Starting phenix.real_space_refine on Sun Sep 29 11:14:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/09_2024/8glj_40195.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/09_2024/8glj_40195.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/09_2024/8glj_40195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/09_2024/8glj_40195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/09_2024/8glj_40195.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/09_2024/8glj_40195.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 13843 2.51 5 N 3662 2.21 5 O 4340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21891 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: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} 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: 12.06, per 1000 atoms: 0.55 Number of scatterers: 21891 At special positions: 0 Unit cell: (119.19, 128.232, 135.63, 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 4340 8.00 N 3662 7.00 C 13843 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: 5.68 Conformation dependent library (CDL) restraints added in 2.8 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5116 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 21 sheets defined 13.4% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.581A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.015A 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: 4.204A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 4.061A 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: 3.561A pdb=" N PHE A 414 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 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: 3.956A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.704A pdb=" N MET A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.825A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.685A 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: 3.659A pdb=" N LEU A1052 " --> pdb=" O GLU A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1089 Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 4.237A pdb=" N ILE A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.529A 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 1438 Processing helix chain 'A' and resid 1573 through 1576 Processing helix chain 'A' and resid 1577 through 1580 removed outlier: 3.608A 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: 3.915A pdb=" N ILE A1629 " --> pdb=" O ARG A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1660 Processing helix chain 'A' and resid 1856 through 1861 Processing helix chain 'A' and resid 1976 through 1981 removed outlier: 3.797A pdb=" N PHE A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1995 Processing helix chain 'A' and resid 2071 through 2075 Processing helix chain 'A' and resid 2084 through 2106 removed outlier: 3.693A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.585A pdb=" N ASN A2136 " --> pdb=" O VAL A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2160 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2186 through 2192 removed outlier: 4.150A pdb=" N TYR A2190 " --> pdb=" O GLY A2186 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A2191 " --> 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 44 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.602A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.708A pdb=" N ASP F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 4.023A 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: 5.800A pdb=" N ILE A 217 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN A 248 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 219 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.558A 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: 5.399A pdb=" N THR A1632 " --> pdb=" O HIS A1672 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS A1672 " --> pdb=" O THR A1632 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG A1634 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU A1670 " --> pdb=" O ARG A1634 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER A1636 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN A1668 " --> pdb=" O SER A1636 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASN A1638 " --> pdb=" O TYR A1666 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR A1666 " --> pdb=" O ASN A1638 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A1640 " --> pdb=" O GLN A1664 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A1664 " --> pdb=" O ILE A1640 " (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: 5.620A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN A1874 " --> pdb=" O GLY A1962 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN A1947 " --> pdb=" O ASN A2020 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A2044 " --> pdb=" O SER A2058 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER A2058 " --> pdb=" O GLN A2044 " (cutoff:3.500A) removed outlier: 5.977A 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: 3.938A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A2302 " --> pdb=" O SER A2319 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER A2319 " --> pdb=" O ASP A2302 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP A2320 " --> pdb=" O TYR A2361 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR A2361 " --> pdb=" O ASP A2320 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN A2322 " --> pdb=" O ALA A2359 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A2359 " --> pdb=" O ASN A2322 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A2324 " --> pdb=" O LEU A2357 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU A2357 " --> pdb=" O LYS A2324 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP A2326 " --> pdb=" O LEU A2355 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A2355 " --> pdb=" O ASP A2326 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A2328 " --> pdb=" O TRP A2353 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP A2353 " --> pdb=" O SER A2328 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG A2330 " --> pdb=" O ASN A2351 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN A2351 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN A2332 " --> pdb=" O GLY A2349 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY A2349 " --> pdb=" O ASN A2332 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR A2334 " --> pdb=" O ALA A2347 " (cutoff:3.500A) removed outlier: 4.360A 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: 3.778A 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: 6.432A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 19.326A pdb=" N TYR A 466 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 23.642A pdb=" N SER A 502 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N LEU A 503 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN A 343 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU A 505 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 345 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET A 507 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 347 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS A 509 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.560A 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 removed outlier: 3.529A pdb=" N GLU A 853 " --> pdb=" O PHE A 850 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 853 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 Processing sheet with id=AB1, 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=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB3, first strand: chain 'A' and resid 938 through 939 removed outlier: 4.564A pdb=" N ILE A 938 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1265 through 1266 removed outlier: 6.941A pdb=" N ARG A1343 " --> pdb=" O LYS A1491 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS A1491 " --> pdb=" O ARG A1343 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A1345 " --> pdb=" O GLY A1489 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY A1489 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS A1347 " --> pdb=" O MET A1487 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N MET A1487 " --> pdb=" O LYS A1347 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A1349 " --> pdb=" O ASN A1485 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN A1485 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id=AB6, first strand: chain 'A' and resid 1862 through 1863 Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 48 removed outlier: 6.931A pdb=" N TYR B 55 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE B 145 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE B 57 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN B 143 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AC1, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.845A pdb=" N ASN F 199 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE F 240 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP F 397 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP F 70 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL F 182 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN F 210 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 118 through 120 Processing sheet with id=AC3, first strand: chain 'D' and resid 514 through 521 712 hydrogen bonds defined for protein. 1875 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: 13.44 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7242 1.34 - 1.46: 4463 1.46 - 1.57: 10573 1.57 - 1.69: 7 1.69 - 1.81: 90 Bond restraints: 22375 Sorted by residual: bond pdb=" C1 LMN F 501 " pdb=" O5 LMN F 501 " ideal model delta sigma weight residual 1.403 1.566 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " ideal model delta sigma weight residual 1.409 1.508 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CCF LMN F 501 " pdb=" OBX LMN F 501 " ideal model delta sigma weight residual 1.410 1.498 -0.088 2.00e-02 2.50e+03 1.95e+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 1.95e+01 bond pdb=" CCR LMN F 501 " pdb=" OBY LMN F 501 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 22370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 30024 2.23 - 4.47: 322 4.47 - 6.70: 26 6.70 - 8.94: 4 8.94 - 11.17: 3 Bond angle restraints: 30379 Sorted by residual: angle pdb=" N SER D 487 " pdb=" CA SER D 487 " pdb=" C SER D 487 " ideal model delta sigma weight residual 110.80 121.97 -11.17 2.13e+00 2.20e-01 2.75e+01 angle pdb=" CA TYR D 486 " pdb=" C TYR D 486 " pdb=" N SER D 487 " ideal model delta sigma weight residual 118.22 114.54 3.68 1.03e+00 9.43e-01 1.28e+01 angle pdb=" CCQ LMN F 501 " pdb=" OCB LMN F 501 " pdb=" CCS LMN F 501 " ideal model delta sigma weight residual 119.65 109.60 10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C TYR D 486 " pdb=" N SER D 487 " pdb=" CA SER D 487 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " pdb=" CCR LMN F 501 " ideal model delta sigma weight residual 120.22 110.36 9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 30374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 12901 23.98 - 47.97: 391 47.97 - 71.95: 71 71.95 - 95.93: 16 95.93 - 119.91: 20 Dihedral angle restraints: 13399 sinusoidal: 5379 harmonic: 8020 Sorted by residual: dihedral pdb=" CA VAL D 463 " pdb=" C VAL D 463 " pdb=" N TYR D 464 " pdb=" CA TYR D 464 " ideal model delta harmonic sigma weight residual 180.00 -142.89 -37.11 0 5.00e+00 4.00e-02 5.51e+01 dihedral pdb=" CA TYR D 486 " pdb=" C TYR D 486 " pdb=" N SER D 487 " pdb=" CA SER D 487 " ideal model delta harmonic sigma weight residual 180.00 148.55 31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA SER D 487 " pdb=" C SER D 487 " pdb=" N LEU D 488 " pdb=" CA LEU D 488 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 13396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2125 0.037 - 0.073: 793 0.073 - 0.110: 273 0.110 - 0.147: 106 0.147 - 0.183: 6 Chirality restraints: 3303 Sorted by residual: chirality pdb=" CA SER D 487 " pdb=" N SER D 487 " pdb=" C SER D 487 " pdb=" CB SER D 487 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 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 6.80e-01 chirality pdb=" CA ILE A1007 " pdb=" N ILE A1007 " pdb=" C ILE A1007 " pdb=" CB ILE A1007 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 3300 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PHE A1639 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C SER A 176 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.016 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 605 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 606 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.022 5.00e-02 4.00e+02 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 390 2.66 - 3.22: 19714 3.22 - 3.78: 33287 3.78 - 4.34: 49672 4.34 - 4.90: 82356 Nonbonded interactions: 185419 Sorted by model distance: nonbonded pdb=" O LYS F 320 " pdb=" OG SER F 346 " model vdw 2.097 3.040 nonbonded pdb=" OH TYR A1015 " pdb=" O ASN A1025 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 982 " pdb=" OG SER A 984 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP A2163 " pdb=" OG SER A2165 " model vdw 2.220 3.040 nonbonded pdb=" O PRO D 465 " pdb=" OG1 THR D 468 " model vdw 2.224 3.040 ... (remaining 185414 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: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.600 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.005 0.163 22375 Z= 0.312 Angle : 0.583 11.172 30379 Z= 0.309 Chirality : 0.046 0.183 3303 Planarity : 0.004 0.039 4022 Dihedral : 13.071 119.915 8283 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.63 % Allowed : 6.59 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2743 helix: -1.22 (0.29), residues: 284 sheet: -0.47 (0.16), residues: 1061 loop : -1.06 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.021 0.001 PHE A1009 TYR 0.019 0.001 TYR A1394 ARG 0.002 0.000 ARG A1556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 346 time to evaluate : 2.324 Fit side-chains REVERT: A 539 ASP cc_start: 0.6512 (t0) cc_final: 0.6173 (t0) REVERT: A 683 LYS cc_start: 0.7873 (mttt) cc_final: 0.7376 (mttp) REVERT: A 745 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6426 (mt-10) REVERT: A 862 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5090 (mt-10) REVERT: A 2185 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7796 (m-40) REVERT: A 2343 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7339 (t0) REVERT: B 30 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 38 TYR cc_start: 0.8732 (t80) cc_final: 0.8373 (t80) REVERT: B 42 ASN cc_start: 0.8615 (m110) cc_final: 0.8292 (m110) REVERT: B 96 ASN cc_start: 0.7250 (t0) cc_final: 0.6986 (t0) REVERT: B 142 ILE cc_start: 0.9289 (tt) cc_final: 0.9079 (tt) REVERT: F 123 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.5670 (p) REVERT: F 128 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: D 474 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: D 505 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7928 (mm) outliers start: 87 outliers final: 35 residues processed: 411 average time/residue: 0.3629 time to fit residues: 231.5937 Evaluate side-chains 280 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 238 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2220 ASP Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2343 ASN Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 514 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 437 ASN A 491 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 GLN A1787 ASN A1826 ASN A1874 ASN B 143 GLN F 209 GLN D 497 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22375 Z= 0.364 Angle : 0.613 11.019 30379 Z= 0.318 Chirality : 0.047 0.280 3303 Planarity : 0.004 0.042 4022 Dihedral : 10.187 102.458 3218 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.00 % Allowed : 9.96 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2743 helix: -1.05 (0.30), residues: 290 sheet: -0.41 (0.16), residues: 1054 loop : -1.07 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 60 HIS 0.009 0.001 HIS D 525 PHE 0.019 0.002 PHE A1242 TYR 0.017 0.002 TYR A1394 ARG 0.005 0.000 ARG A2207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 241 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: A 484 ASP cc_start: 0.7187 (m-30) cc_final: 0.6964 (m-30) REVERT: A 862 GLU cc_start: 0.5494 (OUTLIER) cc_final: 0.4474 (mt-10) REVERT: A 1598 GLU cc_start: 0.6700 (tt0) cc_final: 0.6427 (tt0) REVERT: B 25 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8113 (mtmm) REVERT: B 33 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8195 (tppt) REVERT: B 38 TYR cc_start: 0.8655 (t80) cc_final: 0.8318 (t80) REVERT: B 42 ASN cc_start: 0.8547 (m110) cc_final: 0.8263 (m110) REVERT: B 55 TYR cc_start: 0.8821 (p90) cc_final: 0.8533 (p90) REVERT: B 96 ASN cc_start: 0.7762 (t0) cc_final: 0.7550 (t0) REVERT: B 101 TYR cc_start: 0.8540 (p90) cc_final: 0.8296 (p90) REVERT: F 123 THR cc_start: 0.6500 (OUTLIER) cc_final: 0.5724 (p) REVERT: F 128 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7258 (pt0) REVERT: D 474 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: D 489 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7751 (pp) REVERT: D 505 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8074 (mm) outliers start: 72 outliers final: 44 residues processed: 297 average time/residue: 0.3224 time to fit residues: 154.4666 Evaluate side-chains 270 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 514 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 437 ASN A 491 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN A1787 ASN B 96 ASN B 176 ASN F 209 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 22375 Z= 0.427 Angle : 0.624 10.578 30379 Z= 0.324 Chirality : 0.048 0.310 3303 Planarity : 0.004 0.039 4022 Dihedral : 8.904 75.443 3196 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.25 % Allowed : 10.96 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2743 helix: -1.01 (0.30), residues: 291 sheet: -0.43 (0.16), residues: 1045 loop : -1.14 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1580 HIS 0.004 0.001 HIS D 525 PHE 0.021 0.002 PHE A1480 TYR 0.016 0.002 TYR A1394 ARG 0.005 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 228 time to evaluate : 2.254 Fit side-chains REVERT: B 25 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8158 (mtmm) REVERT: B 38 TYR cc_start: 0.8644 (t80) cc_final: 0.8335 (t80) REVERT: B 101 TYR cc_start: 0.8572 (p90) cc_final: 0.8308 (p90) REVERT: B 141 GLU cc_start: 0.6433 (tm-30) cc_final: 0.6161 (tm-30) REVERT: F 123 THR cc_start: 0.6550 (OUTLIER) cc_final: 0.5901 (p) REVERT: F 128 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7321 (pt0) REVERT: D 474 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7669 (m-80) outliers start: 78 outliers final: 48 residues processed: 288 average time/residue: 0.3183 time to fit residues: 146.8811 Evaluate side-chains 261 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1461 LEU 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 1785 THR Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 339 ASN A 437 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN A 803 ASN ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN A1826 ASN B 96 ASN F 209 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22375 Z= 0.265 Angle : 0.566 10.262 30379 Z= 0.295 Chirality : 0.046 0.316 3303 Planarity : 0.003 0.039 4022 Dihedral : 7.611 73.650 3187 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.75 % Allowed : 11.92 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2743 helix: -0.87 (0.30), residues: 292 sheet: -0.37 (0.16), residues: 1034 loop : -1.03 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1580 HIS 0.005 0.001 HIS D 525 PHE 0.019 0.001 PHE A1242 TYR 0.024 0.001 TYR A2221 ARG 0.006 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 220 time to evaluate : 2.357 Fit side-chains REVERT: A 1580 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.6663 (p-90) REVERT: B 25 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8187 (mtmm) REVERT: B 38 TYR cc_start: 0.8623 (t80) cc_final: 0.8330 (t80) REVERT: B 141 GLU cc_start: 0.6444 (tm-30) cc_final: 0.6109 (tm-30) REVERT: F 123 THR cc_start: 0.6475 (OUTLIER) cc_final: 0.5759 (p) REVERT: F 128 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: D 474 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: D 506 SER cc_start: 0.8385 (m) cc_final: 0.8028 (p) outliers start: 66 outliers final: 44 residues processed: 270 average time/residue: 0.3393 time to fit residues: 148.1454 Evaluate side-chains 255 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 207 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1461 LEU 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 1580 TRP Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 0.0020 chunk 226 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 66 optimal weight: 0.0070 overall best weight: 2.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 339 ASN ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1874 ASN A1882 ASN F 209 GLN D 502 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22375 Z= 0.235 Angle : 0.555 11.252 30379 Z= 0.287 Chirality : 0.046 0.309 3303 Planarity : 0.003 0.038 4022 Dihedral : 7.151 72.903 3186 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.88 % Allowed : 12.21 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2743 helix: -0.79 (0.30), residues: 298 sheet: -0.28 (0.16), residues: 1017 loop : -0.99 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1580 HIS 0.005 0.001 HIS D 525 PHE 0.019 0.001 PHE A1242 TYR 0.015 0.001 TYR A2221 ARG 0.006 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 217 time to evaluate : 2.700 Fit side-chains REVERT: B 33 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8248 (tppt) REVERT: B 38 TYR cc_start: 0.8619 (t80) cc_final: 0.8290 (t80) REVERT: F 123 THR cc_start: 0.6462 (OUTLIER) cc_final: 0.5496 (p) REVERT: F 128 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: D 474 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: D 506 SER cc_start: 0.8378 (m) cc_final: 0.8097 (p) outliers start: 69 outliers final: 44 residues processed: 272 average time/residue: 0.3162 time to fit residues: 139.3082 Evaluate side-chains 248 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 2.636 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1461 LEU 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 1640 ILE Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 792 GLN A1387 ASN A1826 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 22375 Z= 0.544 Angle : 0.662 9.698 30379 Z= 0.342 Chirality : 0.049 0.310 3303 Planarity : 0.004 0.039 4022 Dihedral : 7.276 72.016 3185 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.04 % Allowed : 12.55 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2743 helix: -0.82 (0.30), residues: 291 sheet: -0.50 (0.16), residues: 1051 loop : -1.10 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1580 HIS 0.007 0.001 HIS D 525 PHE 0.025 0.002 PHE A1480 TYR 0.018 0.002 TYR D 517 ARG 0.007 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 207 time to evaluate : 2.680 Fit side-chains REVERT: A 1341 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7010 (t0) REVERT: A 1580 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7177 (p-90) REVERT: B 38 TYR cc_start: 0.8668 (t80) cc_final: 0.8376 (t80) REVERT: B 141 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6346 (tm-30) REVERT: F 123 THR cc_start: 0.6543 (OUTLIER) cc_final: 0.5876 (p) REVERT: F 128 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: D 506 SER cc_start: 0.8328 (m) cc_final: 0.8083 (p) outliers start: 73 outliers final: 52 residues processed: 264 average time/residue: 0.3111 time to fit residues: 135.3402 Evaluate side-chains 253 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1461 LEU 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 1580 TRP Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1887 THR Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A1190 ASN A1826 ASN B 96 ASN F 72 GLN F 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22375 Z= 0.190 Angle : 0.548 9.617 30379 Z= 0.285 Chirality : 0.045 0.290 3303 Planarity : 0.003 0.038 4022 Dihedral : 6.793 71.184 3183 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.38 % Allowed : 13.38 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2743 helix: -0.60 (0.30), residues: 292 sheet: -0.33 (0.16), residues: 1029 loop : -0.97 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2353 HIS 0.005 0.001 HIS D 525 PHE 0.019 0.001 PHE A1242 TYR 0.021 0.001 TYR A1655 ARG 0.006 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 2.533 Fit side-chains revert: symmetry clash REVERT: A 1341 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7006 (t0) REVERT: A 1580 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.6857 (p-90) REVERT: B 32 GLU cc_start: 0.8107 (tp30) cc_final: 0.7494 (tp30) REVERT: B 38 TYR cc_start: 0.8622 (t80) cc_final: 0.8274 (t80) REVERT: B 54 TYR cc_start: 0.8276 (m-80) cc_final: 0.7908 (m-80) REVERT: B 141 GLU cc_start: 0.6470 (tm-30) cc_final: 0.6184 (tm-30) REVERT: F 123 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.5713 (p) REVERT: F 128 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: D 506 SER cc_start: 0.8228 (m) cc_final: 0.8018 (p) outliers start: 57 outliers final: 43 residues processed: 253 average time/residue: 0.3157 time to fit residues: 129.2877 Evaluate side-chains 244 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1318 ASN Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 MET 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 1580 TRP Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 7.9990 chunk 105 optimal weight: 0.3980 chunk 157 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 207 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 792 GLN F 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.004 0.047 22375 Z= 0.227 Angle : 0.553 9.234 30379 Z= 0.286 Chirality : 0.046 0.288 3303 Planarity : 0.003 0.038 4022 Dihedral : 6.665 71.261 3181 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.96 % Allowed : 14.09 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2743 helix: -0.55 (0.31), residues: 292 sheet: -0.29 (0.16), residues: 1030 loop : -0.94 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1580 HIS 0.005 0.001 HIS D 525 PHE 0.022 0.001 PHE D 519 TYR 0.014 0.001 TYR A1655 ARG 0.008 0.000 ARG A2207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 202 time to evaluate : 2.552 Fit side-chains revert: symmetry clash REVERT: A 1341 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.6978 (t0) REVERT: A 1580 TRP cc_start: 0.7672 (OUTLIER) cc_final: 0.6865 (p-90) REVERT: B 32 GLU cc_start: 0.8099 (tp30) cc_final: 0.7595 (tp30) REVERT: B 38 TYR cc_start: 0.8627 (t80) cc_final: 0.8265 (t80) REVERT: B 54 TYR cc_start: 0.8256 (m-80) cc_final: 0.7968 (m-80) REVERT: F 123 THR cc_start: 0.6400 (OUTLIER) cc_final: 0.5676 (p) REVERT: F 128 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: D 506 SER cc_start: 0.8240 (m) cc_final: 0.8015 (p) outliers start: 47 outliers final: 38 residues processed: 239 average time/residue: 0.3220 time to fit residues: 124.2081 Evaluate side-chains 239 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 2.482 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1318 ASN Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1461 LEU 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 1580 TRP Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 148 optimal weight: 0.0050 chunk 107 optimal weight: 0.1980 chunk 193 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 245 optimal weight: 0.8980 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN F 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22375 Z= 0.189 Angle : 0.541 9.236 30379 Z= 0.280 Chirality : 0.045 0.267 3303 Planarity : 0.003 0.038 4022 Dihedral : 6.421 71.074 3179 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.96 % Allowed : 14.21 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2743 helix: -0.53 (0.31), residues: 293 sheet: -0.25 (0.16), residues: 1043 loop : -0.85 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2353 HIS 0.003 0.001 HIS D 525 PHE 0.021 0.001 PHE D 519 TYR 0.016 0.001 TYR D 517 ARG 0.008 0.000 ARG A2207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 206 time to evaluate : 2.257 Fit side-chains REVERT: A 1341 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6980 (t0) REVERT: A 1580 TRP cc_start: 0.7669 (OUTLIER) cc_final: 0.6870 (p-90) REVERT: A 2255 MET cc_start: 0.7077 (ttt) cc_final: 0.6869 (ttt) REVERT: B 32 GLU cc_start: 0.8110 (tp30) cc_final: 0.7626 (tp30) REVERT: B 38 TYR cc_start: 0.8655 (t80) cc_final: 0.8259 (t80) REVERT: B 141 GLU cc_start: 0.6446 (tm-30) cc_final: 0.6212 (tm-30) REVERT: F 123 THR cc_start: 0.6296 (OUTLIER) cc_final: 0.5490 (p) REVERT: F 128 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7353 (pt0) outliers start: 47 outliers final: 37 residues processed: 242 average time/residue: 0.3221 time to fit residues: 125.8564 Evaluate side-chains 236 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1318 ASN Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE 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 1787 ASN Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 272 optimal weight: 20.0000 chunk 251 optimal weight: 0.1980 chunk 217 optimal weight: 0.0970 chunk 22 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 overall best weight: 3.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 437 ASN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN F 72 GLN ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22375 Z= 0.346 Angle : 0.585 9.111 30379 Z= 0.304 Chirality : 0.046 0.265 3303 Planarity : 0.004 0.040 4022 Dihedral : 6.513 71.483 3175 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.88 % Allowed : 14.42 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2743 helix: -0.53 (0.31), residues: 292 sheet: -0.32 (0.16), residues: 1048 loop : -0.91 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1580 HIS 0.004 0.001 HIS D 525 PHE 0.021 0.001 PHE A1242 TYR 0.039 0.002 TYR B 54 ARG 0.008 0.000 ARG A2207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 2.675 Fit side-chains REVERT: A 1341 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7070 (t0) REVERT: A 1580 TRP cc_start: 0.7807 (OUTLIER) cc_final: 0.7113 (p-90) REVERT: A 2255 MET cc_start: 0.7122 (ttt) cc_final: 0.6912 (ttt) REVERT: B 38 TYR cc_start: 0.8650 (t80) cc_final: 0.8278 (t80) REVERT: B 141 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6209 (tm-30) outliers start: 45 outliers final: 37 residues processed: 231 average time/residue: 0.3251 time to fit residues: 121.8110 Evaluate side-chains 232 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 2.340 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1522 ILE 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 1787 ASN Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 2.9990 chunk 231 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 437 ASN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.094850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071340 restraints weight = 41747.174| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.82 r_work: 0.2782 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22375 Z= 0.270 Angle : 0.572 9.096 30379 Z= 0.296 Chirality : 0.046 0.266 3303 Planarity : 0.003 0.040 4022 Dihedral : 6.434 71.386 3174 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.83 % Allowed : 14.34 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2743 helix: -0.52 (0.31), residues: 292 sheet: -0.27 (0.16), residues: 1041 loop : -0.92 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.020 0.001 PHE A1242 TYR 0.031 0.001 TYR B 54 ARG 0.009 0.000 ARG A2207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4368.36 seconds wall clock time: 79 minutes 9.54 seconds (4749.54 seconds total)