Starting phenix.real_space_refine on Sat Aug 23 22:40:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsm_36623/08_2025/8jsm_36623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsm_36623/08_2025/8jsm_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2025/8jsm_36623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2025/8jsm_36623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2025/8jsm_36623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsm_36623/08_2025/8jsm_36623.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: 3.23, per 1000 atoms: 0.22 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: 1.18 Conformation dependent library (CDL) restraints added in 545.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 2.32 Time building geometry restraints manager: 1.55 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: 20184 1.43 - 2.86: 404 2.86 - 4.29: 93 4.29 - 5.72: 29 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 - 35.69: 8986 35.69 - 71.39: 200 71.39 - 107.08: 15 107.08 - 142.77: 0 142.77 - 178.47: 1 Dihedral angle restraints: 9202 sinusoidal: 3739 harmonic: 5463 Sorted by residual: dihedral pdb=" O4' C G 7 " pdb=" C1' C G 7 " pdb=" N1 C G 7 " pdb=" C2 C G 7 " ideal model delta sinusoidal sigma weight residual -128.00 50.47 -178.47 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA SER A 431 " pdb=" C SER A 431 " pdb=" N ASP A 432 " pdb=" CA ASP A 432 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLN E 99 " pdb=" C GLN E 99 " pdb=" N GLN E 100 " pdb=" CA GLN E 100 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 9199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1501 0.030 - 0.059: 599 0.059 - 0.089: 179 0.089 - 0.119: 89 0.119 - 0.148: 15 Chirality restraints: 2383 Sorted by residual: chirality pdb=" CA GLN B 99 " pdb=" N GLN B 99 " pdb=" C GLN B 99 " pdb=" CB GLN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA GLN E 99 " pdb=" N GLN E 99 " pdb=" C GLN E 99 " pdb=" CB GLN E 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ASP A1368 " pdb=" N ASP A1368 " pdb=" C ASP A1368 " pdb=" CB ASP A1368 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (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: 2.770 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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= 0.125 Angle : 0.546 7.145 20721 Z= 0.289 Chirality : 0.038 0.148 2383 Planarity : 0.004 0.055 2616 Dihedral : 15.378 178.467 5656 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 aren 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 covalent geometry : bond 0.00260 (15209) covalent geometry : angle 0.54483 (20719) hydrogen bonds : bond 0.15042 ( 759) hydrogen bonds : angle 4.56326 ( 2173) metal coordination : bond 0.00525 ( 4) metal coordination : angle 3.37321 ( 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 : 0.365 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.1063 time to fit residues: 37.0887 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 : 0.526 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108218 restraints weight = 45180.280| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 6.58 r_work: 0.2695 rms_B_bonded: 6.20 restraints_weight: 2.0000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15213 Z= 0.208 Angle : 0.616 8.823 20721 Z= 0.316 Chirality : 0.043 0.143 2383 Planarity : 0.004 0.040 2616 Dihedral : 9.173 177.621 2164 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.90 % Favored : 92.77 % Rotamer: Outliers : 1.23 % Allowed : 8.18 % Favored : 90.58 % 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 aren not related in a simple way. whole: 0.78 (0.20), residues: 1843 helix: 1.79 (0.17), residues: 996 sheet: 1.17 (0.55), residues: 83 loop : -1.36 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 846 TYR 0.015 0.002 TYR B 142 PHE 0.021 0.002 PHE A 411 TRP 0.014 0.002 TRP A1085 HIS 0.008 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00506 (15209) covalent geometry : angle 0.61316 (20719) hydrogen bonds : bond 0.05751 ( 759) hydrogen bonds : angle 3.85875 ( 2173) metal coordination : bond 0.00944 ( 4) metal coordination : angle 6.41741 ( 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 : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8422 (mtt180) REVERT: A 1083 SER cc_start: 0.9109 (t) cc_final: 0.8768 (m) REVERT: A 1112 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8724 (mp) REVERT: B 230 ASP cc_start: 0.8404 (m-30) cc_final: 0.7375 (m-30) REVERT: B 304 PRO cc_start: 0.7292 (Cg_exo) cc_final: 0.7003 (Cg_endo) outliers start: 20 outliers final: 16 residues processed: 216 average time/residue: 0.1160 time to fit residues: 36.4397 Evaluate side-chains 212 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 0.0670 chunk 59 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 101 optimal weight: 0.0470 chunk 23 optimal weight: 0.6980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3697 r_free = 0.3697 target = 0.148553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110176 restraints weight = 31859.057| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.09 r_work: 0.2858 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15213 Z= 0.112 Angle : 0.534 8.956 20721 Z= 0.276 Chirality : 0.039 0.163 2383 Planarity : 0.004 0.037 2616 Dihedral : 9.066 179.387 2164 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.82 % Favored : 93.86 % Rotamer: Outliers : 0.86 % Allowed : 10.22 % 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 aren not related in a simple way. whole: 1.02 (0.21), residues: 1843 helix: 2.07 (0.17), residues: 987 sheet: 1.15 (0.57), residues: 83 loop : -1.30 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 846 TYR 0.010 0.001 TYR B 142 PHE 0.014 0.001 PHE A 793 TRP 0.009 0.001 TRP A1085 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00237 (15209) covalent geometry : angle 0.53204 (20719) hydrogen bonds : bond 0.04263 ( 759) hydrogen bonds : angle 3.64987 ( 2173) metal coordination : bond 0.00670 ( 4) metal coordination : angle 4.63284 ( 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 217 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 GLU cc_start: 0.8649 (mp0) cc_final: 0.8437 (mp0) REVERT: A 846 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8096 (mtt180) REVERT: A 991 THR cc_start: 0.8845 (m) cc_final: 0.8571 (m) REVERT: A 1083 SER cc_start: 0.8896 (t) cc_final: 0.8526 (m) REVERT: A 1095 ILE cc_start: 0.7912 (mp) cc_final: 0.7683 (mm) REVERT: B 107 LEU cc_start: 0.9064 (tt) cc_final: 0.8692 (pp) REVERT: B 230 ASP cc_start: 0.8184 (m-30) cc_final: 0.6922 (m-30) REVERT: B 304 PRO cc_start: 0.7274 (Cg_exo) cc_final: 0.6993 (Cg_endo) outliers start: 14 outliers final: 11 residues processed: 213 average time/residue: 0.1157 time to fit residues: 35.9718 Evaluate side-chains 205 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1094 ASN Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain C residue 131 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: 3.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.0070 chunk 174 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN B 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109865 restraints weight = 26127.329| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.90 r_work: 0.2923 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1197 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= 0.129 Angle : 0.527 7.186 20721 Z= 0.272 Chirality : 0.039 0.149 2383 Planarity : 0.004 0.037 2616 Dihedral : 9.038 179.955 2164 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.14 % Favored : 93.53 % Rotamer: Outliers : 1.60 % Allowed : 10.77 % 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 aren not related in a simple way. whole: 1.03 (0.21), residues: 1843 helix: 2.07 (0.17), residues: 990 sheet: 1.10 (0.57), residues: 83 loop : -1.30 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 846 TYR 0.012 0.001 TYR B 142 PHE 0.015 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 covalent geometry : bond 0.00299 (15209) covalent geometry : angle 0.52462 (20719) hydrogen bonds : bond 0.04360 ( 759) hydrogen bonds : angle 3.59502 ( 2173) metal coordination : bond 0.00808 ( 4) metal coordination : angle 5.11697 ( 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 225 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 GLU cc_start: 0.8549 (mp0) cc_final: 0.8332 (mp0) REVERT: A 846 ARG cc_start: 0.8391 (mtt-85) cc_final: 0.8125 (mtt180) REVERT: A 991 THR cc_start: 0.8845 (m) cc_final: 0.8587 (m) REVERT: A 1083 SER cc_start: 0.8900 (t) cc_final: 0.8549 (m) REVERT: A 1379 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4690 (tt) REVERT: B 107 LEU cc_start: 0.9091 (tt) cc_final: 0.8698 (pp) REVERT: B 230 ASP cc_start: 0.8212 (m-30) cc_final: 0.6932 (m-30) REVERT: B 304 PRO cc_start: 0.7319 (Cg_exo) cc_final: 0.7051 (Cg_endo) outliers start: 26 outliers final: 16 residues processed: 216 average time/residue: 0.1126 time to fit residues: 35.4890 Evaluate side-chains 212 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 ASN 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 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: 0.9990 chunk 154 optimal weight: 0.0970 chunk 161 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3698 r_free = 0.3698 target = 0.148735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111324 restraints weight = 25281.204| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.07 r_work: 0.2939 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15213 Z= 0.109 Angle : 0.516 10.063 20721 Z= 0.265 Chirality : 0.039 0.170 2383 Planarity : 0.004 0.037 2616 Dihedral : 8.949 178.936 2164 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.92 % Favored : 93.75 % Rotamer: Outliers : 1.60 % Allowed : 11.63 % Favored : 86.77 % 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 aren not related in a simple way. whole: 1.09 (0.21), residues: 1843 helix: 2.13 (0.17), residues: 989 sheet: 1.04 (0.57), residues: 83 loop : -1.27 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 846 TYR 0.010 0.001 TYR B 142 PHE 0.017 0.001 PHE A 793 TRP 0.009 0.001 TRP A 191 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00239 (15209) covalent geometry : angle 0.51355 (20719) hydrogen bonds : bond 0.03879 ( 759) hydrogen bonds : angle 3.50174 ( 2173) metal coordination : bond 0.00765 ( 4) metal coordination : angle 4.68703 ( 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 227 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 GLU cc_start: 0.8543 (mp0) cc_final: 0.8331 (mp0) REVERT: A 846 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.8097 (mtt180) REVERT: A 991 THR cc_start: 0.8800 (m) cc_final: 0.8536 (m) REVERT: A 1083 SER cc_start: 0.8878 (t) cc_final: 0.8522 (m) REVERT: A 1379 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4723 (tt) REVERT: B 107 LEU cc_start: 0.9073 (tt) cc_final: 0.8699 (pp) REVERT: B 230 ASP cc_start: 0.8196 (m-30) cc_final: 0.6871 (m-30) REVERT: B 304 PRO cc_start: 0.7321 (Cg_exo) cc_final: 0.7053 (Cg_endo) REVERT: E 124 MET cc_start: 0.7405 (mtt) cc_final: 0.7191 (mtt) outliers start: 26 outliers final: 15 residues processed: 221 average time/residue: 0.1167 time to fit residues: 37.7314 Evaluate side-chains 212 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 B 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104706 restraints weight = 26146.067| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.06 r_work: 0.2849 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15213 Z= 0.244 Angle : 0.631 11.907 20721 Z= 0.322 Chirality : 0.043 0.161 2383 Planarity : 0.004 0.045 2616 Dihedral : 9.229 175.479 2164 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.01 % Favored : 92.66 % Rotamer: Outliers : 1.97 % Allowed : 12.18 % Favored : 85.85 % 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 aren not related in a simple way. whole: 0.70 (0.21), residues: 1843 helix: 1.76 (0.17), residues: 998 sheet: 0.98 (0.57), residues: 83 loop : -1.44 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.016 0.002 TYR A 153 PHE 0.022 0.002 PHE A 411 TRP 0.011 0.002 TRP A 191 HIS 0.007 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00603 (15209) covalent geometry : angle 0.62652 (20719) hydrogen bonds : bond 0.05905 ( 759) hydrogen bonds : angle 3.82999 ( 2173) metal coordination : bond 0.01113 ( 4) metal coordination : angle 7.42583 ( 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 225 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: A 846 ARG cc_start: 0.8524 (mtt-85) cc_final: 0.8238 (mtt180) REVERT: A 1095 ILE cc_start: 0.7889 (mp) cc_final: 0.7684 (mm) REVERT: A 1269 HIS cc_start: 0.7353 (m90) cc_final: 0.6531 (t70) REVERT: A 1379 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4833 (tt) REVERT: A 1380 ILE cc_start: 0.8172 (mm) cc_final: 0.7909 (mm) REVERT: A 1382 ASP cc_start: 0.7967 (t0) cc_final: 0.7589 (t0) REVERT: B 107 LEU cc_start: 0.9053 (tt) cc_final: 0.8676 (pp) REVERT: E 124 MET cc_start: 0.7513 (mtt) cc_final: 0.7312 (mtt) outliers start: 32 outliers final: 25 residues processed: 217 average time/residue: 0.1042 time to fit residues: 33.3638 Evaluate side-chains 214 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 429 VAL Chi-restraints excluded: chain A residue 474 ILE 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 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 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: 0.7980 chunk 11 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN B 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109937 restraints weight = 39720.113| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 5.87 r_work: 0.2775 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15213 Z= 0.108 Angle : 0.535 9.890 20721 Z= 0.273 Chirality : 0.039 0.165 2383 Planarity : 0.004 0.037 2616 Dihedral : 9.107 179.642 2164 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.92 % Favored : 93.75 % Rotamer: Outliers : 1.66 % Allowed : 12.68 % Favored : 85.66 % 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 aren not related in a simple way. whole: 0.96 (0.21), residues: 1843 helix: 2.04 (0.17), residues: 991 sheet: 1.19 (0.61), residues: 73 loop : -1.35 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.015 0.001 TYR A1088 PHE 0.017 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 covalent geometry : bond 0.00229 (15209) covalent geometry : angle 0.53226 (20719) hydrogen bonds : bond 0.04074 ( 759) hydrogen bonds : angle 3.58653 ( 2173) metal coordination : bond 0.00846 ( 4) metal coordination : angle 5.14465 ( 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 221 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 846 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8312 (mtt180) REVERT: A 991 THR cc_start: 0.8920 (m) cc_final: 0.8697 (m) REVERT: A 1044 LEU cc_start: 0.8990 (tt) cc_final: 0.8674 (mp) REVERT: A 1379 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.5002 (tt) REVERT: A 1382 ASP cc_start: 0.8070 (t0) cc_final: 0.7718 (t0) REVERT: B 107 LEU cc_start: 0.9061 (tt) cc_final: 0.8683 (pp) REVERT: B 204 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7969 (m-30) outliers start: 27 outliers final: 18 residues processed: 215 average time/residue: 0.1100 time to fit residues: 34.6247 Evaluate side-chains 211 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER 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 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 204 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 14 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 74 optimal weight: 0.0010 chunk 42 optimal weight: 0.3980 chunk 144 optimal weight: 0.0570 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 151 optimal weight: 0.0270 overall best weight: 0.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3705 r_free = 0.3705 target = 0.149382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112337 restraints weight = 44107.310| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 6.40 r_work: 0.2772 rms_B_bonded: 6.02 restraints_weight: 2.0000 r_work (final): 0.2772 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1489 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= 0.102 Angle : 0.529 13.158 20721 Z= 0.268 Chirality : 0.038 0.163 2383 Planarity : 0.004 0.036 2616 Dihedral : 8.872 178.189 2164 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.03 % Favored : 93.64 % Rotamer: Outliers : 1.42 % Allowed : 12.86 % 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 aren not related in a simple way. whole: 1.12 (0.21), residues: 1843 helix: 2.21 (0.17), residues: 983 sheet: 1.13 (0.61), residues: 73 loop : -1.28 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.014 0.001 TYR B 122 PHE 0.010 0.001 PHE A 369 TRP 0.010 0.001 TRP A1085 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00209 (15209) covalent geometry : angle 0.52684 (20719) hydrogen bonds : bond 0.03476 ( 759) hydrogen bonds : angle 3.46311 ( 2173) metal coordination : bond 0.00869 ( 4) metal coordination : angle 4.40373 ( 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 220 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 ARG cc_start: 0.8633 (mtt-85) cc_final: 0.8321 (mtt180) REVERT: A 1379 LEU cc_start: 0.5306 (OUTLIER) cc_final: 0.4968 (tt) REVERT: B 107 LEU cc_start: 0.9042 (tt) cc_final: 0.8669 (pp) REVERT: B 122 TYR cc_start: 0.8758 (m-80) cc_final: 0.8509 (m-80) outliers start: 23 outliers final: 15 residues processed: 214 average time/residue: 0.1115 time to fit residues: 35.0791 Evaluate side-chains 210 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 474 ILE 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 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain B residue 198 GLU 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: 1.9990 chunk 22 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 159 optimal weight: 0.2980 chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN B 100 GLN B 213 ASN E 99 GLN E 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109978 restraints weight = 35183.880| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.98 r_work: 0.2818 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15213 Z= 0.123 Angle : 0.535 9.390 20721 Z= 0.274 Chirality : 0.039 0.158 2383 Planarity : 0.004 0.037 2616 Dihedral : 8.859 179.515 2164 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.25 % Favored : 93.42 % Rotamer: Outliers : 1.48 % Allowed : 13.05 % Favored : 85.48 % 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 aren not related in a simple way. whole: 1.08 (0.21), residues: 1843 helix: 2.09 (0.17), residues: 997 sheet: 1.14 (0.62), residues: 73 loop : -1.25 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.012 0.001 TYR B 142 PHE 0.017 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 covalent geometry : bond 0.00283 (15209) covalent geometry : angle 0.53222 (20719) hydrogen bonds : bond 0.04002 ( 759) hydrogen bonds : angle 3.50555 ( 2173) metal coordination : bond 0.00951 ( 4) metal coordination : angle 5.15478 ( 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 217 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8958 (tpp) cc_final: 0.8707 (ttm) REVERT: A 522 GLU cc_start: 0.8703 (mp0) cc_final: 0.8476 (mp0) REVERT: A 846 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.8194 (mtt180) REVERT: A 1269 HIS cc_start: 0.7453 (m90) cc_final: 0.6599 (t70) REVERT: A 1379 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4928 (tt) REVERT: B 122 TYR cc_start: 0.8755 (m-80) cc_final: 0.8474 (m-80) outliers start: 24 outliers final: 20 residues processed: 211 average time/residue: 0.1159 time to fit residues: 35.4407 Evaluate side-chains 213 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 474 ILE 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 728 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 747 THR 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 1094 ASN Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 198 GLU 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 176 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN E 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109639 restraints weight = 33882.498| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 4.61 r_work: 0.2827 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1556 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= 0.126 Angle : 0.539 9.330 20721 Z= 0.276 Chirality : 0.039 0.159 2383 Planarity : 0.004 0.037 2616 Dihedral : 8.860 179.873 2164 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 1.42 % Allowed : 13.11 % Favored : 85.48 % 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 aren not related in a simple way. whole: 1.06 (0.21), residues: 1843 helix: 2.07 (0.17), residues: 997 sheet: 1.16 (0.62), residues: 73 loop : -1.25 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.011 0.001 TYR B 122 PHE 0.015 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 covalent geometry : bond 0.00293 (15209) covalent geometry : angle 0.53679 (20719) hydrogen bonds : bond 0.04086 ( 759) hydrogen bonds : angle 3.51010 ( 2173) metal coordination : bond 0.00927 ( 4) metal coordination : angle 5.19912 ( 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 217 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8946 (tpp) cc_final: 0.8735 (ttm) REVERT: A 846 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.8307 (mtt180) REVERT: A 1269 HIS cc_start: 0.7425 (m90) cc_final: 0.6630 (t70) REVERT: A 1379 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4869 (tt) REVERT: B 122 TYR cc_start: 0.8722 (m-80) cc_final: 0.8451 (m-80) outliers start: 23 outliers final: 20 residues processed: 212 average time/residue: 0.1113 time to fit residues: 34.6047 Evaluate side-chains 213 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 198 GLU 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: 0.9980 chunk 169 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 170 optimal weight: 0.0020 chunk 177 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 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 = 0.147190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110803 restraints weight = 45503.149| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 6.09 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 15213 Z= 0.207 Angle : 0.784 59.184 20721 Z= 0.448 Chirality : 0.049 1.369 2383 Planarity : 0.004 0.037 2616 Dihedral : 8.868 179.875 2164 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.20 % Favored : 93.53 % Rotamer: Outliers : 1.35 % Allowed : 13.29 % Favored : 85.35 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: 1.05 (0.21), residues: 1843 helix: 2.06 (0.17), residues: 997 sheet: 1.16 (0.62), residues: 73 loop : -1.26 (0.23), residues: 773 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 0.015 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 covalent geometry : bond 0.00457 (15209) covalent geometry : angle 0.78211 (20719) hydrogen bonds : bond 0.04163 ( 759) hydrogen bonds : angle 3.51755 ( 2173) metal coordination : bond 0.00965 ( 4) metal coordination : angle 5.20577 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.17 seconds wall clock time: 60 minutes 21.09 seconds (3621.09 seconds total)