Starting phenix.real_space_refine on Thu May 22 01:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gl6_40191/05_2025/8gl6_40191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gl6_40191/05_2025/8gl6_40191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gl6_40191/05_2025/8gl6_40191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gl6_40191/05_2025/8gl6_40191.map" model { file = "/net/cci-nas-00/data/ceres_data/8gl6_40191/05_2025/8gl6_40191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gl6_40191/05_2025/8gl6_40191.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 13840 2.51 5 N 3671 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21896 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.37, per 1000 atoms: 0.52 Number of scatterers: 21896 At special positions: 0 Unit cell: (118.368, 127.41, 134.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 4339 8.00 N 3671 7.00 C 13840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.6 seconds 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 21 sheets defined 14.5% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.722A pdb=" N ASN A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.526A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.105A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.830A pdb=" N ILE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.578A pdb=" N PHE A 414 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 517 through 522 removed outlier: 3.923A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.906A pdb=" N LYS A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 626 through 633 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.867A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.665A pdb=" N TYR A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 5.697A pdb=" N ASP A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 673 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 674 " --> pdb=" O SER A 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 669 through 674' Processing helix chain 'A' and resid 730 through 735 removed outlier: 4.015A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.738A pdb=" N THR A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 982 through 985 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1048 through 1052 removed outlier: 3.710A pdb=" N GLY A1051 " --> pdb=" O TYR A1048 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1052 " --> pdb=" O GLU A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1048 through 1052' Processing helix chain 'A' and resid 1081 through 1089 Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 4.177A pdb=" N ILE A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 removed outlier: 3.513A pdb=" N ALA A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1108' Processing helix chain 'A' and resid 1120 through 1124 removed outlier: 3.504A pdb=" N ALA A1124 " --> pdb=" O TYR A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.515A pdb=" N TYR A1132 " --> pdb=" O VAL A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1427 through 1439 removed outlier: 4.032A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1458 Processing helix chain 'A' and resid 1573 through 1576 Processing helix chain 'A' and resid 1577 through 1580 removed outlier: 3.710A pdb=" N TRP A1580 " --> pdb=" O PRO A1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1577 through 1580' Processing helix chain 'A' and resid 1607 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.961A pdb=" N ILE A1629 " --> pdb=" O ARG A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1658 No H-bonds generated for 'chain 'A' and resid 1656 through 1658' Processing helix chain 'A' and resid 1830 through 1834 removed outlier: 3.648A pdb=" N LYS A1833 " --> pdb=" O PRO A1830 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A1834 " --> pdb=" O ILE A1831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1830 through 1834' Processing helix chain 'A' and resid 1856 through 1861 Processing helix chain 'A' and resid 1976 through 1981 removed outlier: 3.597A pdb=" N VAL A1980 " --> pdb=" O SER A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1995 Processing helix chain 'A' and resid 2071 through 2075 removed outlier: 3.721A pdb=" N THR A2074 " --> pdb=" O MET A2071 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2106 removed outlier: 3.661A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.510A pdb=" N ASN A2136 " --> pdb=" O VAL A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2161 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 3.517A pdb=" N TYR A2190 " --> pdb=" O LEU A2187 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.666A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.981A pdb=" N ASP F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.825A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 319 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 154 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 187 through 194 removed outlier: 6.768A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE A 217 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN A 248 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 219 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 770 through 773 current: chain 'A' and resid 796 through 809 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1559 through 1571 current: chain 'A' and resid 1630 through 1644 removed outlier: 5.417A pdb=" N THR A1632 " --> pdb=" O HIS A1672 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS A1672 " --> pdb=" O THR A1632 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG A1634 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU A1670 " --> pdb=" O ARG A1634 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER A1636 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN A1668 " --> pdb=" O SER A1636 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A1638 " --> pdb=" O TYR A1666 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR A1666 " --> pdb=" O ASN A1638 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A1640 " --> pdb=" O GLN A1664 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A1664 " --> pdb=" O ILE A1640 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A1644 " --> pdb=" O PHE A1660 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A1660 " --> pdb=" O LYS A1644 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1757 through 1760 current: chain 'A' and resid 1779 through 1789 removed outlier: 5.632A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A1945 " --> pdb=" O ASP A2022 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP A2022 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A1947 " --> pdb=" O ASN A2020 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A2023 " --> pdb=" O LEU A2027 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A2027 " --> pdb=" O LEU A2023 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A2044 " --> pdb=" O SER A2058 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A2058 " --> pdb=" O GLN A2044 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER A2046 " --> pdb=" O PRO A2056 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2054 through 2069 current: chain 'A' and resid 2197 through 2217 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2238 through 2240 current: chain 'A' and resid 2264 through 2278 removed outlier: 3.986A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A2302 " --> pdb=" O SER A2319 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N SER A2319 " --> pdb=" O ASP A2302 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP A2320 " --> pdb=" O SER A2362 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A2362 " --> pdb=" O ASP A2320 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A2348 " --> pdb=" O THR A2334 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.876A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.459A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 11.775A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA9, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB1, first strand: chain 'A' and resid 856 through 859 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 856 through 859 current: chain 'A' and resid 1326 through 1334 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1326 through 1334 current: chain 'A' and resid 1423 through 1426 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 866 through 869 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 866 through 869 current: chain 'A' and resid 960 through 969 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 960 through 969 current: chain 'A' and resid 1208 through 1219 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB4, first strand: chain 'A' and resid 938 through 939 removed outlier: 4.416A pdb=" N ILE A 938 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1265 through 1266 removed outlier: 3.997A pdb=" N ARG A1484 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id=AB7, first strand: chain 'A' and resid 1862 through 1863 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 48 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 54 through 59 current: chain 'B' and resid 110 through 113 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 113 current: chain 'B' and resid 166 through 174 Processing sheet with id=AB9, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.770A pdb=" N ASN F 199 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE F 240 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP F 397 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP F 70 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL F 182 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN F 210 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.778A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1363 through 1366 removed outlier: 3.671A pdb=" N THR D1375 " --> pdb=" O LEU D1364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1393 through 1397 removed outlier: 6.873A pdb=" N LEU D1393 " --> pdb=" O ASP D1388 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASP D1388 " --> pdb=" O LEU D1393 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D1395 " --> pdb=" O ILE D1386 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D1419 " --> pdb=" O ARG D1431 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1893 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: 13.03 Time building geometry restraints manager: 5.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7259 1.34 - 1.46: 4909 1.46 - 1.58: 10106 1.58 - 1.69: 6 1.69 - 1.81: 90 Bond restraints: 22370 Sorted by residual: bond pdb=" C1 LMN F 501 " pdb=" O5 LMN F 501 " ideal model delta sigma weight residual 1.403 1.563 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " ideal model delta sigma weight residual 1.409 1.506 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" CCF LMN F 501 " pdb=" OBX LMN F 501 " ideal model delta sigma weight residual 1.410 1.499 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CCS LMN F 501 " pdb=" OBZ LMN F 501 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCR LMN F 501 " pdb=" OBY LMN F 501 " ideal model delta sigma weight residual 1.393 1.475 -0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 22365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 30054 2.07 - 4.13: 283 4.13 - 6.20: 22 6.20 - 8.26: 3 8.26 - 10.33: 2 Bond angle restraints: 30364 Sorted by residual: angle pdb=" N GLY A 759 " pdb=" CA GLY A 759 " pdb=" C GLY A 759 " ideal model delta sigma weight residual 110.96 115.20 -4.24 1.19e+00 7.06e-01 1.27e+01 angle pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " pdb=" CCR LMN F 501 " ideal model delta sigma weight residual 120.22 109.89 10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N GLY A1152 " pdb=" CA GLY A1152 " pdb=" C GLY A1152 " ideal model delta sigma weight residual 112.73 116.83 -4.10 1.20e+00 6.94e-01 1.17e+01 angle pdb=" N VAL A 475 " pdb=" CA VAL A 475 " pdb=" C VAL A 475 " ideal model delta sigma weight residual 113.53 110.29 3.24 9.80e-01 1.04e+00 1.10e+01 angle pdb=" N VAL A1090 " pdb=" CA VAL A1090 " pdb=" C VAL A1090 " ideal model delta sigma weight residual 113.20 110.02 3.18 9.60e-01 1.09e+00 1.09e+01 ... (remaining 30359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 13132 24.42 - 48.84: 219 48.84 - 73.26: 31 73.26 - 97.68: 18 97.68 - 122.10: 19 Dihedral angle restraints: 13419 sinusoidal: 5395 harmonic: 8024 Sorted by residual: dihedral pdb=" CCD LMN F 501 " pdb=" CCS LMN F 501 " pdb=" OBZ LMN F 501 " pdb=" OCB LMN F 501 " ideal model delta sinusoidal sigma weight residual 60.96 -176.94 -122.10 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CCD LMN F 501 " pdb=" CCS LMN F 501 " pdb=" OBZ LMN F 501 " pdb=" CCW LMN F 501 " ideal model delta sinusoidal sigma weight residual -59.55 61.91 -121.46 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CCC LMN F 501 " pdb=" CCR LMN F 501 " pdb=" OBY LMN F 501 " pdb=" O4 LMN F 501 " ideal model delta sinusoidal sigma weight residual 60.74 -179.75 -119.51 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 13416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2065 0.033 - 0.066: 835 0.066 - 0.099: 223 0.099 - 0.132: 177 0.132 - 0.164: 11 Chirality restraints: 3311 Sorted by residual: chirality pdb=" CCV LMN F 501 " pdb=" CCR LMN F 501 " pdb=" CCT LMN F 501 " pdb=" OAU LMN F 501 " both_signs ideal model delta sigma weight residual False 2.28 2.45 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CCQ LMN F 501 " pdb=" CCF LMN F 501 " pdb=" CCH LMN F 501 " pdb=" OCB LMN F 501 " both_signs ideal model delta sigma weight residual False -2.61 -2.46 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CCW LMN F 501 " pdb=" CCS LMN F 501 " pdb=" CCU LMN F 501 " pdb=" OAV LMN F 501 " both_signs ideal model delta sigma weight residual False 2.30 2.45 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 3308 not shown) Planarity restraints: 4017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C PHE A1639 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C SER A 176 " -0.028 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1062 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A1063 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1063 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1063 " -0.022 5.00e-02 4.00e+02 ... (remaining 4014 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 288 2.65 - 3.21: 19405 3.21 - 3.77: 33534 3.77 - 4.34: 50072 4.34 - 4.90: 82233 Nonbonded interactions: 185532 Sorted by model distance: nonbonded pdb=" O LYS F 320 " pdb=" OG SER F 346 " model vdw 2.084 3.040 nonbonded pdb=" OG SER F 109 " pdb=" OD1 ASP F 141 " model vdw 2.180 3.040 nonbonded pdb=" O LEU A2156 " pdb=" OG1 THR A2160 " model vdw 2.213 3.040 nonbonded pdb=" OD2 ASP A2163 " pdb=" OG SER A2165 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A1048 " pdb=" O SER A1071 " model vdw 2.236 3.040 ... (remaining 185527 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.370 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.320 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 22370 Z= 0.163 Angle : 0.498 10.327 30364 Z= 0.268 Chirality : 0.044 0.164 3311 Planarity : 0.003 0.040 4017 Dihedral : 11.295 122.099 8297 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.87 % Allowed : 3.21 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2744 helix: -0.43 (0.33), residues: 271 sheet: 0.31 (0.16), residues: 1075 loop : -0.48 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.017 0.001 PHE A1009 TYR 0.013 0.001 TYR A1394 ARG 0.003 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.12241 ( 710) hydrogen bonds : angle 5.52326 ( 1893) covalent geometry : bond 0.00320 (22370) covalent geometry : angle 0.49832 (30364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 436 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 THR cc_start: 0.7538 (m) cc_final: 0.7298 (p) REVERT: B 47 GLN cc_start: 0.8458 (mp10) cc_final: 0.8229 (mp10) REVERT: B 166 LEU cc_start: 0.9165 (mt) cc_final: 0.8953 (mt) REVERT: D 1420 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8250 (ttmm) outliers start: 21 outliers final: 6 residues processed: 450 average time/residue: 0.3432 time to fit residues: 239.6614 Evaluate side-chains 264 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 258 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1405 LEU Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 308 ASN A 734 GLN A1047 GLN A1056 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 GLN A1302 ASN A1326 GLN ** A1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1604 GLN A1787 ASN A1882 ASN A1984 GLN ** A2350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN F 59 GLN F 122 GLN F 209 GLN D1396 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.073442 restraints weight = 38888.956| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.59 r_work: 0.2738 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.123 22370 Z= 0.529 Angle : 0.785 9.603 30364 Z= 0.408 Chirality : 0.054 0.269 3311 Planarity : 0.005 0.060 4017 Dihedral : 10.176 113.983 3151 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.46 % Allowed : 7.66 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2744 helix: -1.17 (0.29), residues: 291 sheet: -0.05 (0.16), residues: 1086 loop : -0.74 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1996 HIS 0.011 0.002 HIS A2375 PHE 0.032 0.003 PHE A1480 TYR 0.032 0.003 TYR A1120 ARG 0.008 0.001 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 710) hydrogen bonds : angle 5.64321 ( 1893) covalent geometry : bond 0.01204 (22370) covalent geometry : angle 0.78534 (30364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 2.701 Fit side-chains revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8135 (pp20) REVERT: A 438 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8609 (mt-10) REVERT: A 532 GLN cc_start: 0.7602 (mp10) cc_final: 0.7209 (mt0) REVERT: B 45 THR cc_start: 0.7889 (m) cc_final: 0.7496 (p) REVERT: B 101 TYR cc_start: 0.8936 (p90) cc_final: 0.8668 (p90) REVERT: B 112 ASP cc_start: 0.7902 (t70) cc_final: 0.7427 (t70) REVERT: B 141 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7988 (mt-10) outliers start: 59 outliers final: 40 residues processed: 291 average time/residue: 0.3071 time to fit residues: 143.3895 Evaluate side-chains 269 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2032 SER Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1408 SER Chi-restraints excluded: chain D residue 1416 VAL Chi-restraints excluded: chain D residue 1422 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN A1317 ASN A1485 ASN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2350 GLN F 209 GLN ** D1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1415 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.077001 restraints weight = 37652.159| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.63 r_work: 0.2805 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22370 Z= 0.152 Angle : 0.545 7.339 30364 Z= 0.284 Chirality : 0.046 0.304 3311 Planarity : 0.004 0.044 4017 Dihedral : 8.518 107.151 3148 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.92 % Allowed : 9.79 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2744 helix: -0.65 (0.31), residues: 272 sheet: 0.01 (0.16), residues: 1074 loop : -0.63 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1996 HIS 0.003 0.001 HIS A1819 PHE 0.018 0.001 PHE A1242 TYR 0.015 0.001 TYR B 27 ARG 0.004 0.000 ARG D1431 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 710) hydrogen bonds : angle 5.28524 ( 1893) covalent geometry : bond 0.00333 (22370) covalent geometry : angle 0.54457 (30364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 256 time to evaluate : 2.541 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.8981 (m-30) cc_final: 0.8619 (m-30) REVERT: A 271 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8014 (pp20) REVERT: A 458 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8358 (mp0) REVERT: A 968 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8330 (mp0) REVERT: A 1232 ASP cc_start: 0.8164 (p0) cc_final: 0.7887 (p0) REVERT: A 1767 GLN cc_start: 0.8530 (pt0) cc_final: 0.8199 (pm20) REVERT: B 25 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7548 (mtmt) REVERT: B 45 THR cc_start: 0.7826 (m) cc_final: 0.7388 (p) REVERT: B 101 TYR cc_start: 0.8793 (p90) cc_final: 0.8034 (p90) REVERT: B 112 ASP cc_start: 0.7597 (t70) cc_final: 0.6675 (t0) REVERT: B 141 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7834 (mt-10) REVERT: D 1431 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8360 (mtm-85) outliers start: 46 outliers final: 34 residues processed: 283 average time/residue: 0.3182 time to fit residues: 145.7791 Evaluate side-chains 268 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 222 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 227 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN D1385 ASN D1415 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.073522 restraints weight = 38765.870| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.58 r_work: 0.2745 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 22370 Z= 0.338 Angle : 0.635 8.102 30364 Z= 0.329 Chirality : 0.048 0.293 3311 Planarity : 0.004 0.047 4017 Dihedral : 7.855 94.898 3148 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.54 % Allowed : 10.37 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2744 helix: -1.19 (0.29), residues: 299 sheet: -0.14 (0.16), residues: 1085 loop : -0.74 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1996 HIS 0.006 0.001 HIS A2375 PHE 0.024 0.002 PHE A1242 TYR 0.030 0.002 TYR D1395 ARG 0.004 0.001 ARG A1988 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 710) hydrogen bonds : angle 5.44260 ( 1893) covalent geometry : bond 0.00769 (22370) covalent geometry : angle 0.63464 (30364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8262 (t0) cc_final: 0.7804 (p0) REVERT: A 172 ASP cc_start: 0.8988 (m-30) cc_final: 0.8700 (m-30) REVERT: A 180 MET cc_start: 0.7999 (mmt) cc_final: 0.7755 (mmt) REVERT: A 271 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8155 (pp20) REVERT: A 532 GLN cc_start: 0.7682 (mp10) cc_final: 0.7279 (mt0) REVERT: A 968 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8366 (mp0) REVERT: A 1528 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7922 (p0) REVERT: B 45 THR cc_start: 0.7886 (m) cc_final: 0.7493 (p) REVERT: B 101 TYR cc_start: 0.8924 (p90) cc_final: 0.8689 (p90) REVERT: B 112 ASP cc_start: 0.7855 (t70) cc_final: 0.7378 (t70) REVERT: B 141 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8019 (mt-10) REVERT: F 122 GLN cc_start: 0.7944 (mt0) cc_final: 0.7607 (mt0) outliers start: 61 outliers final: 48 residues processed: 271 average time/residue: 0.3171 time to fit residues: 139.1825 Evaluate side-chains 272 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1528 ASN Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2082 THR Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1408 SER Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A1317 ASN A1874 ASN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN D1411 GLN D1415 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.076411 restraints weight = 38003.162| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.63 r_work: 0.2797 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22370 Z= 0.135 Angle : 0.524 8.173 30364 Z= 0.273 Chirality : 0.045 0.316 3311 Planarity : 0.003 0.044 4017 Dihedral : 6.856 83.526 3146 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.29 % Allowed : 11.41 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2744 helix: -0.82 (0.30), residues: 284 sheet: -0.05 (0.16), residues: 1084 loop : -0.64 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2353 HIS 0.003 0.001 HIS F 219 PHE 0.017 0.001 PHE A1242 TYR 0.026 0.001 TYR D1395 ARG 0.006 0.000 ARG D1431 Details of bonding type rmsd hydrogen bonds : bond 0.02661 ( 710) hydrogen bonds : angle 5.20418 ( 1893) covalent geometry : bond 0.00292 (22370) covalent geometry : angle 0.52410 (30364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 2.451 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8313 (t0) cc_final: 0.7811 (p0) REVERT: A 172 ASP cc_start: 0.8936 (m-30) cc_final: 0.8670 (m-30) REVERT: A 180 MET cc_start: 0.7959 (mmt) cc_final: 0.7716 (mmt) REVERT: A 271 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8019 (pp20) REVERT: A 421 GLU cc_start: 0.7937 (tp30) cc_final: 0.7736 (tp30) REVERT: A 1232 ASP cc_start: 0.8269 (p0) cc_final: 0.8063 (p0) REVERT: A 1767 GLN cc_start: 0.8491 (pt0) cc_final: 0.8152 (pm20) REVERT: B 25 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7667 (mtmt) REVERT: B 45 THR cc_start: 0.7851 (m) cc_final: 0.7446 (p) REVERT: B 101 TYR cc_start: 0.8738 (p90) cc_final: 0.8269 (p90) REVERT: B 112 ASP cc_start: 0.7684 (t70) cc_final: 0.7001 (t0) REVERT: B 141 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7877 (mt-10) REVERT: F 122 GLN cc_start: 0.7834 (mt0) cc_final: 0.7471 (mt0) outliers start: 55 outliers final: 37 residues processed: 280 average time/residue: 0.3274 time to fit residues: 148.2500 Evaluate side-chains 268 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2082 THR Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1411 GLN Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 10 optimal weight: 0.0070 chunk 39 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 3.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A1317 ASN A2136 ASN F 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.075003 restraints weight = 38056.997| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.58 r_work: 0.2775 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22370 Z= 0.227 Angle : 0.558 7.750 30364 Z= 0.291 Chirality : 0.047 0.370 3311 Planarity : 0.004 0.043 4017 Dihedral : 6.546 82.580 3146 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.33 % Allowed : 11.87 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2744 helix: -0.86 (0.30), residues: 286 sheet: -0.06 (0.16), residues: 1084 loop : -0.66 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1996 HIS 0.003 0.001 HIS A2375 PHE 0.021 0.001 PHE A1242 TYR 0.027 0.001 TYR D1395 ARG 0.006 0.000 ARG A2398 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 710) hydrogen bonds : angle 5.22728 ( 1893) covalent geometry : bond 0.00511 (22370) covalent geometry : angle 0.55791 (30364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 2.460 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8268 (t0) cc_final: 0.7761 (p0) REVERT: A 172 ASP cc_start: 0.8967 (m-30) cc_final: 0.8706 (m-30) REVERT: A 271 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8044 (pp20) REVERT: A 421 GLU cc_start: 0.7950 (tp30) cc_final: 0.7724 (tp30) REVERT: A 1232 ASP cc_start: 0.8271 (p0) cc_final: 0.8067 (p0) REVERT: A 1767 GLN cc_start: 0.8560 (pt0) cc_final: 0.8236 (pm20) REVERT: B 45 THR cc_start: 0.7893 (m) cc_final: 0.7518 (p) REVERT: B 48 ARG cc_start: 0.8379 (ttt-90) cc_final: 0.8143 (ttt-90) REVERT: B 112 ASP cc_start: 0.7810 (t70) cc_final: 0.7364 (t70) REVERT: B 141 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7915 (mt-10) REVERT: F 122 GLN cc_start: 0.7869 (mt0) cc_final: 0.7509 (mt0) REVERT: D 1411 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6896 (mm110) outliers start: 56 outliers final: 45 residues processed: 268 average time/residue: 0.3207 time to fit residues: 139.5751 Evaluate side-chains 270 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1983 SER Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2082 THR Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1408 SER Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1411 GLN Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 212 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 264 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN D1415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.073731 restraints weight = 38249.970| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.59 r_work: 0.2751 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 22370 Z= 0.307 Angle : 0.605 7.535 30364 Z= 0.315 Chirality : 0.048 0.364 3311 Planarity : 0.004 0.045 4017 Dihedral : 6.516 83.112 3146 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.29 % Allowed : 12.37 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2744 helix: -1.10 (0.29), residues: 299 sheet: -0.17 (0.16), residues: 1076 loop : -0.74 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1996 HIS 0.004 0.001 HIS A2375 PHE 0.023 0.002 PHE A1242 TYR 0.031 0.002 TYR D1395 ARG 0.005 0.001 ARG D1431 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 710) hydrogen bonds : angle 5.34898 ( 1893) covalent geometry : bond 0.00695 (22370) covalent geometry : angle 0.60466 (30364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 2.567 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8295 (t0) cc_final: 0.7720 (p0) REVERT: A 172 ASP cc_start: 0.8923 (m-30) cc_final: 0.8695 (m-30) REVERT: A 180 MET cc_start: 0.8040 (mmt) cc_final: 0.7767 (mmt) REVERT: A 271 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8108 (pp20) REVERT: A 421 GLU cc_start: 0.7993 (tp30) cc_final: 0.7738 (tp30) REVERT: A 1580 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.5262 (p-90) REVERT: A 1813 ILE cc_start: 0.8969 (mt) cc_final: 0.8720 (pt) REVERT: B 32 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 45 THR cc_start: 0.7909 (m) cc_final: 0.7551 (p) REVERT: B 112 ASP cc_start: 0.7859 (t70) cc_final: 0.7344 (t70) REVERT: B 141 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8047 (mt-10) REVERT: F 122 GLN cc_start: 0.7870 (mt0) cc_final: 0.7519 (mt0) REVERT: F 244 TYR cc_start: 0.5403 (p90) cc_final: 0.5203 (p90) outliers start: 55 outliers final: 46 residues processed: 271 average time/residue: 0.3263 time to fit residues: 144.4149 Evaluate side-chains 274 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1983 SER Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2082 THR Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 101 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1317 ASN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN F 72 GLN F 209 GLN D1411 GLN D1415 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.075868 restraints weight = 38150.167| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.58 r_work: 0.2794 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22370 Z= 0.149 Angle : 0.530 8.598 30364 Z= 0.277 Chirality : 0.045 0.327 3311 Planarity : 0.004 0.042 4017 Dihedral : 6.170 80.459 3146 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.29 % Allowed : 12.74 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2744 helix: -0.78 (0.30), residues: 285 sheet: -0.09 (0.16), residues: 1084 loop : -0.64 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1996 HIS 0.003 0.001 HIS F 219 PHE 0.018 0.001 PHE A1242 TYR 0.029 0.001 TYR D1395 ARG 0.006 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 710) hydrogen bonds : angle 5.19481 ( 1893) covalent geometry : bond 0.00330 (22370) covalent geometry : angle 0.52970 (30364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 2.690 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8315 (t0) cc_final: 0.7710 (p0) REVERT: A 172 ASP cc_start: 0.8894 (m-30) cc_final: 0.8690 (m-30) REVERT: A 271 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8015 (pp20) REVERT: A 421 GLU cc_start: 0.7960 (tp30) cc_final: 0.7699 (tp30) REVERT: A 532 GLN cc_start: 0.7368 (mp10) cc_final: 0.6913 (mt0) REVERT: A 741 GLU cc_start: 0.8373 (mp0) cc_final: 0.8103 (mp0) REVERT: A 1767 GLN cc_start: 0.8538 (pt0) cc_final: 0.8201 (pm20) REVERT: A 1813 ILE cc_start: 0.8936 (mt) cc_final: 0.8673 (pt) REVERT: B 23 GLU cc_start: 0.6256 (tm-30) cc_final: 0.5850 (tm-30) REVERT: B 32 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 45 THR cc_start: 0.7907 (m) cc_final: 0.7537 (p) REVERT: B 101 TYR cc_start: 0.8675 (p90) cc_final: 0.8269 (p90) REVERT: B 112 ASP cc_start: 0.7703 (t70) cc_final: 0.7270 (t0) REVERT: B 141 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7948 (mt-10) REVERT: F 122 GLN cc_start: 0.7832 (mt0) cc_final: 0.7481 (mt0) outliers start: 55 outliers final: 48 residues processed: 283 average time/residue: 0.3246 time to fit residues: 149.8781 Evaluate side-chains 282 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1593 GLU Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2082 THR Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1411 GLN Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 20 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 233 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 255 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1323 GLN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 209 GLN D1385 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.076284 restraints weight = 37743.989| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.61 r_work: 0.2798 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22370 Z= 0.139 Angle : 0.523 8.617 30364 Z= 0.274 Chirality : 0.045 0.305 3311 Planarity : 0.004 0.040 4017 Dihedral : 6.014 79.521 3146 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.12 % Allowed : 13.20 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2744 helix: -0.74 (0.30), residues: 290 sheet: -0.06 (0.16), residues: 1084 loop : -0.60 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2353 HIS 0.003 0.001 HIS A1672 PHE 0.018 0.001 PHE A1242 TYR 0.031 0.001 TYR D1395 ARG 0.007 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.02597 ( 710) hydrogen bonds : angle 5.11309 ( 1893) covalent geometry : bond 0.00311 (22370) covalent geometry : angle 0.52291 (30364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 2.330 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8281 (t0) cc_final: 0.7718 (p0) REVERT: A 271 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7993 (pp20) REVERT: A 741 GLU cc_start: 0.8384 (mp0) cc_final: 0.8110 (mp0) REVERT: A 1767 GLN cc_start: 0.8547 (pt0) cc_final: 0.8220 (pm20) REVERT: B 23 GLU cc_start: 0.6331 (tm-30) cc_final: 0.5933 (tm-30) REVERT: B 32 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 45 THR cc_start: 0.7918 (m) cc_final: 0.7551 (p) REVERT: B 101 TYR cc_start: 0.8666 (p90) cc_final: 0.8262 (p90) REVERT: B 112 ASP cc_start: 0.7694 (t70) cc_final: 0.7238 (t0) REVERT: B 141 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7934 (mt-10) REVERT: F 122 GLN cc_start: 0.7801 (mt0) cc_final: 0.7461 (mt0) REVERT: D 1411 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6863 (mm110) outliers start: 51 outliers final: 46 residues processed: 272 average time/residue: 0.3063 time to fit residues: 134.9926 Evaluate side-chains 287 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1593 GLU Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2082 THR Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1408 SER Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1411 GLN Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 166 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 209 GLN D1415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.076302 restraints weight = 37936.976| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.63 r_work: 0.2798 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22370 Z= 0.147 Angle : 0.522 8.482 30364 Z= 0.273 Chirality : 0.045 0.285 3311 Planarity : 0.003 0.041 4017 Dihedral : 5.915 78.876 3146 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.17 % Allowed : 13.16 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2744 helix: -0.73 (0.30), residues: 291 sheet: -0.07 (0.16), residues: 1085 loop : -0.59 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2353 HIS 0.003 0.001 HIS A1672 PHE 0.018 0.001 PHE A1242 TYR 0.029 0.001 TYR D1395 ARG 0.007 0.000 ARG D1431 Details of bonding type rmsd hydrogen bonds : bond 0.02588 ( 710) hydrogen bonds : angle 5.08059 ( 1893) covalent geometry : bond 0.00330 (22370) covalent geometry : angle 0.52155 (30364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 2.466 Fit side-chains revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7994 (pp20) REVERT: A 741 GLU cc_start: 0.8402 (mp0) cc_final: 0.8126 (mp0) REVERT: A 1767 GLN cc_start: 0.8572 (pt0) cc_final: 0.8234 (pm20) REVERT: B 23 GLU cc_start: 0.6340 (tm-30) cc_final: 0.5932 (tm-30) REVERT: B 45 THR cc_start: 0.7924 (m) cc_final: 0.7564 (p) REVERT: B 101 TYR cc_start: 0.8675 (p90) cc_final: 0.8261 (p90) REVERT: B 112 ASP cc_start: 0.7722 (t70) cc_final: 0.7256 (t0) REVERT: B 141 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7932 (mt-10) REVERT: F 122 GLN cc_start: 0.7797 (mt0) cc_final: 0.7458 (mt0) REVERT: D 1425 ASN cc_start: 0.7865 (p0) cc_final: 0.7629 (p0) outliers start: 52 outliers final: 47 residues processed: 278 average time/residue: 0.3135 time to fit residues: 142.4099 Evaluate side-chains 284 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1593 GLU Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2082 THR Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 260 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.074334 restraints weight = 38288.202| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.61 r_work: 0.2760 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 22370 Z= 0.259 Angle : 0.578 7.953 30364 Z= 0.302 Chirality : 0.047 0.279 3311 Planarity : 0.004 0.054 4017 Dihedral : 6.072 78.465 3146 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.21 % Allowed : 13.24 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2744 helix: -0.85 (0.30), residues: 293 sheet: -0.16 (0.16), residues: 1087 loop : -0.65 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1996 HIS 0.003 0.001 HIS A2375 PHE 0.022 0.002 PHE A1242 TYR 0.030 0.002 TYR D1395 ARG 0.007 0.001 ARG A2398 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 710) hydrogen bonds : angle 5.22316 ( 1893) covalent geometry : bond 0.00586 (22370) covalent geometry : angle 0.57778 (30364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10721.89 seconds wall clock time: 186 minutes 50.88 seconds (11210.88 seconds total)