Starting phenix.real_space_refine on Thu May 22 06:36:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glm_40199/05_2025/8glm_40199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glm_40199/05_2025/8glm_40199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8glm_40199/05_2025/8glm_40199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glm_40199/05_2025/8glm_40199.map" model { file = "/net/cci-nas-00/data/ceres_data/8glm_40199/05_2025/8glm_40199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glm_40199/05_2025/8glm_40199.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 13844 2.51 5 N 3668 2.21 5 O 4343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21902 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: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.50, per 1000 atoms: 0.53 Number of scatterers: 21902 At special positions: 0 Unit cell: (118.976, 128.128, 134.784, 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 47 16.00 O 4343 8.00 N 3668 7.00 C 13844 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: 4.83 Conformation dependent library (CDL) restraints added in 2.5 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 23 sheets defined 15.0% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.796A pdb=" N GLN A 202 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.677A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.184A 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: 3.986A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.513A 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 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.983A pdb=" N LYS A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 626 through 634 Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 5.937A pdb=" N ASP A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN A 674 " --> pdb=" O SER A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.765A 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 872 through 876 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 915 through 920 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 Processing helix chain 'A' and resid 1081 through 1089 Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 4.239A 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 1120 through 1124 removed outlier: 3.801A pdb=" N ALA A1124 " --> pdb=" O TYR A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1427 through 1438 Processing helix chain 'A' and resid 1454 through 1458 Processing helix chain 'A' and resid 1573 through 1576 Processing helix chain 'A' and resid 1607 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.618A pdb=" N ALA A1628 " --> pdb=" O ILE A1624 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A1629 " --> pdb=" O ARG A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1658 No H-bonds generated for 'chain 'A' and resid 1656 through 1658' Processing helix chain 'A' and resid 1830 through 1834 removed outlier: 3.510A pdb=" N LYS A1833 " --> pdb=" O PRO A1830 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1861 Processing helix chain 'A' and resid 1976 through 1981 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: 3.635A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 Processing helix chain 'A' and resid 2147 through 2161 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 3.730A pdb=" N ARG A2189 " --> pdb=" O GLY A2186 " (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 'B' and resid 147 through 151 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: 3.667A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 4.039A pdb=" N ASP F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.646A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 319 Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 140 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 138 through 140 current: chain 'A' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 187 through 194 removed outlier: 6.361A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 217 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 247 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS A 219 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR A 245 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU A 221 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 243 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY A 223 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE A 241 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 225 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER A 239 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 754 through 762 current: chain 'A' and resid 770 through 773 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 removed outlier: 3.567A pdb=" N ASN A 830 " --> pdb=" O ASN A1528 " (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: 5.533A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A1945 " --> pdb=" O ASP A2022 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP A2022 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A1947 " --> pdb=" O ASN A2020 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER A2006 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A2023 " --> pdb=" O LEU A2027 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A2027 " --> pdb=" O LEU A2023 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN A2044 " --> pdb=" O SER A2058 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER A2058 " --> pdb=" O GLN A2044 " (cutoff:3.500A) removed outlier: 6.281A 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 2205 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2197 through 2205 current: chain 'A' and resid 2238 through 2240 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: 3.858A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP A2302 " --> pdb=" O SER A2319 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER A2319 " --> pdb=" O ASP A2302 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASP A2320 " --> pdb=" O TYR A2361 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR A2361 " --> pdb=" O ASP A2320 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN A2322 " --> pdb=" O ALA A2359 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A2359 " --> pdb=" O ASN A2322 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A2324 " --> pdb=" O LEU A2357 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A2357 " --> pdb=" O LYS A2324 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP A2326 " --> pdb=" O LEU A2355 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A2355 " --> pdb=" O ASP A2326 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A2328 " --> pdb=" O TRP A2353 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP A2353 " --> pdb=" O SER A2328 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG A2330 " --> pdb=" O ASN A2351 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN A2351 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN A2332 " --> pdb=" O GLY A2349 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A2349 " --> pdb=" O ASN A2332 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR A2334 " --> pdb=" O ALA A2347 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A2379 " --> pdb=" O ASN A2351 " (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: 3.784A 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: 6.252A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 11.777A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N LEU A 503 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN A 343 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A 505 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 345 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET A 507 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 347 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LYS A 509 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.570A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 853 through 859 current: chain 'A' and resid 1326 through 1337 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1326 through 1337 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: 4.590A 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: 7.370A pdb=" N ARG A1343 " --> pdb=" O LYS A1491 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS A1491 " --> pdb=" O ARG A1343 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A1345 " --> pdb=" O GLY A1489 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY A1489 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS A1347 " --> pdb=" O MET A1487 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N MET A1487 " --> pdb=" O LYS A1347 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A1349 " --> pdb=" O ASN A1485 " (cutoff:3.500A) removed outlier: 4.626A 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 1582 through 1583 Processing sheet with id=AB7, first strand: chain 'A' and resid 1862 through 1863 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 48 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 54 through 59 current: chain 'B' and resid 110 through 113 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 113 current: chain 'B' and resid 166 through 174 Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.528A pdb=" N VAL B 160 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.991A pdb=" N ILE F 240 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 387 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP F 397 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP F 70 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL F 182 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.542A 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 removed outlier: 4.180A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 215 through 220 removed outlier: 4.538A pdb=" N TYR F 217 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N SER F 223 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1041 through 1045 Processing sheet with id=AC5, first strand: chain 'D' and resid 1071 through 1075 removed outlier: 6.247A pdb=" N LEU D1071 " --> pdb=" O ASP D1066 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP D1066 " --> pdb=" O LEU D1071 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR D1100 " --> pdb=" O ARG D1060 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL D1062 " --> pdb=" O LYS D1098 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS D1098 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE D1064 " --> pdb=" O ILE D1096 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE D1096 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP D1066 " --> pdb=" O VAL D1094 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL D1094 " --> pdb=" O ASP D1066 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 1899 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: 11.46 Time building geometry restraints manager: 5.71 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: 7248 1.34 - 1.46: 4951 1.46 - 1.58: 10083 1.58 - 1.70: 6 1.70 - 1.82: 92 Bond restraints: 22380 Sorted by residual: bond pdb=" C1 LMN A2501 " pdb=" O5 LMN A2501 " ideal model delta sigma weight residual 1.403 1.565 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.507 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" CCF LMN A2501 " pdb=" OBX LMN A2501 " ideal model delta sigma weight residual 1.410 1.501 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.484 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.474 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 22375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 30079 2.63 - 5.25: 278 5.25 - 7.88: 17 7.88 - 10.50: 4 10.50 - 13.13: 2 Bond angle restraints: 30380 Sorted by residual: angle pdb=" CA PRO F 126 " pdb=" N PRO F 126 " pdb=" CD PRO F 126 " ideal model delta sigma weight residual 112.00 98.87 13.13 1.40e+00 5.10e-01 8.80e+01 angle pdb=" C ILE A2141 " pdb=" N GLY A2142 " pdb=" CA GLY A2142 " ideal model delta sigma weight residual 122.78 113.42 9.36 2.61e+00 1.47e-01 1.29e+01 angle pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " pdb=" CCR LMN A2501 " ideal model delta sigma weight residual 120.22 109.70 10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CA LYS F 294 " pdb=" CB LYS F 294 " pdb=" CG LYS F 294 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 angle pdb=" C PHE A 883 " pdb=" N ILE A 884 " pdb=" CA ILE A 884 " ideal model delta sigma weight residual 122.63 118.55 4.08 1.19e+00 7.06e-01 1.18e+01 ... (remaining 30375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 12263 24.53 - 49.06: 928 49.06 - 73.59: 155 73.59 - 98.12: 52 98.12 - 122.64: 15 Dihedral angle restraints: 13413 sinusoidal: 5391 harmonic: 8022 Sorted by residual: dihedral pdb=" CA ASP A1258 " pdb=" C ASP A1258 " pdb=" N LEU A1259 " pdb=" CA LEU A1259 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA PRO A1063 " pdb=" C PRO A1063 " pdb=" N LEU A1064 " pdb=" CA LEU A1064 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR F 169 " pdb=" C THR F 169 " pdb=" N GLU F 170 " pdb=" CA GLU F 170 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2397 0.047 - 0.093: 650 0.093 - 0.139: 240 0.139 - 0.186: 18 0.186 - 0.232: 2 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB ILE B 100 " pdb=" CA ILE B 100 " pdb=" CG1 ILE B 100 " pdb=" CG2 ILE B 100 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO F 126 " pdb=" N PRO F 126 " pdb=" C PRO F 126 " pdb=" CB PRO F 126 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB ILE A 344 " pdb=" CA ILE A 344 " pdb=" CG1 ILE A 344 " pdb=" CG2 ILE A 344 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 3304 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 125 " 0.070 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO F 126 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO F 126 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 126 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1651 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO A1652 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A1652 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1652 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 605 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 606 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.026 5.00e-02 4.00e+02 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 306 2.65 - 3.21: 19334 3.21 - 3.77: 35303 3.77 - 4.34: 51859 4.34 - 4.90: 82937 Nonbonded interactions: 189739 Sorted by model distance: nonbonded pdb=" OE1 GLN A 865 " pdb=" OH TYR A1006 " model vdw 2.082 3.040 nonbonded pdb=" NH1 ARG A2398 " pdb=" OD1 ASN A2400 " model vdw 2.095 3.120 nonbonded pdb=" ND2 ASN A1392 " pdb=" O GLY A1476 " model vdw 2.097 3.120 nonbonded pdb=" OH TYR A2115 " pdb=" O ILE A2141 " model vdw 2.113 3.040 nonbonded pdb=" OD1 ASN A 492 " pdb=" OG SER A 494 " model vdw 2.135 3.040 ... (remaining 189734 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 49.410 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 0.162 22380 Z= 0.239 Angle : 0.664 13.129 30380 Z= 0.362 Chirality : 0.048 0.232 3307 Planarity : 0.005 0.098 4022 Dihedral : 18.340 122.645 8293 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 2.00 % Allowed : 18.10 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2743 helix: -0.92 (0.29), residues: 303 sheet: 0.72 (0.16), residues: 1065 loop : -0.41 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1996 HIS 0.004 0.001 HIS A 291 PHE 0.022 0.002 PHE A1009 TYR 0.028 0.002 TYR D1042 ARG 0.006 0.001 ARG A2398 Details of bonding type rmsd hydrogen bonds : bond 0.17414 ( 725) hydrogen bonds : angle 7.11632 ( 1899) covalent geometry : bond 0.00507 (22380) covalent geometry : angle 0.66421 (30380) *********************** 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 291 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 2.329 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 282 average time/residue: 1.3372 time to fit residues: 432.2951 Evaluate side-chains 222 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1868 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1040 SER Chi-restraints excluded: chain D residue 1079 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 501 GLN A1326 GLN A1387 ASN A1683 GLN A2012 ASN A2044 GLN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN D1053 ASN D1074 ASN D1084 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070831 restraints weight = 34000.011| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.16 r_work: 0.2802 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 22380 Z= 0.321 Angle : 0.683 11.159 30380 Z= 0.362 Chirality : 0.051 0.292 3307 Planarity : 0.005 0.061 4022 Dihedral : 10.101 95.501 3182 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 3.41 % Allowed : 16.23 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2743 helix: -0.82 (0.30), residues: 298 sheet: 0.67 (0.16), residues: 1031 loop : -0.44 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1580 HIS 0.005 0.001 HIS A1672 PHE 0.025 0.002 PHE A1480 TYR 0.020 0.002 TYR A2159 ARG 0.007 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 725) hydrogen bonds : angle 5.83691 ( 1899) covalent geometry : bond 0.00728 (22380) covalent geometry : angle 0.68306 (30380) *********************** 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 292 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 2.679 Fit side-chains revert: symmetry clash REVERT: A 836 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: A 1722 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6392 (p90) REVERT: A 1946 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8181 (ttmm) REVERT: A 2026 ASP cc_start: 0.6791 (p0) cc_final: 0.6474 (p0) REVERT: A 2081 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: B 25 LYS cc_start: 0.8627 (mttm) cc_final: 0.8405 (mttm) REVERT: B 58 THR cc_start: 0.9097 (m) cc_final: 0.8814 (p) REVERT: B 116 GLU cc_start: 0.8361 (pm20) cc_final: 0.8120 (pm20) REVERT: B 136 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8259 (pp) REVERT: B 141 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6797 (tm-30) REVERT: F 320 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8431 (ttmm) REVERT: F 321 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: D 1066 ASP cc_start: 0.8690 (t0) cc_final: 0.8431 (t0) outliers start: 82 outliers final: 34 residues processed: 276 average time/residue: 1.3430 time to fit residues: 424.5551 Evaluate side-chains 234 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1881 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 87 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN A 272 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN A1528 ASN A1683 GLN A1781 ASN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN B 96 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN D1084 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.095146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.072956 restraints weight = 33747.756| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.15 r_work: 0.2848 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22380 Z= 0.172 Angle : 0.588 8.289 30380 Z= 0.311 Chirality : 0.048 0.414 3307 Planarity : 0.004 0.055 4022 Dihedral : 8.737 83.347 3160 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 3.50 % Allowed : 16.44 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2743 helix: -0.71 (0.31), residues: 292 sheet: 0.50 (0.16), residues: 1046 loop : -0.45 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.019 0.001 PHE A1480 TYR 0.017 0.001 TYR A2159 ARG 0.008 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 725) hydrogen bonds : angle 5.52117 ( 1899) covalent geometry : bond 0.00380 (22380) covalent geometry : angle 0.58848 (30380) *********************** 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 290 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 206 time to evaluate : 2.597 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7924 (mpp) REVERT: A 1020 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: A 1189 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: A 1555 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8640 (mt-10) REVERT: A 1580 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.6482 (p-90) REVERT: A 1722 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6384 (p90) REVERT: A 1946 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8217 (ttmm) REVERT: A 2081 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: A 2340 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8677 (m-30) REVERT: B 25 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: B 116 GLU cc_start: 0.8397 (pm20) cc_final: 0.8184 (pm20) REVERT: F 320 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8441 (ttmm) REVERT: F 321 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8227 (mm-30) outliers start: 84 outliers final: 29 residues processed: 267 average time/residue: 1.3395 time to fit residues: 410.2592 Evaluate side-chains 236 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1849 ASP Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 170 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 199 optimal weight: 0.0370 chunk 168 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 361 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 ASN ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 GLN A2351 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN D1084 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070222 restraints weight = 34336.515| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.15 r_work: 0.2797 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22380 Z= 0.324 Angle : 0.666 10.564 30380 Z= 0.353 Chirality : 0.051 0.318 3307 Planarity : 0.004 0.056 4022 Dihedral : 8.771 87.960 3159 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 3.25 % Allowed : 16.85 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2743 helix: -0.82 (0.31), residues: 293 sheet: 0.44 (0.16), residues: 1037 loop : -0.51 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1580 HIS 0.005 0.001 HIS A1672 PHE 0.026 0.002 PHE A1480 TYR 0.022 0.002 TYR A1104 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 725) hydrogen bonds : angle 5.60680 ( 1899) covalent geometry : bond 0.00735 (22380) covalent geometry : angle 0.66616 (30380) *********************** 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 267 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 189 time to evaluate : 2.681 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: A 884 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 1189 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: A 1197 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: A 1555 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8614 (mt-10) REVERT: A 1580 TRP cc_start: 0.8270 (OUTLIER) cc_final: 0.6646 (p-90) REVERT: A 1722 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6625 (p90) REVERT: A 1946 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8237 (ttmm) REVERT: A 2081 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: B 116 GLU cc_start: 0.8417 (pm20) cc_final: 0.8212 (pm20) REVERT: B 136 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.7961 (pp) REVERT: B 141 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7097 (tm-30) REVERT: F 310 ASP cc_start: 0.1211 (OUTLIER) cc_final: 0.0914 (p0) REVERT: F 321 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8217 (mm-30) outliers start: 78 outliers final: 36 residues processed: 250 average time/residue: 1.4102 time to fit residues: 404.8225 Evaluate side-chains 230 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 21 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 259 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A1528 ASN A1683 GLN B 143 GLN B 155 ASN D1053 ASN D1084 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.073708 restraints weight = 34002.807| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.18 r_work: 0.2866 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22380 Z= 0.133 Angle : 0.557 8.801 30380 Z= 0.294 Chirality : 0.046 0.293 3307 Planarity : 0.004 0.050 4022 Dihedral : 8.135 82.777 3158 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 2.66 % Allowed : 17.23 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2743 helix: -0.81 (0.30), residues: 298 sheet: 0.34 (0.16), residues: 1052 loop : -0.46 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1580 HIS 0.002 0.001 HIS A 291 PHE 0.016 0.001 PHE A1242 TYR 0.015 0.001 TYR A2159 ARG 0.008 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 725) hydrogen bonds : angle 5.34119 ( 1899) covalent geometry : bond 0.00287 (22380) covalent geometry : angle 0.55697 (30380) *********************** 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 267 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 2.433 Fit side-chains revert: symmetry clash REVERT: A 862 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: A 884 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 1189 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: A 1375 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 1448 ASP cc_start: 0.8089 (t0) cc_final: 0.7839 (t0) REVERT: A 1580 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.6468 (p-90) REVERT: A 1722 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6651 (p90) REVERT: A 1946 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8188 (ttmm) REVERT: A 2081 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: A 2324 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8284 (tttp) REVERT: A 2340 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: B 116 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: B 136 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.7956 (pp) REVERT: B 141 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6973 (tm-30) REVERT: F 310 ASP cc_start: 0.1213 (OUTLIER) cc_final: 0.0928 (p0) REVERT: F 321 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8184 (mm-30) outliers start: 64 outliers final: 27 residues processed: 252 average time/residue: 1.3820 time to fit residues: 399.1404 Evaluate side-chains 235 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1881 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2290 MET Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 102 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 171 optimal weight: 0.0980 chunk 174 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 chunk 181 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 818 ASN A1683 GLN A1740 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075498 restraints weight = 33619.989| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.17 r_work: 0.2900 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22380 Z= 0.110 Angle : 0.534 9.052 30380 Z= 0.280 Chirality : 0.046 0.273 3307 Planarity : 0.004 0.053 4022 Dihedral : 7.482 84.839 3156 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 2.54 % Allowed : 17.89 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2743 helix: -0.79 (0.30), residues: 305 sheet: 0.35 (0.16), residues: 1054 loop : -0.42 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1580 HIS 0.002 0.001 HIS A 291 PHE 0.016 0.001 PHE A1242 TYR 0.024 0.001 TYR F 244 ARG 0.011 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 725) hydrogen bonds : angle 5.11469 ( 1899) covalent geometry : bond 0.00243 (22380) covalent geometry : angle 0.53428 (30380) *********************** 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 270 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 2.299 Fit side-chains REVERT: A 523 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.9294 (ttm) REVERT: A 713 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8170 (tp30) REVERT: A 862 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: A 884 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 1189 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: A 1375 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8266 (mm-30) REVERT: A 1580 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.6417 (p-90) REVERT: A 1673 ASP cc_start: 0.8892 (p0) cc_final: 0.8671 (p0) REVERT: A 1722 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6525 (p90) REVERT: A 1946 LYS cc_start: 0.8683 (mtpp) cc_final: 0.8142 (mttm) REVERT: A 2081 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: A 2103 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: A 2340 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8700 (m-30) REVERT: B 116 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: B 136 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7994 (pp) REVERT: F 310 ASP cc_start: 0.1150 (OUTLIER) cc_final: 0.0759 (p0) outliers start: 61 outliers final: 24 residues processed: 257 average time/residue: 1.3560 time to fit residues: 399.3213 Evaluate side-chains 234 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1881 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 2022 ASP Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 227 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 185 optimal weight: 0.0060 chunk 152 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 206 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 0.0470 chunk 256 optimal weight: 9.9990 overall best weight: 0.9696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN A1302 ASN A1683 GLN A1740 ASN A2400 ASN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074605 restraints weight = 33844.114| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.18 r_work: 0.2883 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22380 Z= 0.133 Angle : 0.547 9.577 30380 Z= 0.287 Chirality : 0.046 0.271 3307 Planarity : 0.004 0.048 4022 Dihedral : 7.232 86.027 3156 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 2.16 % Allowed : 18.27 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2743 helix: -0.77 (0.30), residues: 305 sheet: 0.36 (0.16), residues: 1055 loop : -0.42 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.017 0.001 PHE A1242 TYR 0.016 0.001 TYR B 55 ARG 0.009 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 725) hydrogen bonds : angle 5.09816 ( 1899) covalent geometry : bond 0.00298 (22380) covalent geometry : angle 0.54721 (30380) *********************** 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 255 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 2.387 Fit side-chains revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8180 (tp30) REVERT: A 862 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: A 884 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7875 (tp) REVERT: A 1189 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: A 1317 ASN cc_start: 0.8532 (p0) cc_final: 0.8309 (p0) REVERT: A 1375 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8260 (mm-30) REVERT: A 1580 TRP cc_start: 0.8126 (OUTLIER) cc_final: 0.6424 (p-90) REVERT: A 1722 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6495 (p90) REVERT: A 2081 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: A 2199 ARG cc_start: 0.7550 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: A 2324 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8218 (tttm) REVERT: A 2326 ASP cc_start: 0.8479 (m-30) cc_final: 0.8257 (m-30) REVERT: A 2340 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8730 (m-30) REVERT: B 116 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: B 136 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7991 (pp) REVERT: F 310 ASP cc_start: 0.1004 (OUTLIER) cc_final: 0.0641 (p0) outliers start: 52 outliers final: 26 residues processed: 243 average time/residue: 1.3623 time to fit residues: 379.7106 Evaluate side-chains 237 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1881 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 2036 SER Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 114 optimal weight: 0.2980 chunk 216 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN A1683 GLN A1740 ASN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075485 restraints weight = 33812.573| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.19 r_work: 0.2901 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22380 Z= 0.112 Angle : 0.533 9.368 30380 Z= 0.279 Chirality : 0.045 0.264 3307 Planarity : 0.003 0.046 4022 Dihedral : 6.796 88.880 3156 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 1.96 % Allowed : 18.64 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2743 helix: -0.66 (0.30), residues: 299 sheet: 0.38 (0.16), residues: 1059 loop : -0.42 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.023 0.001 PHE A1731 TYR 0.025 0.001 TYR F 244 ARG 0.010 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 725) hydrogen bonds : angle 5.01881 ( 1899) covalent geometry : bond 0.00249 (22380) covalent geometry : angle 0.53330 (30380) *********************** 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 253 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8483 (m-30) cc_final: 0.8221 (m-30) REVERT: A 437 ASN cc_start: 0.8949 (m-40) cc_final: 0.8724 (p0) REVERT: A 713 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8168 (tp30) REVERT: A 836 GLU cc_start: 0.8367 (tt0) cc_final: 0.8165 (tt0) REVERT: A 862 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.5880 (mp0) REVERT: A 884 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 1189 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: A 1317 ASN cc_start: 0.8475 (p0) cc_final: 0.8263 (p0) REVERT: A 1375 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8234 (mm-30) REVERT: A 1580 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.6352 (p-90) REVERT: A 1673 ASP cc_start: 0.8900 (p0) cc_final: 0.8667 (p0) REVERT: A 1722 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6561 (p90) REVERT: A 1946 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8183 (ttmm) REVERT: A 2081 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: A 2199 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7373 (mtm-85) REVERT: A 2324 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8207 (tttm) REVERT: A 2326 ASP cc_start: 0.8485 (m-30) cc_final: 0.8261 (m-30) REVERT: A 2340 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8681 (m-30) REVERT: B 116 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: B 136 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7984 (pp) REVERT: F 310 ASP cc_start: 0.0968 (OUTLIER) cc_final: 0.0602 (p0) outliers start: 47 outliers final: 18 residues processed: 242 average time/residue: 1.4147 time to fit residues: 393.8898 Evaluate side-chains 229 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1881 SER Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN A1683 GLN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.072373 restraints weight = 33977.537| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.18 r_work: 0.2840 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22380 Z= 0.224 Angle : 0.595 10.466 30380 Z= 0.314 Chirality : 0.048 0.266 3307 Planarity : 0.004 0.045 4022 Dihedral : 6.913 88.714 3152 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 1.71 % Allowed : 18.93 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2743 helix: -0.70 (0.31), residues: 293 sheet: 0.36 (0.16), residues: 1051 loop : -0.43 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.024 0.002 PHE A1480 TYR 0.018 0.002 TYR B 55 ARG 0.010 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 725) hydrogen bonds : angle 5.21154 ( 1899) covalent geometry : bond 0.00507 (22380) covalent geometry : angle 0.59522 (30380) *********************** 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 238 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 2.366 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8620 (m-30) cc_final: 0.8369 (m-30) REVERT: A 836 GLU cc_start: 0.8391 (tt0) cc_final: 0.8171 (tt0) REVERT: A 862 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: A 884 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7896 (tp) REVERT: A 1189 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: A 1375 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8250 (mm-30) REVERT: A 1580 TRP cc_start: 0.8145 (OUTLIER) cc_final: 0.6448 (p-90) REVERT: A 1722 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6666 (p90) REVERT: A 1946 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8167 (ttmm) REVERT: A 2081 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: A 2199 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7490 (mtm-85) REVERT: A 2324 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8216 (tttp) REVERT: A 2326 ASP cc_start: 0.8493 (m-30) cc_final: 0.8293 (m-30) REVERT: A 2340 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (m-30) REVERT: A 2360 ASP cc_start: 0.8451 (m-30) cc_final: 0.8018 (p0) REVERT: B 116 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: B 136 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7905 (pp) REVERT: F 310 ASP cc_start: 0.1078 (OUTLIER) cc_final: 0.0713 (p0) outliers start: 41 outliers final: 22 residues processed: 228 average time/residue: 1.3195 time to fit residues: 346.6602 Evaluate side-chains 226 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 2036 SER Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1046 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 210 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 258 optimal weight: 0.0570 chunk 259 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A1317 ASN A1683 GLN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.071672 restraints weight = 34072.279| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.18 r_work: 0.2826 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22380 Z= 0.234 Angle : 0.614 10.687 30380 Z= 0.327 Chirality : 0.048 0.267 3307 Planarity : 0.004 0.046 4022 Dihedral : 6.948 82.875 3152 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 1.91 % Allowed : 18.89 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2743 helix: -0.78 (0.31), residues: 293 sheet: 0.33 (0.16), residues: 1049 loop : -0.48 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.023 0.002 PHE A1480 TYR 0.022 0.002 TYR F 244 ARG 0.010 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 725) hydrogen bonds : angle 5.33497 ( 1899) covalent geometry : bond 0.00528 (22380) covalent geometry : angle 0.61449 (30380) ********************** 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 237 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 2.619 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7898 (mtm110) REVERT: A 836 GLU cc_start: 0.8439 (tt0) cc_final: 0.8228 (tt0) REVERT: A 862 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: A 884 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.7985 (tp) REVERT: A 1189 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: A 1375 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 1580 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.6537 (p-90) REVERT: A 1722 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6909 (p90) REVERT: A 1946 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8148 (ttmm) REVERT: A 2081 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: A 2199 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7480 (mtm-85) REVERT: A 2324 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8232 (tttp) REVERT: A 2326 ASP cc_start: 0.8499 (m-30) cc_final: 0.8276 (m-30) REVERT: A 2340 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8695 (m-30) REVERT: A 2360 ASP cc_start: 0.8459 (m-30) cc_final: 0.8018 (p0) REVERT: B 116 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: B 136 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7891 (pp) REVERT: F 310 ASP cc_start: 0.1241 (OUTLIER) cc_final: 0.0883 (p0) outliers start: 46 outliers final: 22 residues processed: 228 average time/residue: 1.3971 time to fit residues: 364.2146 Evaluate side-chains 218 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1942 LEU Chi-restraints excluded: chain A residue 2036 SER Chi-restraints excluded: chain A residue 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 GLN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.070785 restraints weight = 33888.894| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.16 r_work: 0.2809 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 22380 Z= 0.290 Angle : 0.650 11.255 30380 Z= 0.346 Chirality : 0.050 0.267 3307 Planarity : 0.004 0.046 4022 Dihedral : 6.986 80.792 3152 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 1.71 % Allowed : 18.98 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2743 helix: -0.82 (0.31), residues: 293 sheet: 0.33 (0.16), residues: 1048 loop : -0.53 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1580 HIS 0.006 0.001 HIS A1672 PHE 0.028 0.002 PHE A1480 TYR 0.022 0.002 TYR A1104 ARG 0.010 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 725) hydrogen bonds : angle 5.42306 ( 1899) covalent geometry : bond 0.00654 (22380) covalent geometry : angle 0.64994 (30380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17789.03 seconds wall clock time: 307 minutes 9.33 seconds (18429.33 seconds total)