Starting phenix.real_space_refine on Thu May 1 04:04:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7x_27237/05_2025/8d7x_27237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7x_27237/05_2025/8d7x_27237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7x_27237/05_2025/8d7x_27237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7x_27237/05_2025/8d7x_27237.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7x_27237/05_2025/8d7x_27237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7x_27237/05_2025/8d7x_27237.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 6339 2.51 5 N 1782 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10108 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 7898 Classifications: {'peptide': 1135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 299} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1093} Chain breaks: 1 Unresolved non-hydrogen bonds: 1018 Unresolved non-hydrogen angles: 1299 Unresolved non-hydrogen dihedrals: 818 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 28, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 547 Chain: "B" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2209 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 182} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 330} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 521 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 355 Chain: "B" 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 9616 SG CYS B 323 52.983 27.187 19.376 1.00223.45 S ATOM 9632 SG CYS B 326 49.767 26.700 17.198 1.00251.90 S ATOM 9898 SG CYS B 391 52.987 24.203 17.765 1.00228.20 S ATOM 9914 SG CYS B 394 52.478 27.176 15.244 1.00225.14 S Time building chain proxies: 6.40, per 1000 atoms: 0.63 Number of scatterers: 10108 At special positions: 0 Unit cell: (96.6, 105.8, 148.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 1938 8.00 N 1782 7.00 C 6339 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: 2.28 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " Number of angles added : 6 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 29 sheets defined 11.6% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 1044 through 1062 removed outlier: 3.859A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1061 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1090 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 4.137A pdb=" N GLU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1126 removed outlier: 4.232A pdb=" N ALA A1126 " --> pdb=" O GLU A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1127 through 1138 removed outlier: 3.645A pdb=" N ARG A1138 " --> pdb=" O GLU A1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.028A pdb=" N LYS B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.847A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.634A pdb=" N GLU B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.541A pdb=" N LEU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.630A pdb=" N ARG B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.072A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 5.818A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 65 removed outlier: 6.454A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.797A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 196 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 201 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.797A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 190 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.707A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET A 282 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.622A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 365 Processing sheet with id=AB2, first strand: chain 'A' and resid 396 through 402 removed outlier: 6.747A pdb=" N ILE A 701 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A 401 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU A 699 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 702 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 690 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 682 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.629A pdb=" N THR A 424 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 459 through 461 removed outlier: 4.044A pdb=" N ILE A 469 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 477 " --> pdb=" O GLN A 470 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 476 " --> pdb=" O TRP A 490 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 500 through 503 removed outlier: 4.036A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 511 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN A 520 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN A 528 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N HIS A 522 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.876A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 590 through 594 removed outlier: 3.948A pdb=" N CYS A 604 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.698A pdb=" N VAL A 637 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 652 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.543A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.543A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS A 789 " --> pdb=" O GLN A 806 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN A 806 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU A 791 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 804 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A 793 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.215A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 850 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.215A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.157A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 913 through 917 Processing sheet with id=AC6, first strand: chain 'A' and resid 957 through 959 removed outlier: 6.649A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC8, first strand: chain 'B' and resid 65 through 66 removed outlier: 13.950A pdb=" N THR B 119 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N VAL B 80 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA B 121 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 123 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN B 183 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 167 " --> pdb=" O GLN B 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.738A pdb=" N GLN B 163 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU B 140 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLY B 161 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR B 142 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 159 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR B 144 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 157 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU B 146 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 155 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN B 148 " --> pdb=" O GLU B 153 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU B 153 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 330 through 333 removed outlier: 7.291A pdb=" N GLU B 330 " --> pdb=" O CYS B 323 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS B 323 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 332 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 320 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 322 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.823A pdb=" N LYS B 401 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR B 387 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N TYR B 384 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER B 375 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TRP B 386 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG B 373 " --> pdb=" O TRP B 386 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1026 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: 5.11 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3510 1.34 - 1.46: 2215 1.46 - 1.59: 4485 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 10280 Sorted by residual: bond pdb=" CA SER A 256 " pdb=" CB SER A 256 " ideal model delta sigma weight residual 1.534 1.480 0.054 1.77e-02 3.19e+03 9.30e+00 bond pdb=" N ASP A 795 " pdb=" CA ASP A 795 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.27e-02 6.20e+03 8.97e+00 bond pdb=" N PHE A 733 " pdb=" CA PHE A 733 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.18e-02 7.18e+03 6.92e+00 bond pdb=" N ILE A 794 " pdb=" CA ILE A 794 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.26e-02 6.30e+03 5.92e+00 bond pdb=" N SER A 256 " pdb=" CA SER A 256 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.32e-02 5.74e+03 5.24e+00 ... (remaining 10275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 13638 1.71 - 3.42: 358 3.42 - 5.13: 52 5.13 - 6.84: 9 6.84 - 8.55: 2 Bond angle restraints: 14059 Sorted by residual: angle pdb=" C THR A 257 " pdb=" CA THR A 257 " pdb=" CB THR A 257 " ideal model delta sigma weight residual 110.19 103.25 6.94 1.62e+00 3.81e-01 1.83e+01 angle pdb=" N ILE B 393 " pdb=" CA ILE B 393 " pdb=" C ILE B 393 " ideal model delta sigma weight residual 111.62 108.54 3.08 7.90e-01 1.60e+00 1.52e+01 angle pdb=" CA GLN A 731 " pdb=" C GLN A 731 " pdb=" O GLN A 731 " ideal model delta sigma weight residual 122.27 118.02 4.25 1.16e+00 7.43e-01 1.34e+01 angle pdb=" CA ASP A 795 " pdb=" C ASP A 795 " pdb=" O ASP A 795 " ideal model delta sigma weight residual 121.88 117.88 4.00 1.13e+00 7.83e-01 1.25e+01 angle pdb=" CA LEU A 367 " pdb=" C LEU A 367 " pdb=" O LEU A 367 " ideal model delta sigma weight residual 120.80 117.35 3.45 1.05e+00 9.07e-01 1.08e+01 ... (remaining 14054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 5613 16.71 - 33.42: 419 33.42 - 50.13: 89 50.13 - 66.85: 15 66.85 - 83.56: 11 Dihedral angle restraints: 6147 sinusoidal: 1851 harmonic: 4296 Sorted by residual: dihedral pdb=" CA LYS A 35 " pdb=" C LYS A 35 " pdb=" N ASN A 36 " pdb=" CA ASN A 36 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA CYS B 391 " pdb=" C CYS B 391 " pdb=" N LYS B 392 " pdb=" CA LYS B 392 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE A 876 " pdb=" C PHE A 876 " pdb=" N ASN A 877 " pdb=" CA ASN A 877 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1331 0.058 - 0.116: 295 0.116 - 0.174: 38 0.174 - 0.232: 2 0.232 - 0.289: 3 Chirality restraints: 1669 Sorted by residual: chirality pdb=" CA THR A 257 " pdb=" N THR A 257 " pdb=" C THR A 257 " pdb=" CB THR A 257 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ILE A 794 " pdb=" N ILE A 794 " pdb=" C ILE A 794 " pdb=" CB ILE A 794 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 220 " pdb=" CA ILE A 220 " pdb=" CG1 ILE A 220 " pdb=" CG2 ILE A 220 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1666 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 793 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C ILE A 793 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE A 793 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 794 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 876 " -0.019 2.00e-02 2.50e+03 1.66e-02 4.84e+00 pdb=" CG PHE A 876 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 876 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 876 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 876 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 876 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 876 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 92 " -0.031 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 93 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.027 5.00e-02 4.00e+02 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1373 2.76 - 3.29: 9183 3.29 - 3.83: 15404 3.83 - 4.36: 17379 4.36 - 4.90: 32384 Nonbonded interactions: 75723 Sorted by model distance: nonbonded pdb=" ND2 ASN A 36 " pdb=" OE2 GLU A1002 " model vdw 2.219 3.120 nonbonded pdb=" OD2 ASP A 744 " pdb=" OG SER A 746 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A 3 " pdb=" OE2 GLU A1045 " model vdw 2.220 3.040 nonbonded pdb=" O HIS B 233 " pdb=" ND2 ASN B 236 " model vdw 2.231 3.120 nonbonded pdb=" OD2 ASP A 824 " pdb=" NE1 TRP A 893 " model vdw 2.233 3.120 ... (remaining 75718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.006 0.054 10284 Z= 0.246 Angle : 0.708 17.270 14065 Z= 0.360 Chirality : 0.050 0.289 1669 Planarity : 0.004 0.048 1879 Dihedral : 13.448 83.557 3363 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.60 % Favored : 91.19 % Rotamer: Outliers : 0.60 % Allowed : 0.48 % Favored : 98.92 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.21), residues: 1476 helix: 0.50 (0.45), residues: 151 sheet: -1.34 (0.22), residues: 557 loop : -1.95 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.003 0.001 HIS A1140 PHE 0.038 0.002 PHE A 876 TYR 0.030 0.002 TYR B 282 ARG 0.007 0.000 ARG A 989 Details of bonding type rmsd hydrogen bonds : bond 0.14278 ( 359) hydrogen bonds : angle 6.82474 ( 1026) metal coordination : bond 0.01448 ( 4) metal coordination : angle 13.16700 ( 6) covalent geometry : bond 0.00562 (10280) covalent geometry : angle 0.65335 (14059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.043 Fit side-chains REVERT: A 896 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 251 GLU cc_start: 0.7503 (tp30) cc_final: 0.7114 (tp30) REVERT: B 273 LEU cc_start: 0.7865 (mm) cc_final: 0.7513 (mm) REVERT: B 313 ASP cc_start: 0.8129 (t70) cc_final: 0.7878 (t0) outliers start: 5 outliers final: 3 residues processed: 120 average time/residue: 0.2053 time to fit residues: 35.8861 Evaluate side-chains 100 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 798 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 30.0000 chunk 111 optimal weight: 0.0040 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 133 optimal weight: 0.0770 overall best weight: 1.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 778 HIS A 908 ASN A1070 HIS B 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.163416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125207 restraints weight = 14386.129| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.47 r_work: 0.3367 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10284 Z= 0.149 Angle : 0.620 18.232 14065 Z= 0.297 Chirality : 0.045 0.185 1669 Planarity : 0.004 0.047 1879 Dihedral : 4.579 50.632 1558 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 1.08 % Allowed : 6.48 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1476 helix: 0.51 (0.45), residues: 154 sheet: -1.28 (0.22), residues: 556 loop : -1.80 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.003 0.001 HIS A 778 PHE 0.018 0.001 PHE A 876 TYR 0.020 0.001 TYR B 282 ARG 0.003 0.000 ARG A 989 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 359) hydrogen bonds : angle 5.24976 ( 1026) metal coordination : bond 0.01656 ( 4) metal coordination : angle 13.34121 ( 6) covalent geometry : bond 0.00349 (10280) covalent geometry : angle 0.55540 (14059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.183 Fit side-chains REVERT: B 225 GLN cc_start: 0.7795 (mt0) cc_final: 0.7424 (mt0) REVERT: B 273 LEU cc_start: 0.8539 (mm) cc_final: 0.8180 (mm) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 0.2224 time to fit residues: 36.4417 Evaluate side-chains 98 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 120 optimal weight: 40.0000 chunk 112 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.161657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123648 restraints weight = 14550.802| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.85 r_work: 0.3355 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10284 Z= 0.200 Angle : 0.623 17.083 14065 Z= 0.301 Chirality : 0.046 0.179 1669 Planarity : 0.004 0.046 1879 Dihedral : 4.318 48.819 1554 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 2.16 % Allowed : 9.84 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1476 helix: 0.45 (0.45), residues: 155 sheet: -1.18 (0.22), residues: 545 loop : -1.85 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.003 0.001 HIS A 778 PHE 0.018 0.002 PHE A 876 TYR 0.021 0.002 TYR B 282 ARG 0.003 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 359) hydrogen bonds : angle 5.10344 ( 1026) metal coordination : bond 0.01586 ( 4) metal coordination : angle 12.09191 ( 6) covalent geometry : bond 0.00479 (10280) covalent geometry : angle 0.57142 (14059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.276 Fit side-chains REVERT: B 260 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7805 (tm-30) outliers start: 18 outliers final: 13 residues processed: 112 average time/residue: 0.2430 time to fit residues: 39.5037 Evaluate side-chains 104 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 134 optimal weight: 0.0470 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS B 198 GLN B 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125704 restraints weight = 14388.423| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.28 r_work: 0.3367 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10284 Z= 0.132 Angle : 0.571 15.670 14065 Z= 0.275 Chirality : 0.045 0.147 1669 Planarity : 0.004 0.046 1879 Dihedral : 4.040 40.435 1554 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 2.52 % Allowed : 11.40 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.22), residues: 1476 helix: 0.56 (0.45), residues: 154 sheet: -1.09 (0.22), residues: 545 loop : -1.78 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.002 0.001 HIS A 803 PHE 0.015 0.001 PHE A 829 TYR 0.019 0.001 TYR B 282 ARG 0.002 0.000 ARG A 989 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 359) hydrogen bonds : angle 4.76433 ( 1026) metal coordination : bond 0.01444 ( 4) metal coordination : angle 11.18233 ( 6) covalent geometry : bond 0.00312 (10280) covalent geometry : angle 0.52178 (14059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 876 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: B 198 GLN cc_start: 0.6398 (tp-100) cc_final: 0.6073 (tp40) REVERT: B 225 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: B 260 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7693 (tm-30) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 0.2085 time to fit residues: 36.5583 Evaluate side-chains 107 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.163251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125569 restraints weight = 14530.592| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.88 r_work: 0.3379 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10284 Z= 0.156 Angle : 0.587 15.903 14065 Z= 0.282 Chirality : 0.045 0.146 1669 Planarity : 0.004 0.046 1879 Dihedral : 3.976 30.022 1554 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 2.52 % Allowed : 12.73 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1476 helix: 0.49 (0.44), residues: 155 sheet: -1.12 (0.22), residues: 555 loop : -1.79 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.003 0.001 HIS A 803 PHE 0.015 0.001 PHE A 829 TYR 0.019 0.001 TYR B 282 ARG 0.002 0.000 ARG A 989 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 359) hydrogen bonds : angle 4.70660 ( 1026) metal coordination : bond 0.01485 ( 4) metal coordination : angle 11.54387 ( 6) covalent geometry : bond 0.00372 (10280) covalent geometry : angle 0.53620 (14059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 876 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: B 198 GLN cc_start: 0.6375 (tp-100) cc_final: 0.6118 (tp40) REVERT: B 260 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 386 TRP cc_start: 0.7068 (p90) cc_final: 0.6535 (p90) outliers start: 21 outliers final: 15 residues processed: 115 average time/residue: 0.2367 time to fit residues: 40.1295 Evaluate side-chains 111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 40.0000 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 69 optimal weight: 40.0000 chunk 61 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS B 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114217 restraints weight = 14483.991| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.16 r_work: 0.3303 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10284 Z= 0.241 Angle : 0.637 15.208 14065 Z= 0.312 Chirality : 0.047 0.156 1669 Planarity : 0.004 0.046 1879 Dihedral : 4.149 26.029 1553 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.52 % Allowed : 13.81 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1476 helix: 0.44 (0.44), residues: 155 sheet: -1.22 (0.22), residues: 557 loop : -1.86 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 223 HIS 0.004 0.001 HIS A 803 PHE 0.021 0.002 PHE A 876 TYR 0.023 0.002 TYR B 282 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 359) hydrogen bonds : angle 4.92324 ( 1026) metal coordination : bond 0.01352 ( 4) metal coordination : angle 10.86994 ( 6) covalent geometry : bond 0.00576 (10280) covalent geometry : angle 0.59626 (14059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.379 Fit side-chains REVERT: A 65 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: A 876 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: B 198 GLN cc_start: 0.6571 (tp-100) cc_final: 0.6298 (tp40) REVERT: B 260 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 386 TRP cc_start: 0.6904 (p90) cc_final: 0.6385 (p90) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 0.2299 time to fit residues: 38.8163 Evaluate side-chains 113 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 50.0000 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 113 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.164397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127364 restraints weight = 14702.389| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.78 r_work: 0.3399 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10284 Z= 0.105 Angle : 0.551 14.596 14065 Z= 0.270 Chirality : 0.044 0.146 1669 Planarity : 0.004 0.045 1879 Dihedral : 3.775 23.916 1553 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 2.28 % Allowed : 14.77 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1476 helix: 0.45 (0.44), residues: 160 sheet: -1.11 (0.22), residues: 558 loop : -1.67 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.002 0.001 HIS A 905 PHE 0.015 0.001 PHE A 829 TYR 0.019 0.001 TYR B 282 ARG 0.001 0.000 ARG A 989 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 359) hydrogen bonds : angle 4.50122 ( 1026) metal coordination : bond 0.01302 ( 4) metal coordination : angle 10.07133 ( 6) covalent geometry : bond 0.00243 (10280) covalent geometry : angle 0.51071 (14059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.531 Fit side-chains REVERT: A 65 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: A 876 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 260 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 386 TRP cc_start: 0.7251 (p90) cc_final: 0.6813 (p90) outliers start: 19 outliers final: 14 residues processed: 120 average time/residue: 0.2659 time to fit residues: 46.5122 Evaluate side-chains 113 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 0.0980 chunk 128 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS A1140 HIS B 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.161905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114703 restraints weight = 14580.509| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.50 r_work: 0.3359 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10284 Z= 0.205 Angle : 0.611 14.223 14065 Z= 0.301 Chirality : 0.046 0.146 1669 Planarity : 0.004 0.045 1879 Dihedral : 3.964 25.085 1553 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 3.12 % Allowed : 14.77 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.22), residues: 1476 helix: 0.64 (0.45), residues: 155 sheet: -1.12 (0.22), residues: 554 loop : -1.77 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 224 HIS 0.011 0.001 HIS A1140 PHE 0.022 0.002 PHE A 876 TYR 0.026 0.002 TYR B 282 ARG 0.006 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 359) hydrogen bonds : angle 4.68343 ( 1026) metal coordination : bond 0.01186 ( 4) metal coordination : angle 10.02652 ( 6) covalent geometry : bond 0.00492 (10280) covalent geometry : angle 0.57516 (14059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.272 Fit side-chains REVERT: A 65 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: A 876 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: B 260 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7772 (tm-30) REVERT: B 292 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 386 TRP cc_start: 0.7202 (p90) cc_final: 0.6764 (p90) outliers start: 26 outliers final: 19 residues processed: 115 average time/residue: 0.2375 time to fit residues: 39.7375 Evaluate side-chains 115 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 29 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 62 optimal weight: 50.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS A1140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116221 restraints weight = 14603.012| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.49 r_work: 0.3371 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10284 Z= 0.171 Angle : 0.592 13.762 14065 Z= 0.292 Chirality : 0.045 0.147 1669 Planarity : 0.004 0.045 1879 Dihedral : 3.925 24.691 1553 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.60 % Allowed : 14.89 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1476 helix: 0.69 (0.45), residues: 155 sheet: -1.09 (0.22), residues: 555 loop : -1.74 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 224 HIS 0.006 0.001 HIS A1140 PHE 0.018 0.001 PHE A 876 TYR 0.023 0.002 TYR B 282 ARG 0.013 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 359) hydrogen bonds : angle 4.59787 ( 1026) metal coordination : bond 0.01193 ( 4) metal coordination : angle 9.68673 ( 6) covalent geometry : bond 0.00410 (10280) covalent geometry : angle 0.55737 (14059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 1.187 Fit side-chains REVERT: A 65 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 876 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: B 260 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 292 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7738 (t0) REVERT: B 386 TRP cc_start: 0.7222 (p90) cc_final: 0.6790 (p90) outliers start: 30 outliers final: 24 residues processed: 116 average time/residue: 0.2568 time to fit residues: 43.6896 Evaluate side-chains 121 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 391 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.162703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125192 restraints weight = 14562.632| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.78 r_work: 0.3376 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10284 Z= 0.155 Angle : 0.587 13.356 14065 Z= 0.290 Chirality : 0.045 0.146 1669 Planarity : 0.004 0.050 1879 Dihedral : 3.897 23.884 1553 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.25 % Favored : 92.68 % Rotamer: Outliers : 2.88 % Allowed : 15.37 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1476 helix: 0.69 (0.45), residues: 155 sheet: -1.07 (0.22), residues: 555 loop : -1.72 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 224 HIS 0.007 0.001 HIS A1140 PHE 0.017 0.001 PHE A 876 TYR 0.028 0.001 TYR B 282 ARG 0.012 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 359) hydrogen bonds : angle 4.55008 ( 1026) metal coordination : bond 0.01041 ( 4) metal coordination : angle 9.81809 ( 6) covalent geometry : bond 0.00370 (10280) covalent geometry : angle 0.55088 (14059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.114 Fit side-chains REVERT: A 65 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: A 876 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: B 260 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 386 TRP cc_start: 0.7305 (p90) cc_final: 0.6897 (p90) outliers start: 24 outliers final: 21 residues processed: 114 average time/residue: 0.2182 time to fit residues: 36.4980 Evaluate side-chains 117 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 94 optimal weight: 0.9980 chunk 120 optimal weight: 50.0000 chunk 91 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.0170 chunk 67 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 146 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 HIS B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.166924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130066 restraints weight = 14607.270| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.73 r_work: 0.3433 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10284 Z= 0.094 Angle : 0.539 12.502 14065 Z= 0.267 Chirality : 0.044 0.149 1669 Planarity : 0.004 0.049 1879 Dihedral : 3.573 24.265 1553 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 2.16 % Allowed : 16.09 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1476 helix: 0.64 (0.44), residues: 160 sheet: -1.07 (0.22), residues: 595 loop : -1.56 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.012 0.001 HIS A1140 PHE 0.016 0.001 PHE A 829 TYR 0.021 0.001 TYR B 282 ARG 0.012 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.02553 ( 359) hydrogen bonds : angle 4.24744 ( 1026) metal coordination : bond 0.01028 ( 4) metal coordination : angle 8.92010 ( 6) covalent geometry : bond 0.00213 (10280) covalent geometry : angle 0.50713 (14059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5878.82 seconds wall clock time: 103 minutes 27.46 seconds (6207.46 seconds total)