Starting phenix.real_space_refine on Thu Aug 6 12:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2026/8jsm_36623.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 S 76 5.16 5 C 9442 2.51 5 N 2512 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14856 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10897 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1289} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1989 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2015 Chain: "C" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 737 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 511 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 509 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9157 SG CYS A1150 50.021 51.096 98.488 1.00 96.82 S ATOM 9179 SG CYS A1153 52.834 48.431 97.974 1.00 94.73 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 266 " occ=0.44 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.56 Time building chain proxies: 3.44, per 1000 atoms: 0.23 Number of scatterers: 14856 At special positions: 0 Unit cell: (175.96, 138.61, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 76 16.00 P 10 15.00 O 2815 8.00 N 2512 7.00 C 9442 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: 0.97 Conformation dependent library (CDL) restraints added in 754.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " Number of angles added : 2 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 58.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.672A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.134A pdb=" N CYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.725A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 99 through 122 removed outlier: 4.124A pdb=" N ILE A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.658A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.660A pdb=" N LYS A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 261 removed outlier: 3.597A pdb=" N ILE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.573A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.304A pdb=" N TYR A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.508A pdb=" N HIS A 463 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.745A pdb=" N ILE A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.038A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 515 through 521 removed outlier: 3.576A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.794A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.670A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.590A pdb=" N TYR A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.733A pdb=" N ARG A 691 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN A 692 " --> pdb=" O GLU A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 712 through 731 Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.268A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.939A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.611A pdb=" N ARG A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.922A pdb=" N LEU A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 Processing helix chain 'A' and resid 948 through 955 removed outlier: 4.389A pdb=" N LYS A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 974 through 978 removed outlier: 3.830A pdb=" N SER A 977 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 978 " --> pdb=" O PRO A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 978' Processing helix chain 'A' and resid 980 through 994 removed outlier: 3.609A pdb=" N LEU A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 removed outlier: 3.511A pdb=" N LEU A1004 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.832A pdb=" N ALA A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.582A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1064 removed outlier: 3.536A pdb=" N ASN A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.544A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1100 removed outlier: 3.941A pdb=" N ALA A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1213 through 1230 Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 3.567A pdb=" N LYS A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1254 through 1259 removed outlier: 3.922A pdb=" N MET A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1273 removed outlier: 3.957A pdb=" N ARG A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.661A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1315 through 1331 Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'B' and resid 82 through 119 Processing helix chain 'B' and resid 120 through 123 removed outlier: 4.625A pdb=" N ASP B 123 " --> pdb=" O PRO B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 149 Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.703A pdb=" N ALA B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.723A pdb=" N HIS B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.940A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.667A pdb=" N ASP B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 119 Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.891A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.673A pdb=" N ALA C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 112 removed outlier: 3.682A pdb=" N THR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.820A pdb=" N TYR D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 117 Processing helix chain 'E' and resid 118 through 144 removed outlier: 4.185A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 71 removed outlier: 3.701A pdb=" N LEU A 71 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 231 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.962A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 630 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A 793 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA7, first strand: chain 'A' and resid 1175 through 1176 removed outlier: 3.992A pdb=" N SER A1175 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 removed outlier: 3.950A pdb=" N LYS B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2173 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: 2.59 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3610 1.33 - 1.45: 2981 1.45 - 1.57: 8488 1.57 - 1.69: 19 1.69 - 1.81: 111 Bond restraints: 15209 Sorted by residual: bond pdb=" CA ASN A 959 " pdb=" CB ASN A 959 " ideal model delta sigma weight residual 1.526 1.559 -0.033 1.51e-02 4.39e+03 4.77e+00 bond pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.37e-02 5.33e+03 3.54e+00 bond pdb=" N SER C 179 " pdb=" CA SER C 179 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.34e+00 bond pdb=" CA ASP A 757 " pdb=" CB ASP A 757 " ideal model delta sigma weight residual 1.518 1.546 -0.028 2.08e-02 2.31e+03 1.86e+00 bond pdb=" C GLU C 178 " pdb=" O GLU C 178 " ideal model delta sigma weight residual 1.232 1.249 -0.017 1.32e-02 5.74e+03 1.71e+00 ... (remaining 15204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 20129 1.43 - 2.86: 432 2.86 - 4.29: 113 4.29 - 5.72: 36 5.72 - 7.15: 9 Bond angle restraints: 20719 Sorted by residual: angle pdb=" N GLN B 99 " pdb=" CA GLN B 99 " pdb=" CB GLN B 99 " ideal model delta sigma weight residual 110.40 116.55 -6.15 1.63e+00 3.76e-01 1.42e+01 angle pdb=" N GLU B 115 " pdb=" CA GLU B 115 " pdb=" CB GLU B 115 " ideal model delta sigma weight residual 110.28 116.06 -5.78 1.55e+00 4.16e-01 1.39e+01 angle pdb=" C GLN B 98 " pdb=" N GLN B 99 " pdb=" CA GLN B 99 " ideal model delta sigma weight residual 121.14 114.62 6.52 1.75e+00 3.27e-01 1.39e+01 angle pdb=" C LEU B 114 " pdb=" N GLU B 115 " pdb=" CA GLU B 115 " ideal model delta sigma weight residual 120.31 115.00 5.31 1.52e+00 4.33e-01 1.22e+01 angle pdb=" C SER A 750 " pdb=" N VAL A 751 " pdb=" CA VAL A 751 " ideal model delta sigma weight residual 121.97 128.08 -6.11 1.80e+00 3.09e-01 1.15e+01 ... (remaining 20714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8115 17.97 - 35.94: 830 35.94 - 53.90: 148 53.90 - 71.87: 44 71.87 - 89.84: 17 Dihedral angle restraints: 9154 sinusoidal: 3691 harmonic: 5463 Sorted by residual: dihedral pdb=" C4' G G 3 " pdb=" C3' G G 3 " pdb=" C2' G G 3 " pdb=" C1' G G 3 " ideal model delta sinusoidal sigma weight residual 36.34 -36.08 72.42 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' U G 0 " pdb=" C3' U G 0 " pdb=" C2' U G 0 " pdb=" C1' U G 0 " ideal model delta sinusoidal sigma weight residual 36.34 -35.92 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' C G 7 " pdb=" C3' C G 7 " pdb=" C2' C G 7 " pdb=" C1' C G 7 " ideal model delta sinusoidal sigma weight residual 36.34 -35.73 72.08 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 9151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2068 0.059 - 0.117: 279 0.117 - 0.176: 16 0.176 - 0.234: 5 0.234 - 0.293: 15 Chirality restraints: 2383 Sorted by residual: chirality pdb=" C2' C G 7 " pdb=" C3' C G 7 " pdb=" O2' C G 7 " pdb=" C1' C G 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2' G G 3 " pdb=" C3' G G 3 " pdb=" O2' G G 3 " pdb=" C1' G G 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C2' U G 2 " pdb=" C3' U G 2 " pdb=" O2' U G 2 " pdb=" C1' U G 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2380 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 892 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 893 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 893 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 893 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 959 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ASN A 959 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN A 959 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS A 960 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 314 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 315 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.022 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 119 2.62 - 3.19: 13003 3.19 - 3.76: 21730 3.76 - 4.33: 29295 4.33 - 4.90: 50655 Nonbonded interactions: 114802 Sorted by model distance: nonbonded pdb=" NE2 GLN E 99 " pdb=" OE1 GLN E 100 " model vdw 2.050 3.120 nonbonded pdb=" O ASN A 959 " pdb=" ND2 ASN A 959 " model vdw 2.206 3.120 nonbonded pdb=" O TYR A 32 " pdb=" OG1 THR A 70 " model vdw 2.223 3.040 nonbonded pdb=" O TYR A 667 " pdb=" NE2 GLN A 671 " model vdw 2.270 3.120 nonbonded pdb=" OE1 GLU A1218 " pdb=" NH2 ARG A1247 " model vdw 2.271 3.120 ... (remaining 114797 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 82 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 118 or (resid 119 and (name N or n \ ame CA or name C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 132 or (resid 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 146)) } 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=0.44 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.850 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 : 0.003 0.033 15213 Z= 0.126 Angle : 0.570 7.145 20721 Z= 0.296 Chirality : 0.045 0.293 2383 Planarity : 0.004 0.055 2616 Dihedral : 15.308 89.838 5608 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.71 % Favored : 93.97 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1843 helix: 1.94 (0.17), residues: 965 sheet: 1.32 (0.56), residues: 81 loop : -1.26 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 846 TYR 0.013 0.001 TYR A 800 PHE 0.014 0.001 PHE A 411 TRP 0.023 0.001 TRP A1085 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (15209) covalent geometry : angle 0.56869 / 0.30 (20719) hydrogen bonds : bond 0.15042 / 10.65 ( 759) hydrogen bonds : angle 4.56326 / 3.13 ( 2173) metal coordination : bond 0.00525 / 0.27 ( 4) metal coordination : angle 3.37321 / 1.78 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.468 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.1193 time to fit residues: 42.0366 Evaluate side-chains 202 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 663 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN A1333 ASN B 194 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109269 restraints weight = 45250.599| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 6.31 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15213 Z= 0.214 Angle : 0.719 16.213 20721 Z= 0.342 Chirality : 0.057 1.069 2383 Planarity : 0.004 0.041 2616 Dihedral : 7.528 134.007 2116 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.90 % Favored : 92.77 % Rotamer: Outliers : 1.23 % Allowed : 8.06 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1843 helix: 1.78 (0.17), residues: 996 sheet: 1.17 (0.55), residues: 83 loop : -1.35 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 846 TYR 0.015 0.002 TYR B 142 PHE 0.021 0.002 PHE A 411 TRP 0.013 0.001 TRP A 191 HIS 0.008 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (15209) covalent geometry : angle 0.71666 / 0.34 (20719) hydrogen bonds : bond 0.05827 / 3.87 ( 759) hydrogen bonds : angle 3.85626 / 2.65 ( 2173) metal coordination : bond 0.00957 / 0.49 ( 4) metal coordination : angle 6.42384 / 3.40 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1083 SER cc_start: 0.8608 (t) cc_final: 0.8323 (m) REVERT: A 1112 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 230 ASP cc_start: 0.8298 (m-30) cc_final: 0.7317 (m-30) REVERT: B 304 PRO cc_start: 0.7390 (Cg_exo) cc_final: 0.7162 (Cg_endo) outliers start: 20 outliers final: 16 residues processed: 216 average time/residue: 0.1204 time to fit residues: 38.5222 Evaluate side-chains 213 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 18 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109470 restraints weight = 31886.497| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.26 r_work: 0.2826 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15213 Z= 0.143 Angle : 0.597 11.402 20721 Z= 0.295 Chirality : 0.047 0.608 2383 Planarity : 0.004 0.038 2616 Dihedral : 7.603 144.675 2116 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.92 % Favored : 93.75 % Rotamer: Outliers : 1.05 % Allowed : 10.03 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1843 helix: 1.96 (0.17), residues: 990 sheet: 1.13 (0.57), residues: 83 loop : -1.36 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.012 0.001 TYR A 153 PHE 0.016 0.001 PHE A 411 TRP 0.009 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (15209) covalent geometry : angle 0.59490 / 0.29 (20719) hydrogen bonds : bond 0.04784 / 3.18 ( 759) hydrogen bonds : angle 3.68816 / 2.53 ( 2173) metal coordination : bond 0.00826 / 0.42 ( 4) metal coordination : angle 5.50827 / 2.90 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1044 LEU cc_start: 0.8973 (tt) cc_final: 0.8580 (mp) REVERT: A 1095 ILE cc_start: 0.8003 (mp) cc_final: 0.7784 (mm) REVERT: B 107 LEU cc_start: 0.9115 (tt) cc_final: 0.8728 (pp) REVERT: B 230 ASP cc_start: 0.8310 (m-30) cc_final: 0.7112 (m-30) REVERT: B 304 PRO cc_start: 0.7309 (Cg_exo) cc_final: 0.7031 (Cg_endo) outliers start: 17 outliers final: 14 residues processed: 214 average time/residue: 0.1178 time to fit residues: 37.0412 Evaluate side-chains 209 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108744 restraints weight = 26136.669| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.15 r_work: 0.2901 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15213 Z= 0.146 Angle : 0.577 8.605 20721 Z= 0.287 Chirality : 0.045 0.390 2383 Planarity : 0.004 0.038 2616 Dihedral : 7.621 143.205 2116 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.30 % Favored : 93.37 % Rotamer: Outliers : 1.97 % Allowed : 10.40 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1843 helix: 1.93 (0.17), residues: 997 sheet: 1.11 (0.58), residues: 83 loop : -1.35 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.012 0.001 TYR A 153 PHE 0.016 0.001 PHE A 411 TRP 0.010 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15209) covalent geometry : angle 0.57477 / 0.29 (20719) hydrogen bonds : bond 0.04672 / 3.09 ( 759) hydrogen bonds : angle 3.62842 / 2.50 ( 2173) metal coordination : bond 0.00898 / 0.45 ( 4) metal coordination : angle 5.64622 / 2.98 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1044 LEU cc_start: 0.8855 (tt) cc_final: 0.8523 (mp) REVERT: A 1379 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4757 (tt) REVERT: B 107 LEU cc_start: 0.9074 (tt) cc_final: 0.8702 (pp) REVERT: B 230 ASP cc_start: 0.8225 (m-30) cc_final: 0.6945 (m-30) REVERT: B 304 PRO cc_start: 0.7337 (Cg_exo) cc_final: 0.7051 (Cg_endo) outliers start: 32 outliers final: 21 residues processed: 220 average time/residue: 0.1313 time to fit residues: 42.6854 Evaluate side-chains 216 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109317 restraints weight = 25280.426| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.73 r_work: 0.2928 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15213 Z= 0.136 Angle : 0.569 9.713 20721 Z= 0.285 Chirality : 0.044 0.357 2383 Planarity : 0.004 0.037 2616 Dihedral : 7.602 142.896 2116 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.20 % Favored : 93.48 % Rotamer: Outliers : 2.03 % Allowed : 11.38 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1843 helix: 1.96 (0.17), residues: 997 sheet: 1.06 (0.58), residues: 83 loop : -1.35 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.012 0.001 TYR A 153 PHE 0.016 0.001 PHE A 793 TRP 0.010 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15209) covalent geometry : angle 0.56672 / 0.28 (20719) hydrogen bonds : bond 0.04465 / 2.94 ( 759) hydrogen bonds : angle 3.58570 / 2.46 ( 2173) metal coordination : bond 0.00910 / 0.46 ( 4) metal coordination : angle 5.66272 / 2.98 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: A 1044 LEU cc_start: 0.8884 (tt) cc_final: 0.8572 (mp) REVERT: A 1379 LEU cc_start: 0.5033 (OUTLIER) cc_final: 0.4706 (tt) REVERT: B 107 LEU cc_start: 0.9077 (tt) cc_final: 0.8698 (pp) REVERT: B 230 ASP cc_start: 0.8250 (m-30) cc_final: 0.6960 (m-30) REVERT: B 304 PRO cc_start: 0.7400 (Cg_exo) cc_final: 0.7126 (Cg_endo) outliers start: 33 outliers final: 23 residues processed: 220 average time/residue: 0.1316 time to fit residues: 42.7692 Evaluate side-chains 219 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106671 restraints weight = 26053.800| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.05 r_work: 0.2871 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15213 Z= 0.203 Angle : 0.628 12.936 20721 Z= 0.313 Chirality : 0.046 0.369 2383 Planarity : 0.004 0.040 2616 Dihedral : 7.735 143.069 2116 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.58 % Favored : 93.10 % Rotamer: Outliers : 1.91 % Allowed : 12.37 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1843 helix: 1.81 (0.17), residues: 997 sheet: 1.04 (0.58), residues: 83 loop : -1.43 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.015 0.002 TYR A 153 PHE 0.020 0.002 PHE A 411 TRP 0.011 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.20 (15209) covalent geometry : angle 0.62462 / 0.31 (20719) hydrogen bonds : bond 0.05421 / 3.56 ( 759) hydrogen bonds : angle 3.74581 / 2.57 ( 2173) metal coordination : bond 0.01103 / 0.56 ( 4) metal coordination : angle 6.91451 / 3.66 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: A 800 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7489 (p90) REVERT: A 1269 HIS cc_start: 0.7312 (m90) cc_final: 0.6526 (t70) REVERT: A 1379 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4748 (tt) REVERT: A 1382 ASP cc_start: 0.7928 (t0) cc_final: 0.7581 (t0) REVERT: B 107 LEU cc_start: 0.9055 (tt) cc_final: 0.8672 (pp) REVERT: E 124 MET cc_start: 0.7515 (mtt) cc_final: 0.7283 (mtt) outliers start: 31 outliers final: 26 residues processed: 218 average time/residue: 0.1183 time to fit residues: 38.1533 Evaluate side-chains 217 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110635 restraints weight = 39668.534| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 5.49 r_work: 0.2764 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15213 Z= 0.129 Angle : 0.574 10.008 20721 Z= 0.287 Chirality : 0.043 0.343 2383 Planarity : 0.004 0.038 2616 Dihedral : 7.641 142.724 2116 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.20 % Favored : 93.48 % Rotamer: Outliers : 2.09 % Allowed : 12.68 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1843 helix: 1.96 (0.17), residues: 991 sheet: 1.19 (0.61), residues: 73 loop : -1.38 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.012 0.001 TYR A 153 PHE 0.016 0.001 PHE A 793 TRP 0.009 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15209) covalent geometry : angle 0.57131 / 0.29 (20719) hydrogen bonds : bond 0.04490 / 2.96 ( 759) hydrogen bonds : angle 3.61963 / 2.48 ( 2173) metal coordination : bond 0.00918 / 0.46 ( 4) metal coordination : angle 5.74345 / 3.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: A 1044 LEU cc_start: 0.8961 (tt) cc_final: 0.8651 (mp) REVERT: A 1269 HIS cc_start: 0.7406 (m90) cc_final: 0.6566 (t70) REVERT: A 1379 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.5036 (tt) REVERT: A 1382 ASP cc_start: 0.8077 (t0) cc_final: 0.7722 (t0) REVERT: B 107 LEU cc_start: 0.9049 (tt) cc_final: 0.8669 (pp) outliers start: 34 outliers final: 22 residues processed: 222 average time/residue: 0.1187 time to fit residues: 38.9865 Evaluate side-chains 218 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 14 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 144 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111006 restraints weight = 44042.184| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 6.00 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15213 Z= 0.123 Angle : 0.567 9.837 20721 Z= 0.285 Chirality : 0.042 0.337 2383 Planarity : 0.004 0.036 2616 Dihedral : 7.540 142.312 2116 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.20 % Favored : 93.48 % Rotamer: Outliers : 1.78 % Allowed : 13.23 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1843 helix: 2.01 (0.17), residues: 992 sheet: 1.22 (0.61), residues: 73 loop : -1.35 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 110 TYR 0.014 0.001 TYR B 122 PHE 0.014 0.001 PHE A 411 TRP 0.009 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15209) covalent geometry : angle 0.56473 / 0.28 (20719) hydrogen bonds : bond 0.04203 / 2.78 ( 759) hydrogen bonds : angle 3.57554 / 2.45 ( 2173) metal coordination : bond 0.00959 / 0.48 ( 4) metal coordination : angle 5.48021 / 2.88 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 991 THR cc_start: 0.8563 (m) cc_final: 0.8318 (m) REVERT: A 1044 LEU cc_start: 0.8784 (tt) cc_final: 0.8528 (mp) REVERT: A 1269 HIS cc_start: 0.7440 (m90) cc_final: 0.6653 (t70) REVERT: A 1379 LEU cc_start: 0.5248 (OUTLIER) cc_final: 0.4944 (tt) REVERT: A 1382 ASP cc_start: 0.7777 (t0) cc_final: 0.7431 (t0) REVERT: B 107 LEU cc_start: 0.8862 (tt) cc_final: 0.8582 (pp) outliers start: 29 outliers final: 25 residues processed: 218 average time/residue: 0.1106 time to fit residues: 35.6224 Evaluate side-chains 221 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 52 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 159 optimal weight: 0.0770 chunk 136 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111540 restraints weight = 35051.778| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.60 r_work: 0.2828 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15213 Z= 0.112 Angle : 0.554 9.609 20721 Z= 0.279 Chirality : 0.042 0.330 2383 Planarity : 0.004 0.036 2616 Dihedral : 7.452 142.183 2116 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.20 % Favored : 93.53 % Rotamer: Outliers : 1.72 % Allowed : 13.23 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1843 helix: 2.08 (0.17), residues: 989 sheet: 1.18 (0.61), residues: 73 loop : -1.32 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.013 0.001 TYR A1088 PHE 0.019 0.001 PHE A 793 TRP 0.009 0.001 TRP A1019 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15209) covalent geometry : angle 0.55211 / 0.28 (20719) hydrogen bonds : bond 0.03920 / 2.60 ( 759) hydrogen bonds : angle 3.53108 / 2.42 ( 2173) metal coordination : bond 0.00936 / 0.47 ( 4) metal coordination : angle 5.06510 / 2.67 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: A 1269 HIS cc_start: 0.7422 (m90) cc_final: 0.6641 (t70) REVERT: A 1379 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4932 (tt) REVERT: A 1382 ASP cc_start: 0.7895 (t0) cc_final: 0.7502 (t0) REVERT: B 107 LEU cc_start: 0.9056 (tt) cc_final: 0.8670 (pp) outliers start: 28 outliers final: 22 residues processed: 219 average time/residue: 0.1058 time to fit residues: 33.9909 Evaluate side-chains 220 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 176 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108736 restraints weight = 33760.756| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.35 r_work: 0.2814 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 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 : 0.003 0.028 15213 Z= 0.141 Angle : 0.581 13.260 20721 Z= 0.290 Chirality : 0.043 0.343 2383 Planarity : 0.004 0.037 2616 Dihedral : 7.454 142.033 2116 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.20 % Favored : 93.53 % Rotamer: Outliers : 1.72 % Allowed : 13.29 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1843 helix: 1.99 (0.17), residues: 997 sheet: 1.28 (0.62), residues: 73 loop : -1.32 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 990 TYR 0.013 0.001 TYR B 122 PHE 0.016 0.001 PHE A 411 TRP 0.009 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15209) covalent geometry : angle 0.57801 / 0.29 (20719) hydrogen bonds : bond 0.04432 / 2.93 ( 759) hydrogen bonds : angle 3.58997 / 2.47 ( 2173) metal coordination : bond 0.01020 / 0.51 ( 4) metal coordination : angle 5.78410 / 3.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: A 991 THR cc_start: 0.8853 (m) cc_final: 0.8577 (m) REVERT: A 1269 HIS cc_start: 0.7472 (m90) cc_final: 0.6668 (t70) REVERT: A 1379 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.4912 (tt) REVERT: A 1382 ASP cc_start: 0.7956 (t0) cc_final: 0.7567 (t0) REVERT: B 122 TYR cc_start: 0.8722 (m-80) cc_final: 0.8479 (m-80) outliers start: 28 outliers final: 25 residues processed: 217 average time/residue: 0.1077 time to fit residues: 34.6218 Evaluate side-chains 219 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 169 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107654 restraints weight = 45176.136| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 6.53 r_work: 0.2686 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15213 Z= 0.186 Angle : 0.624 13.285 20721 Z= 0.312 Chirality : 0.045 0.356 2383 Planarity : 0.004 0.040 2616 Dihedral : 7.601 142.513 2116 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.52 % Favored : 93.21 % Rotamer: Outliers : 1.91 % Allowed : 13.17 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1843 helix: 1.90 (0.17), residues: 989 sheet: 1.19 (0.62), residues: 73 loop : -1.44 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 990 TYR 0.015 0.002 TYR A 153 PHE 0.021 0.002 PHE A 793 TRP 0.010 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (15209) covalent geometry : angle 0.62073 / 0.31 (20719) hydrogen bonds : bond 0.05313 / 3.50 ( 759) hydrogen bonds : angle 3.74087 / 2.58 ( 2173) metal coordination : bond 0.01108 / 0.56 ( 4) metal coordination : angle 6.74821 / 3.56 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.98 seconds wall clock time: 62 minutes 45.00 seconds (3765.00 seconds total)