Starting phenix.real_space_refine on Sun Oct 12 07:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glm_40199/10_2025/8glm_40199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glm_40199/10_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_40199/10_2025/8glm_40199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glm_40199/10_2025/8glm_40199.map" model { file = "/net/cci-nas-00/data/ceres_data/8glm_40199/10_2025/8glm_40199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glm_40199/10_2025/8glm_40199.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.13, per 1000 atoms: 0.23 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 1.27 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: 6.35 Time building geometry restraints manager: 2.30 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- 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 : 7.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (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 ARG 0.006 0.001 ARG A2398 TYR 0.028 0.002 TYR D1042 PHE 0.022 0.002 PHE A1009 TRP 0.019 0.002 TRP A1996 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00507 (22380) covalent geometry : angle 0.66421 (30380) hydrogen bonds : bond 0.17414 ( 725) hydrogen bonds : angle 7.11632 ( 1899) *********************** 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 : 0.915 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 282 average time/residue: 0.6615 time to fit residues: 212.9724 Evaluate side-chains 221 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 272 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A1326 GLN A1387 ASN A1528 ASN A1683 GLN A2012 ASN ** 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 = 0.3364 r_free = 0.3364 target = 0.095274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.072813 restraints weight = 33971.046| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.17 r_work: 0.2838 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22380 Z= 0.219 Angle : 0.629 8.860 30380 Z= 0.333 Chirality : 0.049 0.301 3307 Planarity : 0.004 0.058 4022 Dihedral : 9.832 94.011 3182 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 3.29 % Allowed : 16.40 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 2743 helix: -0.68 (0.31), residues: 291 sheet: 0.63 (0.16), residues: 1043 loop : -0.40 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 235 TYR 0.020 0.002 TYR A2159 PHE 0.021 0.002 PHE A1480 TRP 0.020 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00493 (22380) covalent geometry : angle 0.62908 (30380) hydrogen bonds : bond 0.04105 ( 725) hydrogen bonds : angle 5.72225 ( 1899) *********************** 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 289 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 1448 ASP cc_start: 0.7955 (t0) cc_final: 0.7744 (t0) REVERT: A 1722 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6330 (p90) REVERT: A 1946 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8165 (ttmm) REVERT: A 2081 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: B 25 LYS cc_start: 0.8609 (mttm) cc_final: 0.8389 (mttm) REVERT: B 58 THR cc_start: 0.9094 (m) cc_final: 0.8807 (p) REVERT: B 116 GLU cc_start: 0.8362 (pm20) cc_final: 0.8137 (pm20) REVERT: B 141 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6776 (tm-30) REVERT: F 321 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8216 (mm-30) REVERT: D 1066 ASP cc_start: 0.8663 (t0) cc_final: 0.8423 (t0) outliers start: 79 outliers final: 32 residues processed: 275 average time/residue: 0.6458 time to fit residues: 202.4341 Evaluate side-chains 232 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 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 747 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 827 VAL 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 1849 ASP 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 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 173 VAL Chi-restraints excluded: chain F residue 241 PHE 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 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 197 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 18 optimal weight: 0.0020 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 overall best weight: 0.9528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 361 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A1528 ASN A1683 GLN A1781 ASN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN B 143 GLN B 155 ASN F 353 GLN 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 = 0.3393 r_free = 0.3393 target = 0.096876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074552 restraints weight = 33891.755| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.18 r_work: 0.2875 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1317 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= 0.136 Angle : 0.562 8.278 30380 Z= 0.295 Chirality : 0.047 0.407 3307 Planarity : 0.004 0.050 4022 Dihedral : 8.431 86.108 3159 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 3.04 % Allowed : 16.77 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 2743 helix: -0.61 (0.31), residues: 291 sheet: 0.51 (0.16), residues: 1055 loop : -0.39 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 235 TYR 0.016 0.001 TYR A2159 PHE 0.017 0.001 PHE A1242 TRP 0.015 0.001 TRP A1580 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00301 (22380) covalent geometry : angle 0.56160 (30380) hydrogen bonds : bond 0.03504 ( 725) hydrogen bonds : angle 5.41406 ( 1899) *********************** 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 281 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7973 (mpp) REVERT: A 1020 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: A 1409 CYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6018 (p) REVERT: A 1448 ASP cc_start: 0.7917 (t0) cc_final: 0.7642 (t0) REVERT: A 1722 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6237 (p90) REVERT: A 1946 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8162 (ttmm) REVERT: A 2081 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: B 25 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8330 (mttm) REVERT: B 58 THR cc_start: 0.9091 (m) cc_final: 0.8868 (p) REVERT: B 116 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: B 136 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.7953 (pp) REVERT: B 141 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6884 (tm-30) REVERT: F 321 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8196 (mm-30) outliers start: 73 outliers final: 28 residues processed: 258 average time/residue: 0.6397 time to fit residues: 188.1788 Evaluate side-chains 236 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 1020 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1409 CYS 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 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 2396 THR 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 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 76 ILE Chi-restraints excluded: chain F residue 241 PHE 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 Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 181 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 501 GLN A1528 ASN A1683 GLN A2044 GLN A2351 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN D1084 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.071715 restraints weight = 34165.874| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.16 r_work: 0.2826 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22380 Z= 0.251 Angle : 0.612 8.979 30380 Z= 0.323 Chirality : 0.049 0.317 3307 Planarity : 0.004 0.052 4022 Dihedral : 8.409 87.299 3157 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 3.12 % Allowed : 16.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.16), residues: 2743 helix: -0.69 (0.31), residues: 287 sheet: 0.46 (0.16), residues: 1046 loop : -0.41 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1556 TYR 0.019 0.002 TYR A1104 PHE 0.025 0.002 PHE A1480 TRP 0.021 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00565 (22380) covalent geometry : angle 0.61216 (30380) hydrogen bonds : bond 0.03865 ( 725) hydrogen bonds : angle 5.45631 ( 1899) *********************** 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 275 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8128 (tp30) REVERT: A 862 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: A 1448 ASP cc_start: 0.8064 (t0) cc_final: 0.7776 (t0) REVERT: A 1580 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.6558 (p-90) REVERT: A 1722 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6422 (p90) REVERT: A 1946 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8235 (ttmm) REVERT: A 2081 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: A 2324 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8254 (tttm) REVERT: B 58 THR cc_start: 0.9099 (m) cc_final: 0.8813 (p) REVERT: B 116 GLU cc_start: 0.8392 (pm20) cc_final: 0.8160 (pm20) REVERT: B 136 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.7989 (pp) REVERT: B 141 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6898 (tm-30) REVERT: F 321 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8197 (mm-30) outliers start: 75 outliers final: 38 residues processed: 257 average time/residue: 0.6404 time to fit residues: 187.4862 Evaluate side-chains 236 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 537 LYS 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 931 SER Chi-restraints excluded: chain A residue 1102 SER 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 1811 LEU Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2022 ASP 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 2290 MET 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 93 LEU 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 76 ILE Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE 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 Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 190 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.0010 chunk 131 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- 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** A1528 ASN A1683 GLN B 143 GLN B 155 ASN D1053 ASN D1084 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.072726 restraints weight = 33710.764| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.17 r_work: 0.2845 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22380 Z= 0.183 Angle : 0.579 9.274 30380 Z= 0.306 Chirality : 0.047 0.292 3307 Planarity : 0.004 0.051 4022 Dihedral : 8.097 83.795 3157 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 2.79 % Allowed : 17.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.16), residues: 2743 helix: -0.77 (0.31), residues: 293 sheet: 0.40 (0.16), residues: 1052 loop : -0.44 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 235 TYR 0.016 0.001 TYR B 55 PHE 0.020 0.001 PHE A1480 TRP 0.019 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00410 (22380) covalent geometry : angle 0.57887 (30380) hydrogen bonds : bond 0.03509 ( 725) hydrogen bonds : angle 5.37269 ( 1899) *********************** 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 272 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8126 (tp30) REVERT: A 862 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.5995 (mp0) REVERT: A 884 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 1189 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: A 1375 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 1448 ASP cc_start: 0.8044 (t0) cc_final: 0.7795 (t0) REVERT: A 1580 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.6487 (p-90) REVERT: A 1722 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6509 (p90) REVERT: A 1946 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8202 (ttmm) REVERT: A 2081 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: A 2324 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8253 (tttp) REVERT: B 58 THR cc_start: 0.9107 (m) cc_final: 0.8803 (p) REVERT: B 116 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: B 136 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.7932 (pp) REVERT: B 141 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6867 (tm-30) REVERT: F 321 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8190 (mm-30) outliers start: 67 outliers final: 38 residues processed: 254 average time/residue: 0.5934 time to fit residues: 172.1030 Evaluate side-chains 245 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 537 LYS 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 1241 MET 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 1881 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2022 ASP 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 2290 MET 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 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 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE 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 Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 17 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN A1683 GLN B 96 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.071188 restraints weight = 33930.013| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.17 r_work: 0.2816 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22380 Z= 0.262 Angle : 0.624 9.450 30380 Z= 0.330 Chirality : 0.049 0.287 3307 Planarity : 0.004 0.053 4022 Dihedral : 8.000 84.368 3157 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 3.16 % Allowed : 16.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2743 helix: -0.75 (0.31), residues: 287 sheet: 0.39 (0.16), residues: 1046 loop : -0.46 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 235 TYR 0.021 0.002 TYR F 244 PHE 0.025 0.002 PHE A1480 TRP 0.024 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00593 (22380) covalent geometry : angle 0.62385 (30380) hydrogen bonds : bond 0.03848 ( 725) hydrogen bonds : angle 5.44805 ( 1899) *********************** 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 267 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 191 time to evaluate : 0.846 Fit side-chains REVERT: A 713 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8119 (tp30) REVERT: A 836 GLU cc_start: 0.8361 (tt0) cc_final: 0.8155 (tt0) REVERT: A 862 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: A 884 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8026 (tp) REVERT: A 1189 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: A 1432 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8600 (ttm170) REVERT: A 1448 ASP cc_start: 0.8088 (t0) cc_final: 0.7818 (t0) REVERT: A 1580 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.6523 (p-90) REVERT: A 1722 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6624 (p90) REVERT: A 2081 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: B 116 GLU cc_start: 0.8422 (pm20) cc_final: 0.8183 (pm20) REVERT: B 136 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.7952 (pp) REVERT: B 141 GLU cc_start: 0.7310 (tm-30) cc_final: 0.7073 (tm-30) REVERT: F 321 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8202 (mm-30) outliers start: 76 outliers final: 42 residues processed: 250 average time/residue: 0.6415 time to fit residues: 182.8407 Evaluate side-chains 239 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 401 ASN Chi-restraints excluded: chain A residue 537 LYS 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 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1432 ARG 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 1849 ASP 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 2290 MET 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 106 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 76 ILE Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE 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 Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 6 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 722 GLN A1683 GLN B 143 GLN B 155 ASN D1053 ASN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072240 restraints weight = 34036.283| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.18 r_work: 0.2836 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22380 Z= 0.197 Angle : 0.590 9.812 30380 Z= 0.311 Chirality : 0.047 0.279 3307 Planarity : 0.004 0.052 4022 Dihedral : 7.620 85.046 3157 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 2.83 % Allowed : 17.31 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2743 helix: -0.80 (0.31), residues: 293 sheet: 0.37 (0.16), residues: 1055 loop : -0.48 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 235 TYR 0.016 0.001 TYR A2159 PHE 0.019 0.001 PHE A1480 TRP 0.021 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00442 (22380) covalent geometry : angle 0.58956 (30380) hydrogen bonds : bond 0.03512 ( 725) hydrogen bonds : angle 5.36299 ( 1899) *********************** 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 267 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 199 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7864 (mtm110) REVERT: A 713 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8150 (tp30) REVERT: A 836 GLU cc_start: 0.8345 (tt0) cc_final: 0.8098 (tt0) REVERT: A 862 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: A 884 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 1189 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: A 1197 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8501 (mt-10) REVERT: A 1317 ASN cc_start: 0.8627 (p0) cc_final: 0.8417 (p0) REVERT: A 1432 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8597 (ttm170) REVERT: A 1448 ASP cc_start: 0.8115 (t0) cc_final: 0.7868 (t0) REVERT: A 1580 TRP cc_start: 0.8217 (OUTLIER) cc_final: 0.6537 (p-90) REVERT: A 1722 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6659 (p90) REVERT: A 1946 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8222 (ttmm) REVERT: A 2081 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: A 2324 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8175 (tttm) REVERT: B 116 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: B 136 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.7934 (pp) REVERT: B 141 GLU cc_start: 0.7250 (tm-30) cc_final: 0.7038 (tm-30) REVERT: F 321 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: F 331 MET cc_start: 0.8729 (tpt) cc_final: 0.8462 (tpt) outliers start: 68 outliers final: 41 residues processed: 249 average time/residue: 0.6111 time to fit residues: 173.2705 Evaluate side-chains 245 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 401 ASN Chi-restraints excluded: chain A residue 537 LYS 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 996 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1432 ARG Chi-restraints excluded: chain A residue 1531 ASP 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 1881 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER 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 2290 MET 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 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 23 GLU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE 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 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 206 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 257 optimal weight: 0.0970 chunk 267 optimal weight: 2.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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** A1683 GLN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.072430 restraints weight = 33777.572| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.17 r_work: 0.2841 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22380 Z= 0.184 Angle : 0.580 10.177 30380 Z= 0.306 Chirality : 0.047 0.273 3307 Planarity : 0.004 0.050 4022 Dihedral : 7.313 86.735 3157 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 2.83 % Allowed : 17.48 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2743 helix: -0.72 (0.31), residues: 287 sheet: 0.37 (0.16), residues: 1056 loop : -0.46 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 235 TYR 0.024 0.001 TYR F 244 PHE 0.020 0.001 PHE A1480 TRP 0.020 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00412 (22380) covalent geometry : angle 0.58015 (30380) hydrogen bonds : bond 0.03426 ( 725) hydrogen bonds : angle 5.31761 ( 1899) *********************** 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 265 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.8407 (mpp) cc_final: 0.8159 (mmt) REVERT: A 331 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7856 (mtm110) REVERT: A 713 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8160 (tp30) REVERT: A 836 GLU cc_start: 0.8348 (tt0) cc_final: 0.8121 (tt0) REVERT: A 862 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.5952 (mp0) REVERT: A 884 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.7928 (tp) REVERT: A 1189 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: A 1317 ASN cc_start: 0.8599 (p0) cc_final: 0.8379 (p0) REVERT: A 1375 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 1432 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8601 (ttm170) REVERT: A 1580 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.6512 (p-90) REVERT: A 1722 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6645 (p90) REVERT: A 1946 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8222 (ttmm) REVERT: A 2081 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: A 2324 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8222 (tttp) REVERT: A 2326 ASP cc_start: 0.8566 (m-30) cc_final: 0.8365 (m-30) REVERT: B 116 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: B 136 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.7954 (pp) REVERT: B 141 GLU cc_start: 0.7258 (tm-30) cc_final: 0.7044 (tm-30) REVERT: F 321 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8192 (mm-30) outliers start: 68 outliers final: 44 residues processed: 248 average time/residue: 0.6488 time to fit residues: 182.9993 Evaluate side-chains 249 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 537 LYS 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 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 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1432 ARG Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1733 THR Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1849 ASP 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 2022 ASP 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 2290 MET 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 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 23 GLU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE 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 Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 199 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070035 restraints weight = 34059.930| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.14 r_work: 0.2797 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 22380 Z= 0.338 Angle : 0.674 11.254 30380 Z= 0.358 Chirality : 0.051 0.275 3307 Planarity : 0.004 0.049 4022 Dihedral : 7.566 88.915 3157 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 2.70 % Allowed : 17.60 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.16), residues: 2743 helix: -0.91 (0.30), residues: 300 sheet: 0.35 (0.16), residues: 1047 loop : -0.55 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 235 TYR 0.023 0.002 TYR A1104 PHE 0.030 0.002 PHE A1480 TRP 0.029 0.002 TRP A1580 HIS 0.005 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00767 (22380) covalent geometry : angle 0.67410 (30380) hydrogen bonds : bond 0.04135 ( 725) hydrogen bonds : angle 5.53659 ( 1899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7898 (mtm110) REVERT: A 395 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: A 713 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8143 (tp30) REVERT: A 747 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8748 (m-40) REVERT: A 862 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.5946 (mp0) REVERT: A 884 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 1432 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8593 (ttm170) REVERT: A 1580 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.6646 (p-90) REVERT: A 1722 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6936 (p90) REVERT: A 1745 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8589 (ptp-110) REVERT: A 1946 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8232 (ttmm) REVERT: A 2081 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: A 2324 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8267 (tttp) REVERT: A 2360 ASP cc_start: 0.8502 (m-30) cc_final: 0.8060 (p0) REVERT: B 45 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 136 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.7943 (pp) REVERT: B 141 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7083 (tm-30) REVERT: F 321 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: F 348 MET cc_start: 0.8222 (mpp) cc_final: 0.7801 (ttt) REVERT: D 1066 ASP cc_start: 0.8660 (t0) cc_final: 0.8449 (t0) outliers start: 65 outliers final: 39 residues processed: 240 average time/residue: 0.6821 time to fit residues: 185.6040 Evaluate side-chains 234 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 537 LYS 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 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 1432 ARG Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1733 THR Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1752 ILE 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 2290 MET 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 106 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 23 GLU Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE 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 Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 206 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 230 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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** A1317 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 = 0.3389 r_free = 0.3389 target = 0.096321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.073991 restraints weight = 33742.835| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.18 r_work: 0.2871 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22380 Z= 0.117 Angle : 0.564 9.324 30380 Z= 0.299 Chirality : 0.046 0.265 3307 Planarity : 0.004 0.049 4022 Dihedral : 7.047 89.954 3156 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 2.04 % Allowed : 18.27 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.16), residues: 2743 helix: -0.80 (0.30), residues: 293 sheet: 0.32 (0.16), residues: 1055 loop : -0.48 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 235 TYR 0.021 0.001 TYR F 244 PHE 0.016 0.001 PHE A1242 TRP 0.017 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00257 (22380) covalent geometry : angle 0.56431 (30380) hydrogen bonds : bond 0.03081 ( 725) hydrogen bonds : angle 5.28484 ( 1899) ********************** 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 255 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7867 (mtm110) REVERT: A 713 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8169 (tp30) REVERT: A 779 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8558 (ttm) REVERT: A 862 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: A 884 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7874 (tp) REVERT: A 1375 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 1432 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8597 (ttm170) REVERT: A 1580 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.6370 (p-90) REVERT: A 1722 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6804 (p90) REVERT: A 1946 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8246 (ttmm) REVERT: A 2081 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: A 2199 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7186 (ptt90) REVERT: A 2324 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8219 (tttp) REVERT: A 2326 ASP cc_start: 0.8584 (m-30) cc_final: 0.8384 (m-30) REVERT: B 58 THR cc_start: 0.9053 (m) cc_final: 0.8632 (p) REVERT: B 136 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7944 (pp) REVERT: B 141 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6791 (tm-30) REVERT: F 321 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: F 348 MET cc_start: 0.8221 (mpp) cc_final: 0.7767 (ttt) outliers start: 49 outliers final: 24 residues processed: 245 average time/residue: 0.6665 time to fit residues: 185.7923 Evaluate side-chains 231 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 779 MET 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 996 SER Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1432 ARG 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 2081 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2290 MET Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 106 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 23 GLU Chi-restraints excluded: chain F residue 241 PHE 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 Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 A1734 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070050 restraints weight = 34004.925| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.16 r_work: 0.2797 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 22380 Z= 0.356 Angle : 0.683 11.904 30380 Z= 0.363 Chirality : 0.051 0.268 3307 Planarity : 0.004 0.048 4022 Dihedral : 7.341 89.462 3154 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 1.91 % Allowed : 18.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.16), residues: 2743 helix: -0.90 (0.30), residues: 300 sheet: 0.36 (0.16), residues: 1047 loop : -0.56 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 235 TYR 0.023 0.002 TYR A1104 PHE 0.028 0.002 PHE A1480 TRP 0.029 0.002 TRP A1580 HIS 0.006 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00811 (22380) covalent geometry : angle 0.68320 (30380) hydrogen bonds : bond 0.04109 ( 725) hydrogen bonds : angle 5.49044 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8987.76 seconds wall clock time: 153 minutes 32.60 seconds (9212.60 seconds total)