Starting phenix.real_space_refine on Thu May 22 06:36:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gln_40201/05_2025/8gln_40201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gln_40201/05_2025/8gln_40201.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/8gln_40201/05_2025/8gln_40201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gln_40201/05_2025/8gln_40201.map" model { file = "/net/cci-nas-00/data/ceres_data/8gln_40201/05_2025/8gln_40201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gln_40201/05_2025/8gln_40201.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 13844 2.51 5 N 3668 2.21 5 O 4343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21902 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.55, per 1000 atoms: 0.53 Number of scatterers: 21902 At special positions: 0 Unit cell: (118.976, 129.792, 135.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 4343 8.00 N 3668 7.00 C 13844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.97 Conformation dependent library (CDL) restraints added in 2.7 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 23 sheets defined 14.6% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.597A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.025A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.579A 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 removed outlier: 3.746A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.970A 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 730 through 735 removed outlier: 3.578A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.802A 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: 4.102A pdb=" N ILE A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 Processing helix chain 'A' and resid 1127 through 1132 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 1628 removed outlier: 3.608A pdb=" N ALA A1628 " --> pdb=" O ILE A1624 " (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: 3.786A pdb=" N LYS A1833 " --> pdb=" O PRO A1830 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A1834 " --> pdb=" O ILE A1831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1830 through 1834' Processing helix chain 'A' and resid 1856 through 1861 Processing helix chain 'A' and resid 1941 through 1943 No H-bonds generated for 'chain 'A' and resid 1941 through 1943' Processing helix chain 'A' and resid 1976 through 1981 Processing helix chain 'A' and resid 1987 through 1994 Processing helix chain 'A' and resid 2071 through 2075 Processing helix chain 'A' and resid 2084 through 2106 removed outlier: 3.681A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.513A pdb=" N ASN A2136 " --> pdb=" O VAL A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2161 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 3.560A pdb=" N ARG A2189 " --> pdb=" O GLY A2186 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A2190 " --> pdb=" O LEU A2187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2186 through 2190' 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: 3.643A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.756A pdb=" N ASP F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.754A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 319 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 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: 6.304A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 217 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A 248 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 219 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N MET A 227 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLN A 238 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 770 through 773 current: chain 'A' and resid 798 through 809 removed outlier: 3.850A 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: 5.608A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2007 through 2015 current: chain 'A' and resid 2027 through 2032 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2027 through 2032 current: chain 'A' and resid 2054 through 2069 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2054 through 2069 current: chain 'A' and resid 2197 through 2217 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2238 through 2240 current: chain 'A' and resid 2264 through 2278 removed outlier: 4.030A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A2302 " --> pdb=" O SER A2319 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER A2319 " --> pdb=" O ASP A2302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.884A 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: 6.203A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 11.832A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 19.582A pdb=" N TYR A 466 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 23.885A pdb=" N SER A 502 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.553A 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: 4.606A 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 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 1581 through 1583 removed outlier: 4.261A pdb=" N GLY A1581 " --> pdb=" O ASP A1645 " (cutoff:3.500A) 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 167 through 174 Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AC1, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.685A pdb=" N ASN F 199 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE F 240 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 387 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP F 397 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASP F 70 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL F 182 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.657A 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: 4.161A 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: 4.484A pdb=" N TYR F 217 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 9.612A 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 removed outlier: 3.633A pdb=" N ILE D1050 " --> pdb=" O VAL D1085 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1071 through 1075 removed outlier: 5.933A pdb=" N LEU D1071 " --> pdb=" O ASP D1066 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP D1066 " --> pdb=" O LEU D1071 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN D1093 " --> pdb=" O PHE D1113 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.83 Time building geometry restraints manager: 5.87 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: 7258 1.34 - 1.46: 5215 1.46 - 1.58: 9810 1.58 - 1.70: 5 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 6.54e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.506 -0.097 2.00e-02 2.50e+03 2.36e+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 2.07e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.476 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 22375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 29951 2.09 - 4.17: 376 4.17 - 6.26: 43 6.26 - 8.35: 7 8.35 - 10.44: 3 Bond angle restraints: 30380 Sorted by residual: angle pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " pdb=" CCR LMN A2501 " ideal model delta sigma weight residual 120.22 109.78 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C GLN A 538 " pdb=" N ASP A 539 " pdb=" CA ASP A 539 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CCQ LMN A2501 " pdb=" OCB LMN A2501 " pdb=" CCS LMN A2501 " ideal model delta sigma weight residual 119.65 110.13 9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C ILE B 100 " pdb=" CA ILE B 100 " pdb=" CB ILE B 100 " ideal model delta sigma weight residual 111.29 116.49 -5.20 1.64e+00 3.72e-01 1.01e+01 angle pdb=" C SER A2050 " pdb=" N THR A2051 " pdb=" CA THR A2051 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.58e+00 ... (remaining 30375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.78: 12444 24.78 - 49.56: 785 49.56 - 74.34: 115 74.34 - 99.12: 53 99.12 - 123.90: 16 Dihedral angle restraints: 13413 sinusoidal: 5391 harmonic: 8022 Sorted by residual: dihedral pdb=" CA PRO A1063 " pdb=" C PRO A1063 " pdb=" N LEU A1064 " pdb=" CA LEU A1064 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASP A1258 " pdb=" C ASP A1258 " pdb=" N LEU A1259 " pdb=" CA LEU A1259 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE A1078 " pdb=" C PHE A1078 " pdb=" N ASP A1079 " pdb=" CA ASP A1079 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2158 0.035 - 0.071: 735 0.071 - 0.106: 288 0.106 - 0.141: 119 0.141 - 0.177: 7 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CA ASP A1281 " pdb=" N ASP A1281 " pdb=" C ASP A1281 " pdb=" CB ASP A1281 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 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 2.82 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CCV LMN A2501 " pdb=" CCR LMN A2501 " pdb=" CCT LMN A2501 " pdb=" OAU LMN A2501 " both_signs ideal model delta sigma weight residual False 2.28 2.45 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 3304 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1651 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A1652 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1652 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1652 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 125 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO F 126 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 126 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 126 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 133 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 134 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " 0.025 5.00e-02 4.00e+02 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 293 2.65 - 3.21: 19477 3.21 - 3.77: 35211 3.77 - 4.34: 51199 4.34 - 4.90: 82613 Nonbonded interactions: 188793 Sorted by model distance: nonbonded pdb=" ND2 ASN A 343 " pdb=" O GLU A 429 " model vdw 2.084 3.120 nonbonded pdb=" OE2 GLU B 32 " pdb=" OH TYR B 54 " model vdw 2.154 3.040 nonbonded pdb=" OG SER F 75 " pdb=" OG1 THR F 95 " model vdw 2.155 3.040 nonbonded pdb=" ND2 ASN A1392 " pdb=" O GLY A1476 " model vdw 2.161 3.120 nonbonded pdb=" OH TYR A2115 " pdb=" O ILE A2141 " model vdw 2.169 3.040 ... (remaining 188788 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.310 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.004 0.162 22380 Z= 0.177 Angle : 0.585 10.435 30380 Z= 0.304 Chirality : 0.045 0.177 3307 Planarity : 0.004 0.053 4022 Dihedral : 17.394 123.900 8293 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 1.04 % Allowed : 10.94 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2743 helix: -0.51 (0.30), residues: 291 sheet: 0.82 (0.16), residues: 1061 loop : -0.33 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1996 HIS 0.005 0.001 HIS A 291 PHE 0.015 0.001 PHE A1480 TYR 0.020 0.001 TYR A 534 ARG 0.010 0.000 ARG A2264 Details of bonding type rmsd hydrogen bonds : bond 0.19444 ( 723) hydrogen bonds : angle 7.32232 ( 1920) covalent geometry : bond 0.00368 (22380) covalent geometry : angle 0.58514 (30380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 2.396 Fit side-chains revert: symmetry clash REVERT: A 2400 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8144 (m110) REVERT: D 1053 ASN cc_start: 0.7407 (m110) cc_final: 0.7102 (m-40) outliers start: 25 outliers final: 10 residues processed: 282 average time/residue: 1.3289 time to fit residues: 431.1296 Evaluate side-chains 217 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 1878 ASN 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 119 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 248 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 375 ASN A 418 ASN A 437 ASN A 727 GLN A 865 GLN A1222 GLN A1316 ASN A1324 ASN A1326 GLN A1348 ASN A1485 ASN ** A1650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1880 ASN A1955 ASN A2136 ASN B 96 ASN B 155 ASN F 245 ASN D1089 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.072311 restraints weight = 35367.957| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.21 r_work: 0.2849 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22380 Z= 0.247 Angle : 0.657 9.399 30380 Z= 0.345 Chirality : 0.050 0.342 3307 Planarity : 0.005 0.050 4022 Dihedral : 9.910 105.318 3161 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 2.62 % Allowed : 11.74 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2743 helix: -0.57 (0.30), residues: 293 sheet: 0.58 (0.16), residues: 1062 loop : -0.40 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1996 HIS 0.004 0.001 HIS A 291 PHE 0.023 0.002 PHE A1480 TYR 0.019 0.002 TYR A2159 ARG 0.007 0.001 ARG A2264 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 723) hydrogen bonds : angle 5.86153 ( 1920) covalent geometry : bond 0.00561 (22380) covalent geometry : angle 0.65668 (30380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8309 (mtpp) REVERT: A 576 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8757 (mm-40) REVERT: A 741 GLU cc_start: 0.8700 (mp0) cc_final: 0.8153 (mp0) REVERT: A 779 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8410 (tmm) REVERT: A 884 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8050 (tp) REVERT: A 1164 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8785 (mmt180) REVERT: A 1448 ASP cc_start: 0.7835 (t0) cc_final: 0.7600 (t70) REVERT: A 2083 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: A 2400 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8565 (m110) REVERT: B 32 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8656 (mm-30) REVERT: B 54 TYR cc_start: 0.8603 (m-80) cc_final: 0.8366 (m-80) REVERT: F 294 LYS cc_start: 0.7899 (pptt) cc_final: 0.7685 (pptt) REVERT: D 1053 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8400 (m-40) REVERT: D 1082 GLU cc_start: 0.8110 (tt0) cc_final: 0.7783 (tt0) outliers start: 63 outliers final: 30 residues processed: 254 average time/residue: 1.3718 time to fit residues: 398.9522 Evaluate side-chains 240 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 576 GLN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1878 ASN Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE 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 1053 ASN Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 87 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 230 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 437 ASN A1316 ASN A1650 GLN A1695 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 143 GLN B 155 ASN D1089 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.072219 restraints weight = 35229.178| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.21 r_work: 0.2854 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22380 Z= 0.209 Angle : 0.622 9.533 30380 Z= 0.326 Chirality : 0.048 0.311 3307 Planarity : 0.004 0.046 4022 Dihedral : 9.242 97.579 3157 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.50 % Allowed : 11.69 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2743 helix: -0.70 (0.30), residues: 299 sheet: 0.46 (0.16), residues: 1060 loop : -0.47 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1996 HIS 0.004 0.001 HIS A 291 PHE 0.022 0.001 PHE A1480 TYR 0.016 0.001 TYR A2159 ARG 0.008 0.001 ARG A2264 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 723) hydrogen bonds : angle 5.67242 ( 1920) covalent geometry : bond 0.00470 (22380) covalent geometry : angle 0.62203 (30380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7817 (mtp180) REVERT: A 537 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8318 (mtpp) REVERT: A 741 GLU cc_start: 0.8709 (mp0) cc_final: 0.8169 (mp0) REVERT: A 779 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8439 (tmm) REVERT: A 884 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 1258 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: A 1448 ASP cc_start: 0.7907 (t0) cc_final: 0.7614 (t70) REVERT: A 2083 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: B 32 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8715 (mm-30) REVERT: B 54 TYR cc_start: 0.8639 (m-80) cc_final: 0.8404 (m-80) REVERT: B 169 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8558 (mt-10) REVERT: F 294 LYS cc_start: 0.7947 (pptt) cc_final: 0.7725 (pptt) REVERT: D 1053 ASN cc_start: 0.8682 (m110) cc_final: 0.8348 (m-40) REVERT: D 1082 GLU cc_start: 0.8225 (tt0) cc_final: 0.7943 (tt0) outliers start: 60 outliers final: 33 residues processed: 256 average time/residue: 1.3717 time to fit residues: 402.2357 Evaluate side-chains 236 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1878 ASN Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 193 ILE 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 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 170 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 199 optimal weight: 7.9990 chunk 168 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 576 GLN A1387 ASN A1695 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 143 GLN B 155 ASN D1074 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.072897 restraints weight = 35533.184| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.21 r_work: 0.2867 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22380 Z= 0.172 Angle : 0.592 9.658 30380 Z= 0.309 Chirality : 0.047 0.350 3307 Planarity : 0.004 0.046 4022 Dihedral : 8.623 85.600 3153 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.41 % Allowed : 12.40 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2743 helix: -0.70 (0.30), residues: 299 sheet: 0.42 (0.16), residues: 1055 loop : -0.48 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1996 HIS 0.004 0.001 HIS A 291 PHE 0.019 0.001 PHE A1480 TYR 0.015 0.001 TYR A2159 ARG 0.006 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 723) hydrogen bonds : angle 5.50338 ( 1920) covalent geometry : bond 0.00386 (22380) covalent geometry : angle 0.59237 (30380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7803 (mtp180) REVERT: A 331 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7786 (ptp-110) REVERT: A 537 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8344 (mtpp) REVERT: A 613 GLN cc_start: 0.8863 (tp40) cc_final: 0.8661 (tp-100) REVERT: A 741 GLU cc_start: 0.8706 (mp0) cc_final: 0.8220 (mp0) REVERT: A 779 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8390 (tmm) REVERT: A 870 MET cc_start: 0.9400 (mmp) cc_final: 0.9171 (mmm) REVERT: A 1258 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: A 1448 ASP cc_start: 0.7939 (t0) cc_final: 0.7620 (t70) REVERT: A 1946 LYS cc_start: 0.8074 (mttp) cc_final: 0.7807 (mtmt) REVERT: A 2199 ARG cc_start: 0.7584 (ptt90) cc_final: 0.7293 (ptt90) REVERT: A 2365 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8714 (pttm) REVERT: B 54 TYR cc_start: 0.8661 (m-80) cc_final: 0.8415 (m-80) REVERT: F 294 LYS cc_start: 0.8021 (pptt) cc_final: 0.7744 (pptt) outliers start: 58 outliers final: 32 residues processed: 257 average time/residue: 1.3333 time to fit residues: 392.6585 Evaluate side-chains 240 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1878 ASN Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 113 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 128 GLU Chi-restraints excluded: chain F residue 193 ILE 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 1047 ASP Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 21 optimal weight: 0.3980 chunk 170 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 418 ASN A 437 ASN A 495 ASN A 532 GLN A 818 ASN A 865 GLN A1123 ASN A1650 GLN A1695 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1880 ASN A2040 ASN A2331 ASN B 96 ASN B 155 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.069567 restraints weight = 35806.786| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.23 r_work: 0.2804 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 22380 Z= 0.348 Angle : 0.694 10.963 30380 Z= 0.365 Chirality : 0.052 0.357 3307 Planarity : 0.005 0.046 4022 Dihedral : 8.494 84.787 3151 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.62 % Allowed : 12.28 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2743 helix: -0.72 (0.30), residues: 294 sheet: 0.32 (0.16), residues: 1062 loop : -0.53 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1580 HIS 0.007 0.002 HIS A1672 PHE 0.025 0.002 PHE A1480 TYR 0.021 0.002 TYR A1104 ARG 0.006 0.001 ARG A1556 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 723) hydrogen bonds : angle 5.71791 ( 1920) covalent geometry : bond 0.00792 (22380) covalent geometry : angle 0.69442 (30380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 202 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.7850 (mtp180) REVERT: A 331 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7809 (ptp-110) REVERT: A 537 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8283 (mtpp) REVERT: A 741 GLU cc_start: 0.8743 (mp0) cc_final: 0.8176 (mp0) REVERT: A 779 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8471 (tmm) REVERT: A 1448 ASP cc_start: 0.8077 (t0) cc_final: 0.7777 (t70) REVERT: A 2083 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: A 2199 ARG cc_start: 0.7656 (ptt90) cc_final: 0.7326 (ptt90) REVERT: A 2360 ASP cc_start: 0.8490 (t0) cc_final: 0.7771 (p0) REVERT: A 2365 LYS cc_start: 0.9010 (ttpp) cc_final: 0.8729 (pttm) REVERT: B 138 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8813 (t) REVERT: F 294 LYS cc_start: 0.7981 (pptt) cc_final: 0.7698 (pptt) REVERT: D 1089 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7069 (tt0) outliers start: 63 outliers final: 35 residues processed: 248 average time/residue: 1.4480 time to fit residues: 409.8924 Evaluate side-chains 237 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR 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 1179 ILE Chi-restraints excluded: chain A residue 1878 ASN Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 331 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 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Chi-restraints excluded: chain D residue 1089 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 102 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 576 GLN A 865 GLN A1583 ASN A1650 GLN A1695 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2350 GLN B 96 ASN B 143 GLN B 155 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073151 restraints weight = 35093.438| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.20 r_work: 0.2879 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22380 Z= 0.139 Angle : 0.580 10.063 30380 Z= 0.302 Chirality : 0.047 0.366 3307 Planarity : 0.004 0.048 4022 Dihedral : 7.589 85.406 3151 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.91 % Allowed : 13.61 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2743 helix: -0.61 (0.31), residues: 286 sheet: 0.33 (0.16), residues: 1054 loop : -0.50 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.015 0.001 PHE A1242 TYR 0.011 0.001 TYR A2159 ARG 0.005 0.000 ARG A1643 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 723) hydrogen bonds : angle 5.45715 ( 1920) covalent geometry : bond 0.00309 (22380) covalent geometry : angle 0.58010 (30380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7846 (mtp180) REVERT: A 331 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7830 (ptp-110) REVERT: A 741 GLU cc_start: 0.8697 (mp0) cc_final: 0.8224 (mp0) REVERT: A 884 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7973 (tp) REVERT: A 1448 ASP cc_start: 0.7955 (t0) cc_final: 0.7738 (t0) REVERT: A 1878 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8110 (t0) REVERT: A 2199 ARG cc_start: 0.7626 (ptt90) cc_final: 0.7295 (ptt90) REVERT: A 2360 ASP cc_start: 0.8450 (t0) cc_final: 0.7743 (p0) REVERT: A 2365 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8697 (pttm) REVERT: B 138 SER cc_start: 0.9146 (m) cc_final: 0.8886 (t) REVERT: B 169 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8552 (mt-10) REVERT: F 128 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7817 (pp20) REVERT: F 294 LYS cc_start: 0.7994 (pptt) cc_final: 0.7735 (pptt) outliers start: 46 outliers final: 23 residues processed: 248 average time/residue: 1.4468 time to fit residues: 408.5455 Evaluate side-chains 234 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1878 ASN Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2106 TYR Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE 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 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 227 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 109 optimal weight: 0.0040 chunk 256 optimal weight: 9.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 437 ASN A 532 GLN A 613 GLN A 865 GLN A1695 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2350 GLN B 96 ASN B 143 GLN B 149 HIS B 155 ASN D1089 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.072159 restraints weight = 35345.916| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.21 r_work: 0.2859 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22380 Z= 0.183 Angle : 0.595 9.983 30380 Z= 0.311 Chirality : 0.047 0.369 3307 Planarity : 0.004 0.046 4022 Dihedral : 7.358 84.369 3151 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.62 % Allowed : 14.27 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2743 helix: -0.73 (0.30), residues: 300 sheet: 0.31 (0.16), residues: 1064 loop : -0.46 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.004 0.001 HIS A 291 PHE 0.021 0.001 PHE A1480 TYR 0.017 0.001 TYR B 55 ARG 0.008 0.000 ARG A1643 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 723) hydrogen bonds : angle 5.42413 ( 1920) covalent geometry : bond 0.00412 (22380) covalent geometry : angle 0.59509 (30380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7835 (mtp180) REVERT: A 331 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7829 (ptp-110) REVERT: A 741 GLU cc_start: 0.8716 (mp0) cc_final: 0.8243 (mp0) REVERT: A 884 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7975 (tp) REVERT: A 1448 ASP cc_start: 0.7977 (t0) cc_final: 0.7746 (t0) REVERT: A 2199 ARG cc_start: 0.7646 (ptt90) cc_final: 0.7278 (ptt90) REVERT: A 2273 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8314 (mtm180) REVERT: A 2360 ASP cc_start: 0.8467 (t0) cc_final: 0.7775 (p0) REVERT: A 2365 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8696 (pttm) REVERT: B 32 GLU cc_start: 0.9037 (tp30) cc_final: 0.8513 (tp30) REVERT: B 138 SER cc_start: 0.9201 (m) cc_final: 0.8916 (t) REVERT: B 169 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8589 (mt-10) REVERT: F 128 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7835 (pp20) REVERT: F 294 LYS cc_start: 0.7977 (pptt) cc_final: 0.7746 (pptt) REVERT: F 320 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7917 (tttm) outliers start: 39 outliers final: 25 residues processed: 241 average time/residue: 1.4743 time to fit residues: 405.7744 Evaluate side-chains 238 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2106 TYR Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 320 LYS 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 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 114 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 532 GLN A 865 GLN A1695 GLN A1880 ASN A2350 GLN B 96 ASN B 143 GLN B 155 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072496 restraints weight = 35456.355| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.20 r_work: 0.2867 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22380 Z= 0.168 Angle : 0.589 9.991 30380 Z= 0.307 Chirality : 0.047 0.347 3307 Planarity : 0.004 0.047 4022 Dihedral : 6.961 83.558 3149 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.54 % Allowed : 14.69 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2743 helix: -0.70 (0.30), residues: 299 sheet: 0.31 (0.16), residues: 1065 loop : -0.46 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.019 0.001 PHE A1480 TYR 0.018 0.001 TYR B 55 ARG 0.008 0.000 ARG A1643 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 723) hydrogen bonds : angle 5.38618 ( 1920) covalent geometry : bond 0.00378 (22380) covalent geometry : angle 0.58934 (30380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7804 (mtp180) REVERT: A 331 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7840 (ptp-110) REVERT: A 378 ASP cc_start: 0.8758 (m-30) cc_final: 0.8525 (m-30) REVERT: A 741 GLU cc_start: 0.8704 (mp0) cc_final: 0.8231 (mp0) REVERT: A 884 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7962 (tp) REVERT: A 1448 ASP cc_start: 0.7999 (t0) cc_final: 0.7760 (t0) REVERT: A 1946 LYS cc_start: 0.8133 (mttt) cc_final: 0.7920 (mptt) REVERT: A 2199 ARG cc_start: 0.7625 (ptt90) cc_final: 0.7392 (ptt90) REVERT: A 2273 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8318 (mtm180) REVERT: A 2360 ASP cc_start: 0.8462 (t0) cc_final: 0.7776 (p0) REVERT: A 2365 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8683 (pttm) REVERT: B 138 SER cc_start: 0.9159 (m) cc_final: 0.8933 (t) REVERT: B 169 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8563 (mt-10) REVERT: F 128 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: F 320 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7913 (tttm) outliers start: 37 outliers final: 24 residues processed: 242 average time/residue: 1.3812 time to fit residues: 381.7085 Evaluate side-chains 240 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 320 LYS 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 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 110 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 532 GLN A 865 GLN A1695 GLN A1880 ASN A2350 GLN B 96 ASN B 143 GLN B 155 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072759 restraints weight = 35337.794| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.22 r_work: 0.2869 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22380 Z= 0.161 Angle : 0.590 9.300 30380 Z= 0.308 Chirality : 0.047 0.319 3307 Planarity : 0.004 0.047 4022 Dihedral : 6.837 83.019 3149 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.83 % Allowed : 14.77 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2743 helix: -0.65 (0.30), residues: 295 sheet: 0.29 (0.16), residues: 1067 loop : -0.44 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.019 0.001 PHE A1480 TYR 0.017 0.001 TYR B 55 ARG 0.007 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 723) hydrogen bonds : angle 5.36070 ( 1920) covalent geometry : bond 0.00363 (22380) covalent geometry : angle 0.59042 (30380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7803 (mtp180) REVERT: A 331 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7839 (ptp-110) REVERT: A 378 ASP cc_start: 0.8750 (m-30) cc_final: 0.8516 (m-30) REVERT: A 741 GLU cc_start: 0.8710 (mp0) cc_final: 0.8241 (mp0) REVERT: A 779 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8447 (tmm) REVERT: A 815 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.8223 (mtp180) REVERT: A 884 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7945 (tp) REVERT: A 1258 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8345 (m-30) REVERT: A 1448 ASP cc_start: 0.7994 (t0) cc_final: 0.7786 (t0) REVERT: A 1946 LYS cc_start: 0.8109 (mttt) cc_final: 0.7840 (mptt) REVERT: A 2199 ARG cc_start: 0.7672 (ptt90) cc_final: 0.7418 (ptt90) REVERT: A 2273 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8308 (mtm180) REVERT: A 2360 ASP cc_start: 0.8457 (t0) cc_final: 0.7774 (p0) REVERT: A 2365 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8682 (pttm) REVERT: B 169 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8589 (mt-10) REVERT: F 128 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7871 (pp20) outliers start: 44 outliers final: 27 residues processed: 244 average time/residue: 1.4276 time to fit residues: 398.2382 Evaluate side-chains 241 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2106 TYR Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2332 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 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE 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 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 210 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 437 ASN A 532 GLN A 865 GLN A1695 GLN A1880 ASN A2350 GLN B 96 ASN B 143 GLN B 155 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.070826 restraints weight = 35713.526| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.21 r_work: 0.2833 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22380 Z= 0.258 Angle : 0.648 10.140 30380 Z= 0.339 Chirality : 0.049 0.305 3307 Planarity : 0.004 0.047 4022 Dihedral : 7.019 83.034 3149 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.62 % Allowed : 15.15 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2743 helix: -0.71 (0.31), residues: 295 sheet: 0.23 (0.16), residues: 1067 loop : -0.48 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1580 HIS 0.005 0.001 HIS A1672 PHE 0.024 0.002 PHE A1480 TYR 0.020 0.002 TYR B 55 ARG 0.012 0.001 ARG A2264 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 723) hydrogen bonds : angle 5.50755 ( 1920) covalent geometry : bond 0.00586 (22380) covalent geometry : angle 0.64754 (30380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7808 (mtp180) REVERT: A 331 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7839 (ptp-110) REVERT: A 741 GLU cc_start: 0.8729 (mp0) cc_final: 0.8242 (mp0) REVERT: A 779 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8447 (tmm) REVERT: A 1448 ASP cc_start: 0.8049 (t0) cc_final: 0.7803 (t0) REVERT: A 1592 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: A 2083 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: A 2199 ARG cc_start: 0.7654 (ptt90) cc_final: 0.7314 (ptt90) REVERT: A 2360 ASP cc_start: 0.8479 (t0) cc_final: 0.7793 (p0) REVERT: A 2365 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8688 (pttm) REVERT: B 54 TYR cc_start: 0.8481 (m-80) cc_final: 0.8259 (m-80) REVERT: B 169 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8632 (mt-10) REVERT: F 128 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: F 294 LYS cc_start: 0.7945 (pptt) cc_final: 0.7682 (pttp) outliers start: 39 outliers final: 29 residues processed: 238 average time/residue: 1.4761 time to fit residues: 398.0974 Evaluate side-chains 241 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2332 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 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE 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 1056 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 201 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 437 ASN A1583 ASN A1695 GLN A2350 GLN B 96 ASN B 143 GLN B 155 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070929 restraints weight = 35388.074| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.21 r_work: 0.2836 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 22380 Z= 0.257 Angle : 0.788 59.199 30380 Z= 0.440 Chirality : 0.048 0.410 3307 Planarity : 0.004 0.047 4022 Dihedral : 7.018 83.011 3149 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.62 % Allowed : 15.31 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2743 helix: -0.71 (0.30), residues: 295 sheet: 0.22 (0.16), residues: 1067 loop : -0.48 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.024 0.002 PHE A1480 TYR 0.019 0.002 TYR B 55 ARG 0.009 0.000 ARG A2264 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 723) hydrogen bonds : angle 5.51130 ( 1920) covalent geometry : bond 0.00551 (22380) covalent geometry : angle 0.78755 (30380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18392.26 seconds wall clock time: 319 minutes 1.55 seconds (19141.55 seconds total)