356 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 643 SER 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 1043 VAL Chi-restraints excluded: chain A residue 1140 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 1445 VAL Chi-restraints excluded: chain A residue 1543 ILE Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1646 ILE 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 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 274 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 626 LEU 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 43 GLU Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 45 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A1657 ASN A1703 ASN 2 226 ASN ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.133879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.116016 restraints weight = 59487.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.116000 restraints weight = 39955.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.116217 restraints weight = 32943.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.116622 restraints weight = 31459.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.116783 restraints weight = 27914.880| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19993 Z= 0.160 Angle : 0.687 10.713 27159 Z= 0.355 Chirality : 0.045 0.179 3135 Planarity : 0.005 0.093 3496 Dihedral : 5.392 29.339 2715 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.68 % Allowed : 18.81 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.15), residues: 2531 helix: -0.32 (0.17), residues: 933 sheet: -1.84 (0.33), residues: 245 loop : -3.10 (0.14), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 738 TYR 0.030 0.001 TYR A1884 PHE 0.019 0.002 PHE A1112 TRP 0.014 0.001 TRP A1627 HIS 0.013 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00350 (19986) covalent geometry : angle 0.68438 (27153) SS BOND : bond 0.00717 ( 3) SS BOND : angle 3.70026 ( 6) hydrogen bonds : bond 0.05473 ( 735) hydrogen bonds : angle 5.44585 ( 2121) metal coordination : bond 0.00254 ( 3) Misc. bond : bond 0.00591 ( 1) *********************** 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 268 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7055 (p) REVERT: A 82 MET cc_start: 0.6336 (ptt) cc_final: 0.6070 (ptt) REVERT: A 177 MET cc_start: 0.5637 (mtp) cc_final: 0.5404 (mtp) REVERT: A 643 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7541 (p) REVERT: A 987 LYS cc_start: 0.6463 (pttm) cc_final: 0.5955 (tptt) REVERT: A 1155 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6849 (mm110) REVERT: A 1436 ARG cc_start: 0.5381 (ptt180) cc_final: 0.4856 (ptt90) REVERT: A 1551 ASP cc_start: 0.7114 (p0) cc_final: 0.6824 (p0) REVERT: 2 218 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5722 (t80) REVERT: 2 224 LEU cc_start: 0.8543 (mp) cc_final: 0.8211 (mt) REVERT: 2 274 LEU cc_start: 0.3752 (OUTLIER) cc_final: 0.3425 (tt) REVERT: 2 481 MET cc_start: 0.6867 (mmp) cc_final: 0.6630 (mmm) REVERT: 2 544 ASP cc_start: 0.6794 (p0) cc_final: 0.6587 (p0) REVERT: 2 681 LYS cc_start: 0.7890 (mppt) cc_final: 0.7663 (mtpt) REVERT: 3 51 GLU cc_start: 0.8090 (tp30) cc_final: 0.7692 (tm-30) outliers start: 75 outliers final: 44 residues processed: 252 average time/residue: 0.1164 time to fit residues: 48.6148 Evaluate side-chains 228 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL 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 515 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 643 SER 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 1012 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1155 GLN 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 1547 SER Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1580 LEU Chi-restraints excluded: chain A residue 1613 VAL 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 1848 VAL 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 229 VAL 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 626 LEU Chi-restraints excluded: chain 2 residue 659 ILE Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 132 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS A1296 ASN A1413 ASN 4 23 GLN ** 4 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.132887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.115454 restraints weight = 59254.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.114614 restraints weight = 46337.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.115276 restraints weight = 38974.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.115776 restraints weight = 32800.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.115897 restraints weight = 30579.462| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19993 Z= 0.175 Angle : 0.705 13.061 27159 Z= 0.361 Chirality : 0.045 0.232 3135 Planarity : 0.005 0.140 3496 Dihedral : 5.405 29.943 2715 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.03 % Allowed : 19.40 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.16), residues: 2531 helix: -0.08 (0.17), residues: 937 sheet: -1.86 (0.33), residues: 248 loop : -3.08 (0.14), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1289 TYR 0.029 0.002 TYR A1884 PHE 0.030 0.002 PHE A1596 TRP 0.011 0.001 TRP A1627 HIS 0.013 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00387 (19986) covalent geometry : angle 0.70032 (27153) SS BOND : bond 0.01400 ( 3) SS BOND : angle 5.37181 ( 6) hydrogen bonds : bond 0.05456 ( 735) hydrogen bonds : angle 5.38709 ( 2121) metal coordination : bond 0.00319 ( 3) Misc. bond : bond 0.00563 ( 1) *********************** 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 to be fit. rotamer outliers: 82 poor density : 194 time to evaluate : 0.772 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 56 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.7083 (p) REVERT: A 164 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 830 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6205 (t80) REVERT: A 844 MET cc_start: 0.6919 (tmm) cc_final: 0.6658 (tmm) REVERT: A 987 LYS cc_start: 0.6504 (pttm) cc_final: 0.5863 (tptt) REVERT: A 1155 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6943 (mm110) REVERT: A 1436 ARG cc_start: 0.5427 (ptt180) cc_final: 0.4884 (ptt90) REVERT: A 1600 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6353 (tt) REVERT: A 1618 ASN cc_start: 0.7104 (OUTLIER) cc_final: 0.6773 (m-40) REVERT: A 1702 GLN cc_start: 0.7788 (mp10) cc_final: 0.7570 (mp10) REVERT: 2 218 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5734 (t80) REVERT: 2 224 LEU cc_start: 0.8588 (mp) cc_final: 0.8252 (mt) REVERT: 2 274 LEU cc_start: 0.3754 (OUTLIER) cc_final: 0.3511 (tt) REVERT: 2 544 ASP cc_start: 0.7228 (p0) cc_final: 0.6984 (p0) REVERT: 2 681 LYS cc_start: 0.7991 (mppt) cc_final: 0.7780 (mtpt) REVERT: 3 51 GLU cc_start: 0.8075 (tp30) cc_final: 0.7671 (tm-30) outliers start: 82 outliers final: 56 residues processed: 256 average time/residue: 0.1180 time to fit residues: 48.9382 Evaluate side-chains 245 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 181 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 134 VAL 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 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 643 SER 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 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 1012 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1155 GLN Chi-restraints excluded: chain A residue 1289 ARG 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 1547 SER Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1580 LEU Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1613 VAL Chi-restraints excluded: chain A residue 1618 ASN Chi-restraints excluded: chain A residue 1646 ILE 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 1848 VAL 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 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 497 LEU Chi-restraints excluded: chain 2 residue 503 LEU 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 43 GLU Chi-restraints excluded: chain 4 residue 55 ILE Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 122 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 523 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.131802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.114201 restraints weight = 59170.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.113378 restraints weight = 46940.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.114200 restraints weight = 38378.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.114654 restraints weight = 31214.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.114683 restraints weight = 29073.948| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19993 Z= 0.184 Angle : 0.714 15.007 27159 Z= 0.367 Chirality : 0.046 0.217 3135 Planarity : 0.005 0.111 3496 Dihedral : 5.482 27.954 2715 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.96 % Allowed : 19.30 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.16), residues: 2531 helix: 0.04 (0.17), residues: 938 sheet: -2.01 (0.32), residues: 265 loop : -2.99 (0.15), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1289 TYR 0.030 0.002 TYR 2 688 PHE 0.019 0.002 PHE A 399 TRP 0.014 0.001 TRP A1627 HIS 0.014 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00408 (19986) covalent geometry : angle 0.71162 (27153) SS BOND : bond 0.00656 ( 3) SS BOND : angle 3.89430 ( 6) hydrogen bonds : bond 0.05429 ( 735) hydrogen bonds : angle 5.36190 ( 2121) metal coordination : bond 0.00320 ( 3) Misc. bond : bond 0.00490 ( 1) *********************** 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 296 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 195 time to evaluate : 0.743 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: 0.8156 (OUTLIER) cc_final: 0.7666 (mm) REVERT: A 386 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8421 (t80) REVERT: A 457 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7196 (pt0) REVERT: A 844 MET cc_start: 0.6890 (tmm) cc_final: 0.6563 (tmm) REVERT: A 1436 ARG cc_start: 0.5244 (ptt180) cc_final: 0.4701 (ptt90) REVERT: A 1618 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6809 (m-40) REVERT: 2 218 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5693 (t80) REVERT: 2 274 LEU cc_start: 0.3653 (OUTLIER) cc_final: 0.3452 (tt) REVERT: 2 681 LYS cc_start: 0.8188 (mppt) cc_final: 0.7788 (mtpt) REVERT: 3 51 GLU cc_start: 0.8178 (tp30) cc_final: 0.7736 (tm-30) outliers start: 101 outliers final: 66 residues processed: 272 average time/residue: 0.1081 time to fit residues: 48.6921 Evaluate side-chains 249 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 177 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 134 VAL 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 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 308 ILE Chi-restraints excluded: chain A residue 386 PHE 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 643 SER 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 1043 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1155 GLN 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 1547 SER Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1580 LEU 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 1635 LEU Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1791 LEU Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1805 GLU 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 2194 ILE Chi-restraints excluded: chain 2 residue 218 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 328 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 431 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 659 ILE Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 2 residue 669 ARG Chi-restraints excluded: chain 2 residue 682 THR Chi-restraints excluded: chain 3 residue 43 GLU Chi-restraints excluded: chain 4 residue 36 SER Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 163 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 90 optimal weight: 0.0020 chunk 24 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A1489 HIS A1638 HIS A1703 ASN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN ** 4 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.134262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.116501 restraints weight = 59258.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.115925 restraints weight = 47607.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.116782 restraints weight = 36908.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.117195 restraints weight = 29974.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.117351 restraints weight = 27437.464| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19993 Z= 0.129 Angle : 0.673 13.049 27159 Z= 0.342 Chirality : 0.044 0.202 3135 Planarity : 0.005 0.166 3496 Dihedral : 5.213 30.857 2715 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.49 % Allowed : 21.51 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.16), residues: 2531 helix: 0.22 (0.17), residues: 949 sheet: -1.82 (0.32), residues: 260 loop : -2.88 (0.15), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1289 TYR 0.028 0.001 TYR A1884 PHE 0.037 0.001 PHE A1596 TRP 0.020 0.001 TRP A1627 HIS 0.014 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00274 (19986) covalent geometry : angle 0.67163 (27153) SS BOND : bond 0.00691 ( 3) SS BOND : angle 3.27639 ( 6) hydrogen bonds : bond 0.04982 ( 735) hydrogen bonds : angle 5.19021 ( 2121) metal coordination : bond 0.00135 ( 3) Misc. bond : bond 0.00037 ( 1) *********************** 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 279 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 208 time to evaluate : 0.535 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 135 TYR cc_start: 0.6715 (t80) cc_final: 0.6358 (t80) REVERT: A 164 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7517 (mm) REVERT: A 457 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: A 830 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6169 (t80) REVERT: A 987 LYS cc_start: 0.6301 (pttm) cc_final: 0.5309 (tptt) REVERT: A 1436 ARG cc_start: 0.5472 (ptt180) cc_final: 0.4867 (ptt90) REVERT: A 1618 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6680 (m-40) REVERT: 2 218 PHE cc_start: 0.6016 (OUTLIER) cc_final: 0.5744 (t80) REVERT: 2 681 LYS cc_start: 0.8032 (mppt) cc_final: 0.7540 (mtpp) REVERT: 3 51 GLU cc_start: 0.8092 (tp30) cc_final: 0.7670 (tm-30) outliers start: 71 outliers final: 51 residues processed: 263 average time/residue: 0.1173 time to fit residues: 50.4593 Evaluate side-chains 244 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 134 VAL 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 308 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 643 SER 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 1140 ILE Chi-restraints excluded: chain A residue 1155 GLN 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 1528 LEU Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1580 LEU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1618 ASN Chi-restraints excluded: chain A residue 1635 LEU Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1703 ASN Chi-restraints excluded: chain A residue 1801 GLU 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 2213 LEU Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 321 VAL Chi-restraints excluded: chain 2 residue 328 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 625 ASP Chi-restraints excluded: chain 2 residue 626 LEU Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 2 residue 669 ARG Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 36 SER 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 139 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 161 optimal weight: 0.4980 chunk 194 optimal weight: 6.9990 chunk 101 optimal weight: 0.0030 chunk 61 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.132884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.115331 restraints weight = 59162.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.115200 restraints weight = 42597.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.115994 restraints weight = 34034.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.116340 restraints weight = 30441.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.116404 restraints weight = 27992.719| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19993 Z= 0.157 Angle : 0.711 20.245 27159 Z= 0.362 Chirality : 0.045 0.230 3135 Planarity : 0.006 0.192 3496 Dihedral : 5.262 28.265 2715 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.78 % Allowed : 21.51 % Favored : 74.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.16), residues: 2531 helix: 0.32 (0.17), residues: 945 sheet: -1.84 (0.33), residues: 263 loop : -2.86 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1289 TYR 0.028 0.001 TYR A1884 PHE 0.043 0.002 PHE A1076 TRP 0.014 0.001 TRP A1627 HIS 0.014 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00345 (19986) covalent geometry : angle 0.70422 (27153) SS BOND : bond 0.00880 ( 3) SS BOND : angle 6.60946 ( 6) hydrogen bonds : bond 0.05132 ( 735) hydrogen bonds : angle 5.19009 ( 2121) metal coordination : bond 0.00364 ( 3) Misc. bond : bond 0.00960 ( 1) *********************** 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 265 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 0.754 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: 0.8013 (OUTLIER) cc_final: 0.7574 (mm) REVERT: A 457 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7258 (pt0) REVERT: A 830 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 987 LYS cc_start: 0.6001 (pttm) cc_final: 0.5037 (tptt) REVERT: A 1436 ARG cc_start: 0.5397 (ptt180) cc_final: 0.4857 (ptt90) REVERT: A 1618 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6677 (m-40) REVERT: 2 218 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5480 (t80) REVERT: 2 222 TYR cc_start: 0.7022 (t80) cc_final: 0.6728 (t80) REVERT: 2 681 LYS cc_start: 0.8119 (mppt) cc_final: 0.7618 (mtpp) REVERT: 3 51 GLU cc_start: 0.8115 (tp30) cc_final: 0.7683 (tm-30) outliers start: 77 outliers final: 60 residues processed: 249 average time/residue: 0.1070 time to fit residues: 44.0349 Evaluate side-chains 247 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 182 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 134 VAL 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 457 GLU Chi-restraints excluded: chain A residue 470 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 640 ASP Chi-restraints excluded: chain A residue 643 SER 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 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 1140 ILE Chi-restraints excluded: chain A residue 1155 GLN 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 1547 SER Chi-restraints excluded: chain A residue 1580 LEU 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 1635 LEU Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1791 LEU Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1884 TYR Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 321 VAL Chi-restraints excluded: chain 2 residue 328 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 431 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 659 ILE Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 3 residue 70 SER Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 252 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 148 optimal weight: 0.3980 chunk 238 optimal weight: 0.3980 chunk 200 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.131520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.113631 restraints weight = 59121.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.113960 restraints weight = 42419.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.114471 restraints weight = 35059.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.114779 restraints weight = 31550.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.114885 restraints weight = 28884.645| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19993 Z= 0.186 Angle : 0.732 15.045 27159 Z= 0.375 Chirality : 0.046 0.208 3135 Planarity : 0.005 0.071 3496 Dihedral : 5.439 35.414 2715 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.78 % Allowed : 21.61 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.16), residues: 2531 helix: 0.23 (0.17), residues: 950 sheet: -1.85 (0.33), residues: 258 loop : -2.91 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A1289 TYR 0.028 0.002 TYR A1884 PHE 0.047 0.002 PHE A1596 TRP 0.019 0.001 TRP A1627 HIS 0.018 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00413 (19986) covalent geometry : angle 0.72727 (27153) SS BOND : bond 0.00724 ( 3) SS BOND : angle 5.77877 ( 6) hydrogen bonds : bond 0.05363 ( 735) hydrogen bonds : angle 5.33003 ( 2121) metal coordination : bond 0.00404 ( 3) Misc. bond : bond 0.01110 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 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 262 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 185 time to evaluate : 0.721 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: 0.8112 (OUTLIER) cc_final: 0.7704 (mm) REVERT: A 457 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7202 (pt0) REVERT: A 987 LYS cc_start: 0.6248 (pttm) cc_final: 0.5165 (tptt) REVERT: A 1436 ARG cc_start: 0.5238 (ptt180) cc_final: 0.4721 (ptt90) REVERT: A 1618 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6662 (m110) REVERT: 2 218 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.5432 (t80) REVERT: 2 222 TYR cc_start: 0.7330 (t80) cc_final: 0.6961 (t80) REVERT: 2 224 LEU cc_start: 0.8732 (mp) cc_final: 0.8419 (mt) REVERT: 3 51 GLU cc_start: 0.8184 (tp30) cc_final: 0.7720 (tm-30) outliers start: 77 outliers final: 64 residues processed: 247 average time/residue: 0.1111 time to fit residues: 46.5623 Evaluate side-chains 246 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 134 VAL 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 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 643 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 ILE 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 1043 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1155 GLN 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 1547 SER Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1580 LEU 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 1635 LEU Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1791 LEU Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1884 TYR Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 321 VAL Chi-restraints excluded: chain 2 residue 328 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 431 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 635 ILE Chi-restraints excluded: chain 2 residue 659 ILE Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 3 residue 43 GLU Chi-restraints excluded: chain 3 residue 70 SER Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 9 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 48 ASN ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.132561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.114707 restraints weight = 59697.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.114714 restraints weight = 43766.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.115398 restraints weight = 34427.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.115733 restraints weight = 30722.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.115777 restraints weight = 28175.783| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19993 Z= 0.150 Angle : 0.703 14.580 27159 Z= 0.356 Chirality : 0.045 0.215 3135 Planarity : 0.005 0.072 3496 Dihedral : 5.302 33.218 2715 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.63 % Allowed : 22.20 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.16), residues: 2531 helix: 0.30 (0.17), residues: 952 sheet: -1.69 (0.35), residues: 240 loop : -2.85 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1289 TYR 0.028 0.001 TYR A1884 PHE 0.039 0.002 PHE A1076 TRP 0.032 0.001 TRP A1627 HIS 0.015 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00331 (19986) covalent geometry : angle 0.69891 (27153) SS BOND : bond 0.00736 ( 3) SS BOND : angle 5.26335 ( 6) hydrogen bonds : bond 0.05083 ( 735) hydrogen bonds : angle 5.23438 ( 2121) metal coordination : bond 0.00217 ( 3) Misc. bond : bond 0.00741 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 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 262 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 188 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6433 (ptt) cc_final: 0.6170 (ptt) REVERT: A 164 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7614 (mm) REVERT: A 457 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: A 987 LYS cc_start: 0.6049 (pttm) cc_final: 0.4962 (tptt) REVERT: A 1436 ARG cc_start: 0.5295 (ptt180) cc_final: 0.4702 (ptt90) REVERT: A 1618 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6627 (m-40) REVERT: 2 218 PHE cc_start: 0.5784 (OUTLIER) cc_final: 0.5468 (t80) REVERT: 2 222 TYR cc_start: 0.7197 (t80) cc_final: 0.6790 (t80) REVERT: 2 681 LYS cc_start: 0.8175 (mppt) cc_final: 0.7693 (mtpp) REVERT: 3 51 GLU cc_start: 0.8128 (tp30) cc_final: 0.7674 (tm-30) outliers start: 74 outliers final: 64 residues processed: 248 average time/residue: 0.1098 time to fit residues: 46.3690 Evaluate side-chains 247 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 134 VAL 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 457 GLU Chi-restraints excluded: chain A residue 470 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 640 ASP Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 ILE 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 1140 ILE Chi-restraints excluded: chain A residue 1155 GLN 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 1547 SER Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1580 LEU 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 1635 LEU Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1653 SER Chi-restraints excluded: chain A residue 1665 LEU Chi-restraints excluded: chain A residue 1674 VAL Chi-restraints excluded: chain A residue 1791 LEU Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1884 TYR Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2137 PHE Chi-restraints excluded: chain 2 residue 218 PHE Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 298 LEU Chi-restraints excluded: chain 2 residue 321 VAL Chi-restraints excluded: chain 2 residue 328 VAL Chi-restraints excluded: chain 2 residue 365 LEU Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 431 LEU Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 503 LEU Chi-restraints excluded: chain 2 residue 635 ILE Chi-restraints excluded: chain 2 residue 666 HIS Chi-restraints excluded: chain 3 residue 43 GLU Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 4 residue 31 LEU Chi-restraints excluded: chain 4 residue 61 LEU Chi-restraints excluded: chain 4 residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 125 optimal weight: 0.0370 chunk 142 optimal weight: 0.0040 chunk 3 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 103 optimal weight: 0.0040 chunk 176 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN A1648 HIS A1703 ASN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2145 HIS 4 23 GLN ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.135110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.117210 restraints weight = 59106.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.117400 restraints weight = 43033.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.118164 restraints weight = 33058.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.118433 restraints weight = 29533.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.118590 restraints weight = 27211.119| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19993 Z= 0.124 Angle : 0.688 12.886 27159 Z= 0.343 Chirality : 0.045 0.244 3135 Planarity : 0.004 0.072 3496 Dihedral : 5.073 29.510 2715 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.00 % Allowed : 23.28 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.16), residues: 2531 helix: 0.48 (0.17), residues: 948 sheet: -1.72 (0.34), residues: 249 loop : -2.68 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1289 TYR 0.028 0.001 TYR A1884 PHE 0.056 0.001 PHE A1596 TRP 0.037 0.001 TRP A1627 HIS 0.011 0.001 HIS 2 666 Details of bonding type rmsd covalent geometry : bond 0.00268 (19986) covalent geometry : angle 0.68399 (27153) SS BOND : bond 0.00743 ( 3) SS BOND : angle 4.80751 ( 6) hydrogen bonds : bond 0.04749 ( 735) hydrogen bonds : angle 5.09978 ( 2121) metal coordination : bond 0.00163 ( 3) Misc. bond : bond 0.00501 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.32 seconds wall clock time: 51 minutes 59.92 seconds (3119.92 seconds total)