Starting phenix.real_space_refine on Sun Oct 12 07:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glj_40195/10_2025/8glj_40195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glj_40195/10_2025/8glj_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/cci-nas-00/data/ceres_data/8glj_40195/10_2025/8glj_40195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glj_40195/10_2025/8glj_40195.map" model { file = "/net/cci-nas-00/data/ceres_data/8glj_40195/10_2025/8glj_40195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glj_40195/10_2025/8glj_40195.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.04, per 1000 atoms: 0.23 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.23 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: 6.13 Time building geometry restraints manager: 2.70 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: 2.380 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.950 ------------------------------------------------------------------------------- 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= 0.225 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 : 7.72 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A1556 TYR 0.019 0.001 TYR A1394 PHE 0.021 0.001 PHE A1009 TRP 0.015 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00483 (22375) covalent geometry : angle 0.58291 (30379) hydrogen bonds : bond 0.12343 ( 712) hydrogen bonds : angle 6.17363 ( 1875) *********************** 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 to be fit. rotamer outliers: 87 poor density : 346 time to evaluate : 0.877 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: 0.7377 (mttp) REVERT: A 745 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6422 (mt-10) REVERT: A 862 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5089 (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: 0.7338 (t0) REVERT: B 38 TYR cc_start: 0.8732 (t80) cc_final: 0.8380 (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: 0.9080 (tt) REVERT: F 123 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.5669 (p) REVERT: F 128 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: D 474 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: D 505 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7928 (mm) outliers start: 87 outliers final: 36 residues processed: 411 average time/residue: 0.1611 time to fit residues: 102.6498 Evaluate side-chains 280 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 836 GLU 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 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 437 ASN A 491 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN A1224 GLN A1787 ASN A1826 ASN A1874 ASN B 96 ASN B 143 GLN B 176 ASN F 209 GLN D 497 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.092778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.069156 restraints weight = 42318.613| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.80 r_work: 0.2741 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 22375 Z= 0.376 Angle : 0.689 10.702 30379 Z= 0.356 Chirality : 0.049 0.321 3303 Planarity : 0.005 0.044 4022 Dihedral : 10.083 98.114 3221 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.21 % Allowed : 10.13 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.16), residues: 2743 helix: -1.11 (0.30), residues: 284 sheet: -0.55 (0.16), residues: 1053 loop : -1.16 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.019 0.002 TYR A1394 PHE 0.024 0.002 PHE A1480 TRP 0.021 0.002 TRP A1580 HIS 0.009 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00843 (22375) covalent geometry : angle 0.68893 (30379) hydrogen bonds : bond 0.03551 ( 712) hydrogen bonds : angle 5.65467 ( 1875) *********************** 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 309 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 232 time to evaluate : 0.673 Fit side-chains REVERT: A 180 MET cc_start: 0.7637 (mmt) cc_final: 0.6912 (mmt) REVERT: A 190 ASN cc_start: 0.7896 (m110) cc_final: 0.7221 (m110) REVERT: A 484 ASP cc_start: 0.8131 (m-30) cc_final: 0.7858 (m-30) REVERT: A 539 ASP cc_start: 0.7725 (t0) cc_final: 0.7401 (t0) REVERT: A 741 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 1263 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 1598 GLU cc_start: 0.8392 (tt0) cc_final: 0.8155 (tt0) REVERT: A 1675 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8218 (mm-30) REVERT: A 2333 GLU cc_start: 0.7795 (mp0) cc_final: 0.7534 (mp0) REVERT: A 2365 LYS cc_start: 0.8863 (tmmt) cc_final: 0.8504 (tptp) REVERT: B 25 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8085 (mtmm) REVERT: B 34 GLU cc_start: 0.8681 (tp30) cc_final: 0.8421 (mt-10) REVERT: B 38 TYR cc_start: 0.8202 (t80) cc_final: 0.7810 (t80) REVERT: B 47 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7238 (tp-100) REVERT: B 55 TYR cc_start: 0.9116 (p90) cc_final: 0.8587 (p90) REVERT: B 96 ASN cc_start: 0.7699 (t0) cc_final: 0.7409 (t0) REVERT: B 102 LYS cc_start: 0.8898 (tttt) cc_final: 0.8416 (tttt) REVERT: B 113 GLU cc_start: 0.7560 (tp30) cc_final: 0.7202 (tp30) REVERT: B 141 GLU cc_start: 0.6244 (tm-30) cc_final: 0.6025 (tm-30) REVERT: B 169 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: B 174 SER cc_start: 0.8843 (m) cc_final: 0.8528 (p) REVERT: F 123 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.5578 (p) REVERT: F 128 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6859 (pt0) REVERT: F 137 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 472 ILE cc_start: 0.8797 (mm) cc_final: 0.8499 (mm) REVERT: D 495 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8237 (mm-30) REVERT: D 532 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7872 (tptp) outliers start: 77 outliers final: 46 residues processed: 292 average time/residue: 0.1475 time to fit residues: 69.9360 Evaluate side-chains 264 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 407 ILE 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 754 THR Chi-restraints excluded: chain A residue 779 MET 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 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 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1644 LYS 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 2219 PHE 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 B residue 146 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 75 SER 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 510 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 339 ASN A 437 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1787 ASN A1826 ASN A2248 GLN F 209 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.094281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.070851 restraints weight = 42428.660| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.80 r_work: 0.2786 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22375 Z= 0.124 Angle : 0.555 10.562 30379 Z= 0.287 Chirality : 0.046 0.353 3303 Planarity : 0.003 0.038 4022 Dihedral : 8.119 73.623 3185 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.75 % Allowed : 11.59 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.16), residues: 2743 helix: -0.87 (0.30), residues: 289 sheet: -0.38 (0.16), residues: 1040 loop : -1.02 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.019 0.001 TYR A 806 PHE 0.018 0.001 PHE D 461 TRP 0.012 0.001 TRP A2353 HIS 0.005 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00269 (22375) covalent geometry : angle 0.55504 (30379) hydrogen bonds : bond 0.02713 ( 712) hydrogen bonds : angle 5.34933 ( 1875) *********************** 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 300 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.7556 (mmt) cc_final: 0.6873 (mmt) REVERT: A 190 ASN cc_start: 0.7874 (m110) cc_final: 0.7069 (m110) REVERT: A 271 GLU cc_start: 0.7742 (tt0) cc_final: 0.7462 (tt0) REVERT: A 484 ASP cc_start: 0.8100 (m-30) cc_final: 0.7808 (m-30) REVERT: A 539 ASP cc_start: 0.7577 (t0) cc_final: 0.7344 (t0) REVERT: A 741 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 745 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 752 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8490 (mt0) REVERT: A 1263 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 2333 GLU cc_start: 0.7793 (mp0) cc_final: 0.7504 (mp0) REVERT: A 2365 LYS cc_start: 0.8827 (tmmt) cc_final: 0.8469 (tptp) REVERT: A 2374 ASP cc_start: 0.8110 (m-30) cc_final: 0.7900 (m-30) REVERT: B 25 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8217 (mttt) REVERT: B 34 GLU cc_start: 0.8730 (tp30) cc_final: 0.8436 (mt-10) REVERT: B 38 TYR cc_start: 0.8187 (t80) cc_final: 0.7855 (t80) REVERT: B 47 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7348 (tp-100) REVERT: B 55 TYR cc_start: 0.9124 (p90) cc_final: 0.8419 (p90) REVERT: B 96 ASN cc_start: 0.7786 (t0) cc_final: 0.7461 (t0) REVERT: B 101 TYR cc_start: 0.8652 (p90) cc_final: 0.8376 (p90) REVERT: B 141 GLU cc_start: 0.6308 (tm-30) cc_final: 0.6016 (tm-30) REVERT: B 174 SER cc_start: 0.8878 (m) cc_final: 0.8577 (p) REVERT: F 123 THR cc_start: 0.6614 (OUTLIER) cc_final: 0.5561 (p) REVERT: F 128 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: F 388 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8938 (ttm-80) REVERT: D 472 ILE cc_start: 0.8851 (mm) cc_final: 0.8647 (mm) REVERT: D 502 ASN cc_start: 0.7736 (t0) cc_final: 0.7354 (p0) REVERT: D 526 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8274 (mtmt) outliers start: 66 outliers final: 40 residues processed: 286 average time/residue: 0.1508 time to fit residues: 69.4417 Evaluate side-chains 263 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 593 ASP 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 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 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 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 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 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 388 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 184 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 231 optimal weight: 0.0370 chunk 74 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 A 437 ASN A 792 GLN A 803 ASN A1190 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.072641 restraints weight = 42022.134| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.79 r_work: 0.2821 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22375 Z= 0.099 Angle : 0.525 10.759 30379 Z= 0.270 Chirality : 0.045 0.287 3303 Planarity : 0.003 0.039 4022 Dihedral : 6.969 73.301 3183 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.67 % Allowed : 12.26 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 2743 helix: -0.70 (0.30), residues: 292 sheet: -0.26 (0.16), residues: 1031 loop : -0.92 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.012 0.001 TYR A 806 PHE 0.017 0.001 PHE A1242 TRP 0.011 0.001 TRP A2353 HIS 0.003 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00219 (22375) covalent geometry : angle 0.52532 (30379) hydrogen bonds : bond 0.02429 ( 712) hydrogen bonds : angle 5.13754 ( 1875) *********************** 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 297 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 133 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8235 (m-40) REVERT: A 180 MET cc_start: 0.7527 (mmt) cc_final: 0.6859 (mmt) REVERT: A 190 ASN cc_start: 0.7896 (m110) cc_final: 0.7049 (m110) REVERT: A 271 GLU cc_start: 0.7694 (tt0) cc_final: 0.7416 (tt0) REVERT: A 539 ASP cc_start: 0.7533 (t0) cc_final: 0.7280 (t0) REVERT: A 741 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 745 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 1263 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 1827 TYR cc_start: 0.8168 (t80) cc_final: 0.7820 (t80) REVERT: A 1949 GLN cc_start: 0.7892 (tp40) cc_final: 0.7527 (mm110) REVERT: A 2175 PHE cc_start: 0.8541 (m-80) cc_final: 0.8257 (t80) REVERT: A 2333 GLU cc_start: 0.7814 (mp0) cc_final: 0.7566 (mp0) REVERT: B 25 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8185 (mtmm) REVERT: B 34 GLU cc_start: 0.8751 (tp30) cc_final: 0.8453 (mt-10) REVERT: B 38 TYR cc_start: 0.8199 (t80) cc_final: 0.7779 (t80) REVERT: B 47 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7373 (tp-100) REVERT: B 96 ASN cc_start: 0.7869 (t0) cc_final: 0.7572 (t0) REVERT: B 101 TYR cc_start: 0.8685 (p90) cc_final: 0.8407 (p90) REVERT: B 141 GLU cc_start: 0.6296 (tm-30) cc_final: 0.5954 (tm-30) REVERT: B 174 SER cc_start: 0.8902 (m) cc_final: 0.8555 (p) REVERT: F 123 THR cc_start: 0.6557 (OUTLIER) cc_final: 0.5216 (p) REVERT: F 137 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7744 (mt-10) REVERT: F 333 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8703 (mm-40) REVERT: F 388 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8923 (ttm-80) REVERT: D 472 ILE cc_start: 0.8905 (mm) cc_final: 0.8589 (mm) REVERT: D 480 THR cc_start: 0.8076 (p) cc_final: 0.7765 (t) REVERT: D 502 ASN cc_start: 0.7784 (t0) cc_final: 0.7391 (p0) REVERT: D 506 SER cc_start: 0.9277 (m) cc_final: 0.8832 (p) REVERT: D 532 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7816 (tptp) outliers start: 64 outliers final: 34 residues processed: 283 average time/residue: 0.1548 time to fit residues: 69.9300 Evaluate side-chains 255 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN 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 593 ASP 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 1221 SER Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1565 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 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 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 323 THR Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 388 ARG Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 102 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 241 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 76 optimal weight: 0.0370 chunk 164 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 3.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 272 ASN A 339 ASN A 437 ASN A1882 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.069488 restraints weight = 42492.343| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.81 r_work: 0.2762 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22375 Z= 0.220 Angle : 0.568 9.382 30379 Z= 0.293 Chirality : 0.046 0.305 3303 Planarity : 0.004 0.038 4022 Dihedral : 6.724 72.551 3175 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.88 % Allowed : 12.38 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.16), residues: 2743 helix: -0.68 (0.30), residues: 298 sheet: -0.26 (0.16), residues: 1033 loop : -0.89 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2207 TYR 0.016 0.001 TYR F 81 PHE 0.020 0.001 PHE A1242 TRP 0.013 0.001 TRP A1580 HIS 0.003 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00495 (22375) covalent geometry : angle 0.56799 (30379) hydrogen bonds : bond 0.02828 ( 712) hydrogen bonds : angle 5.17103 ( 1875) *********************** 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 291 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.7570 (mmt) cc_final: 0.7099 (mmt) REVERT: A 190 ASN cc_start: 0.7970 (m110) cc_final: 0.6972 (m-40) REVERT: A 539 ASP cc_start: 0.7628 (t0) cc_final: 0.7319 (t0) REVERT: A 741 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 745 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7415 (mt-10) REVERT: A 1263 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 1341 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7064 (t0) REVERT: A 1827 TYR cc_start: 0.8235 (t80) cc_final: 0.7915 (t80) REVERT: A 2175 PHE cc_start: 0.8547 (m-80) cc_final: 0.8325 (t80) REVERT: B 25 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8206 (mtmm) REVERT: B 34 GLU cc_start: 0.8778 (tp30) cc_final: 0.8452 (mt-10) REVERT: B 38 TYR cc_start: 0.8200 (t80) cc_final: 0.7802 (t80) REVERT: B 47 GLN cc_start: 0.7741 (tp-100) cc_final: 0.7355 (tp-100) REVERT: B 96 ASN cc_start: 0.7861 (t0) cc_final: 0.7558 (t0) REVERT: B 101 TYR cc_start: 0.8866 (p90) cc_final: 0.8477 (p90) REVERT: B 141 GLU cc_start: 0.6591 (tm-30) cc_final: 0.6134 (tm-30) REVERT: B 169 GLU cc_start: 0.8722 (mp0) cc_final: 0.8261 (mp0) REVERT: B 174 SER cc_start: 0.8933 (m) cc_final: 0.8515 (p) REVERT: F 123 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.6085 (p) REVERT: F 125 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7272 (p0) REVERT: F 137 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7840 (mt-10) REVERT: D 502 ASN cc_start: 0.7803 (t0) cc_final: 0.7409 (p0) REVERT: D 506 SER cc_start: 0.9288 (m) cc_final: 0.8869 (p) REVERT: D 532 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7872 (tptp) outliers start: 69 outliers final: 44 residues processed: 279 average time/residue: 0.1475 time to fit residues: 66.1500 Evaluate side-chains 256 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 593 ASP 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 820 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1221 SER 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 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 1887 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 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR 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 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 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 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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 A 437 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1826 ASN A2248 GLN F 72 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.094128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.070305 restraints weight = 42023.023| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.83 r_work: 0.2757 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22375 Z= 0.267 Angle : 0.601 9.438 30379 Z= 0.309 Chirality : 0.047 0.293 3303 Planarity : 0.004 0.038 4022 Dihedral : 6.734 71.652 3173 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.79 % Allowed : 12.92 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.16), residues: 2743 helix: -0.68 (0.30), residues: 299 sheet: -0.36 (0.16), residues: 1042 loop : -0.92 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2207 TYR 0.014 0.002 TYR A1394 PHE 0.021 0.002 PHE A1242 TRP 0.017 0.002 TRP A1580 HIS 0.005 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00598 (22375) covalent geometry : angle 0.60076 (30379) hydrogen bonds : bond 0.02990 ( 712) hydrogen bonds : angle 5.30828 ( 1875) *********************** 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 277 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 0.778 Fit side-chains REVERT: A 180 MET cc_start: 0.7544 (mmt) cc_final: 0.7044 (mmt) REVERT: A 190 ASN cc_start: 0.7969 (m110) cc_final: 0.6869 (m-40) REVERT: A 264 GLN cc_start: 0.8040 (tt0) cc_final: 0.7773 (tt0) REVERT: A 539 ASP cc_start: 0.7631 (t0) cc_final: 0.7321 (t0) REVERT: A 741 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 745 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 914 ASP cc_start: 0.9095 (t70) cc_final: 0.8679 (t0) REVERT: A 1263 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 1341 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7015 (t0) REVERT: A 1580 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.7041 (p-90) REVERT: A 1827 TYR cc_start: 0.8161 (t80) cc_final: 0.7828 (t80) REVERT: A 2288 LYS cc_start: 0.8032 (mttm) cc_final: 0.7829 (mtmm) REVERT: A 2333 GLU cc_start: 0.7662 (mp0) cc_final: 0.7310 (mp0) REVERT: B 25 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8167 (mtmm) REVERT: B 34 GLU cc_start: 0.8805 (tp30) cc_final: 0.8430 (mt-10) REVERT: B 38 TYR cc_start: 0.8175 (t80) cc_final: 0.7812 (t80) REVERT: B 47 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7335 (tp-100) REVERT: B 96 ASN cc_start: 0.7691 (t0) cc_final: 0.7434 (t0) REVERT: B 101 TYR cc_start: 0.8970 (p90) cc_final: 0.8590 (p90) REVERT: B 169 GLU cc_start: 0.8658 (mp0) cc_final: 0.8132 (mp0) REVERT: B 174 SER cc_start: 0.8899 (m) cc_final: 0.8422 (p) REVERT: F 125 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7213 (p0) REVERT: F 137 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7888 (mt-10) REVERT: F 209 GLN cc_start: 0.8357 (mt0) cc_final: 0.8040 (mt0) REVERT: D 480 THR cc_start: 0.8145 (p) cc_final: 0.7843 (t) REVERT: D 498 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8694 (mm) REVERT: D 506 SER cc_start: 0.9248 (m) cc_final: 0.8841 (p) REVERT: D 532 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7829 (tptp) outliers start: 67 outliers final: 47 residues processed: 263 average time/residue: 0.1540 time to fit residues: 65.0188 Evaluate side-chains 253 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 433 LYS Chi-restraints excluded: chain A residue 544 ASN 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 1011 VAL Chi-restraints excluded: chain A residue 1171 ILE 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 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 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 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 72 GLN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 125 ASP 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 483 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 A 437 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.071548 restraints weight = 41728.824| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.84 r_work: 0.2785 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22375 Z= 0.172 Angle : 0.560 9.371 30379 Z= 0.290 Chirality : 0.046 0.291 3303 Planarity : 0.003 0.038 4022 Dihedral : 6.503 70.898 3171 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.33 % Allowed : 13.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.16), residues: 2743 helix: -0.51 (0.31), residues: 293 sheet: -0.29 (0.16), residues: 1033 loop : -0.90 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2207 TYR 0.011 0.001 TYR A1394 PHE 0.020 0.001 PHE A1242 TRP 0.014 0.001 TRP A1580 HIS 0.007 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00382 (22375) covalent geometry : angle 0.56035 (30379) hydrogen bonds : bond 0.02726 ( 712) hydrogen bonds : angle 5.23005 ( 1875) *********************** 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 to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.7542 (mmt) cc_final: 0.6964 (mmt) REVERT: A 190 ASN cc_start: 0.7950 (m110) cc_final: 0.6829 (m-40) REVERT: A 741 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 745 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7457 (tp30) REVERT: A 1263 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7905 (mt-10) REVERT: A 1341 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7000 (t0) REVERT: A 1827 TYR cc_start: 0.8112 (t80) cc_final: 0.7771 (t80) REVERT: A 2175 PHE cc_start: 0.8555 (m-80) cc_final: 0.8329 (t80) REVERT: A 2288 LYS cc_start: 0.8038 (mttm) cc_final: 0.7826 (mtmm) REVERT: A 2333 GLU cc_start: 0.7695 (mp0) cc_final: 0.7319 (mp0) REVERT: B 25 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8164 (mtmm) REVERT: B 32 GLU cc_start: 0.8685 (tp30) cc_final: 0.8231 (tp30) REVERT: B 34 GLU cc_start: 0.8802 (tp30) cc_final: 0.8418 (mt-10) REVERT: B 38 TYR cc_start: 0.8114 (t80) cc_final: 0.7733 (t80) REVERT: B 47 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7359 (tp-100) REVERT: B 54 TYR cc_start: 0.8765 (m-80) cc_final: 0.8235 (m-80) REVERT: B 96 ASN cc_start: 0.7660 (t0) cc_final: 0.7427 (t0) REVERT: B 101 TYR cc_start: 0.8865 (p90) cc_final: 0.8664 (p90) REVERT: B 141 GLU cc_start: 0.6410 (tm-30) cc_final: 0.6135 (tm-30) REVERT: B 169 GLU cc_start: 0.8643 (mp0) cc_final: 0.8272 (mp0) REVERT: B 174 SER cc_start: 0.8923 (m) cc_final: 0.8449 (p) REVERT: F 125 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.7659 (p0) REVERT: F 137 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7835 (mt-10) REVERT: F 183 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: F 209 GLN cc_start: 0.8251 (mt0) cc_final: 0.7868 (mt0) REVERT: D 480 THR cc_start: 0.8093 (p) cc_final: 0.7798 (t) REVERT: D 498 ILE cc_start: 0.8938 (mm) cc_final: 0.8726 (mm) REVERT: D 506 SER cc_start: 0.9246 (m) cc_final: 0.8838 (p) REVERT: D 532 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7798 (tptp) outliers start: 56 outliers final: 45 residues processed: 256 average time/residue: 0.1519 time to fit residues: 62.3788 Evaluate side-chains 250 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL 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 433 LYS 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 1011 VAL Chi-restraints excluded: chain A residue 1171 ILE 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 1785 THR Chi-restraints excluded: chain A residue 1787 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 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 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 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 183 ASP 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 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 437 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1826 ASN ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.071869 restraints weight = 41419.713| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.81 r_work: 0.2801 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22375 Z= 0.132 Angle : 0.541 9.228 30379 Z= 0.279 Chirality : 0.045 0.293 3303 Planarity : 0.003 0.038 4022 Dihedral : 6.274 70.868 3169 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.17 % Allowed : 13.67 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.16), residues: 2743 helix: -0.46 (0.31), residues: 293 sheet: -0.28 (0.16), residues: 1041 loop : -0.85 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2207 TYR 0.012 0.001 TYR B 104 PHE 0.019 0.001 PHE A1242 TRP 0.012 0.001 TRP A2353 HIS 0.004 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00295 (22375) covalent geometry : angle 0.54097 (30379) hydrogen bonds : bond 0.02576 ( 712) hydrogen bonds : angle 5.15277 ( 1875) *********************** 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 to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7515 (mmt) cc_final: 0.7020 (mmt) REVERT: A 741 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7924 (tm-30) REVERT: A 745 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7434 (tp30) REVERT: A 1263 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7888 (mt-10) REVERT: A 1341 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.6970 (t0) REVERT: A 1580 TRP cc_start: 0.8111 (OUTLIER) cc_final: 0.6959 (p-90) REVERT: A 1827 TYR cc_start: 0.8107 (t80) cc_final: 0.7806 (t80) REVERT: A 2175 PHE cc_start: 0.8513 (m-80) cc_final: 0.8312 (t80) REVERT: A 2240 MET cc_start: 0.8984 (pmm) cc_final: 0.8767 (pmm) REVERT: B 25 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8210 (mtmm) REVERT: B 32 GLU cc_start: 0.8698 (tp30) cc_final: 0.8185 (tp30) REVERT: B 34 GLU cc_start: 0.8821 (tp30) cc_final: 0.8422 (mt-10) REVERT: B 38 TYR cc_start: 0.8123 (t80) cc_final: 0.7739 (t80) REVERT: B 47 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7331 (tp-100) REVERT: B 54 TYR cc_start: 0.8752 (m-80) cc_final: 0.8171 (m-80) REVERT: B 96 ASN cc_start: 0.7732 (t0) cc_final: 0.7532 (t0) REVERT: B 131 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8124 (mt-10) REVERT: B 141 GLU cc_start: 0.6442 (tm-30) cc_final: 0.6130 (tm-30) REVERT: B 169 GLU cc_start: 0.8637 (mp0) cc_final: 0.8060 (mp0) REVERT: F 125 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7774 (p0) REVERT: F 137 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7814 (mt-10) REVERT: F 183 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: F 209 GLN cc_start: 0.8164 (mt0) cc_final: 0.7795 (mt0) REVERT: D 506 SER cc_start: 0.9257 (m) cc_final: 0.8867 (p) REVERT: D 532 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7797 (tptp) outliers start: 52 outliers final: 41 residues processed: 238 average time/residue: 0.1538 time to fit residues: 58.7044 Evaluate side-chains 239 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL 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 433 LYS 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 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 1286 ASP 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 1785 THR Chi-restraints excluded: chain A residue 1787 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 2219 PHE Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2341 TYR 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 125 ASP Chi-restraints excluded: chain F residue 183 ASP 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 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** A1826 ASN F 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.072429 restraints weight = 41533.109| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.80 r_work: 0.2812 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22375 Z= 0.128 Angle : 0.535 9.352 30379 Z= 0.276 Chirality : 0.045 0.267 3303 Planarity : 0.003 0.039 4022 Dihedral : 6.026 71.328 3166 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.13 % Allowed : 13.67 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.16), residues: 2743 helix: -0.43 (0.31), residues: 293 sheet: -0.20 (0.16), residues: 1036 loop : -0.81 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2207 TYR 0.013 0.001 TYR D 464 PHE 0.019 0.001 PHE A1242 TRP 0.011 0.001 TRP A2353 HIS 0.003 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00287 (22375) covalent geometry : angle 0.53493 (30379) hydrogen bonds : bond 0.02491 ( 712) hydrogen bonds : angle 5.07510 ( 1875) *********************** 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 to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.7511 (mmt) cc_final: 0.6780 (mmt) REVERT: A 190 ASN cc_start: 0.7937 (m110) cc_final: 0.6848 (m-40) REVERT: A 262 LYS cc_start: 0.8797 (mmtp) cc_final: 0.8503 (mmtm) REVERT: A 741 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 745 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7509 (tp30) REVERT: A 914 ASP cc_start: 0.9088 (t70) cc_final: 0.8662 (t0) REVERT: A 1263 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 1341 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7012 (t0) REVERT: A 1827 TYR cc_start: 0.8074 (t80) cc_final: 0.7768 (t80) REVERT: A 2175 PHE cc_start: 0.8532 (m-80) cc_final: 0.8263 (t80) REVERT: A 2240 MET cc_start: 0.9038 (pmm) cc_final: 0.8835 (pmm) REVERT: A 2255 MET cc_start: 0.8502 (ttt) cc_final: 0.7977 (ttt) REVERT: B 25 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8185 (mtmm) REVERT: B 32 GLU cc_start: 0.8719 (tp30) cc_final: 0.8206 (tp30) REVERT: B 34 GLU cc_start: 0.8820 (tp30) cc_final: 0.8419 (mt-10) REVERT: B 38 TYR cc_start: 0.8148 (t80) cc_final: 0.7761 (t80) REVERT: B 47 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7308 (tp-100) REVERT: B 54 TYR cc_start: 0.8737 (m-80) cc_final: 0.8179 (m-80) REVERT: B 131 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8103 (mt-10) REVERT: B 141 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6079 (tm-30) REVERT: B 169 GLU cc_start: 0.8561 (mp0) cc_final: 0.7994 (mp0) REVERT: F 125 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7877 (p0) REVERT: D 502 ASN cc_start: 0.7722 (t0) cc_final: 0.7360 (p0) REVERT: D 506 SER cc_start: 0.9265 (m) cc_final: 0.8894 (p) REVERT: D 532 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7784 (tptp) outliers start: 51 outliers final: 44 residues processed: 244 average time/residue: 0.1620 time to fit residues: 63.5147 Evaluate side-chains 241 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 367 SER 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 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 1286 ASP 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 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 1787 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 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 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 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 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 505 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 218 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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 792 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 ASN B 96 ASN F 72 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.070135 restraints weight = 41960.365| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.81 r_work: 0.2764 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22375 Z= 0.255 Angle : 0.596 9.195 30379 Z= 0.308 Chirality : 0.047 0.285 3303 Planarity : 0.004 0.040 4022 Dihedral : 6.218 71.411 3166 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.17 % Allowed : 13.84 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.16), residues: 2743 helix: -0.44 (0.31), residues: 292 sheet: -0.27 (0.17), residues: 1044 loop : -0.89 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2207 TYR 0.022 0.002 TYR A1655 PHE 0.021 0.002 PHE A1480 TRP 0.018 0.002 TRP A1580 HIS 0.006 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00571 (22375) covalent geometry : angle 0.59573 (30379) hydrogen bonds : bond 0.02931 ( 712) hydrogen bonds : angle 5.24329 ( 1875) ********************** 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 248 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.7538 (mmt) cc_final: 0.6856 (mmt) REVERT: A 190 ASN cc_start: 0.7958 (m110) cc_final: 0.6886 (m-40) REVERT: A 741 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 745 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7375 (tp30) REVERT: A 914 ASP cc_start: 0.9099 (t70) cc_final: 0.8693 (t0) REVERT: A 1341 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7037 (t0) REVERT: A 1461 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8774 (tt) REVERT: A 1580 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7201 (p-90) REVERT: A 1827 TYR cc_start: 0.8099 (t80) cc_final: 0.7779 (t80) REVERT: A 2333 GLU cc_start: 0.7749 (mp0) cc_final: 0.7507 (mp0) REVERT: B 25 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8200 (mtmm) REVERT: B 32 GLU cc_start: 0.8713 (tp30) cc_final: 0.8304 (tp30) REVERT: B 34 GLU cc_start: 0.8827 (tp30) cc_final: 0.8415 (mt-10) REVERT: B 38 TYR cc_start: 0.8167 (t80) cc_final: 0.7799 (t80) REVERT: B 47 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7298 (tp-100) REVERT: B 54 TYR cc_start: 0.8773 (m-80) cc_final: 0.8272 (m-80) REVERT: B 169 GLU cc_start: 0.8499 (mp0) cc_final: 0.7895 (mp0) REVERT: F 125 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7789 (p0) REVERT: F 183 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: D 506 SER cc_start: 0.9228 (m) cc_final: 0.8837 (p) REVERT: D 532 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7767 (tptp) outliers start: 52 outliers final: 42 residues processed: 238 average time/residue: 0.1526 time to fit residues: 58.2743 Evaluate side-chains 241 residues out of total 2399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 367 SER 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 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 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 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 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 125 ASP Chi-restraints excluded: chain F residue 183 ASP 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 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 78 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.8722 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071359 restraints weight = 41654.394| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.82 r_work: 0.2794 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22375 Z= 0.149 Angle : 0.559 9.170 30379 Z= 0.288 Chirality : 0.045 0.267 3303 Planarity : 0.003 0.040 4022 Dihedral : 6.124 71.475 3166 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.13 % Allowed : 13.80 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.16), residues: 2743 helix: -0.40 (0.31), residues: 292 sheet: -0.24 (0.17), residues: 1039 loop : -0.86 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2207 TYR 0.014 0.001 TYR D 464 PHE 0.019 0.001 PHE A1242 TRP 0.013 0.001 TRP A1580 HIS 0.006 0.001 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00331 (22375) covalent geometry : angle 0.55910 (30379) hydrogen bonds : bond 0.02684 ( 712) hydrogen bonds : angle 5.19814 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4222.03 seconds wall clock time: 73 minutes 40.10 seconds (4420.10 seconds total)