Starting phenix.real_space_refine on Fri Feb 14 12:49:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7x_27237/02_2025/8d7x_27237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7x_27237/02_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_27237/02_2025/8d7x_27237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7x_27237/02_2025/8d7x_27237.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7x_27237/02_2025/8d7x_27237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7x_27237/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.38, 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: 1.80 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: 5.19 Time building geometry restraints manager: 2.70 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- 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 10280 Z= 0.380 Angle : 0.653 8.549 14059 Z= 0.356 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 *********************** 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 : 1.243 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: 0.2183 time to fit residues: 37.8840 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 : 1.241 ------------------------------------------------------------------------------- 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: 0.8186 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 : 0.003 0.030 10280 Z= 0.235 Angle : 0.555 6.054 14059 Z= 0.293 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 *********************** 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 : 1.222 Fit side-chains REVERT: B 225 GLN cc_start: 0.7793 (mt0) cc_final: 0.7421 (mt0) REVERT: B 273 LEU cc_start: 0.8544 (mm) cc_final: 0.8185 (mm) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 0.2248 time to fit residues: 36.7067 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 : 1.109 ------------------------------------------------------------------------------- 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: 0.9980 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 120 optimal weight: 40.0000 chunk 112 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.161233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123199 restraints weight = 14556.190| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.84 r_work: 0.3347 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10280 Z= 0.352 Angle : 0.584 6.858 14059 Z= 0.304 Chirality : 0.046 0.187 1669 Planarity : 0.004 0.046 1879 Dihedral : 4.371 49.721 1554 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.86 % Favored : 92.07 % Rotamer: Outliers : 2.04 % Allowed : 9.72 % Favored : 88.24 % 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: -2.06 (0.21), residues: 1476 helix: 0.42 (0.45), residues: 155 sheet: -1.20 (0.22), residues: 545 loop : -1.87 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.004 0.001 HIS A 803 PHE 0.019 0.002 PHE A 876 TYR 0.021 0.002 TYR B 282 ARG 0.003 0.000 ARG A 947 *********************** 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 114 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.980 Fit side-chains REVERT: A 908 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8108 (t160) REVERT: B 260 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7805 (tm-30) outliers start: 17 outliers final: 12 residues processed: 109 average time/residue: 0.2255 time to fit residues: 35.5179 Evaluate side-chains 103 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 908 ASN 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: 3.9990 chunk 104 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 0.0050 chunk 97 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 overall best weight: 0.7274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS A1055 GLN B 198 GLN B 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.164301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126595 restraints weight = 14384.806| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.26 r_work: 0.3384 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10280 Z= 0.175 Angle : 0.510 5.984 14059 Z= 0.266 Chirality : 0.044 0.147 1669 Planarity : 0.004 0.046 1879 Dihedral : 3.987 41.077 1554 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 2.40 % Allowed : 11.28 % Favored : 86.31 % 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: 0.58 (0.45), residues: 154 sheet: -1.15 (0.22), residues: 555 loop : -1.73 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.002 0.001 HIS A 905 PHE 0.015 0.001 PHE A 829 TYR 0.018 0.001 TYR B 282 ARG 0.001 0.000 ARG A 989 *********************** 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 126 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 876 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: A 908 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8115 (t160) REVERT: B 198 GLN cc_start: 0.6285 (tp-100) cc_final: 0.5976 (tp40) REVERT: B 225 GLN cc_start: 0.8079 (mt0) cc_final: 0.7703 (mt0) REVERT: B 260 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7890 (tm-30) REVERT: B 313 ASP cc_start: 0.8277 (t0) cc_final: 0.8076 (t0) REVERT: B 314 ILE cc_start: 0.8675 (mm) cc_final: 0.8424 (mm) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 0.2160 time to fit residues: 38.1105 Evaluate side-chains 109 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 908 ASN 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 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 11 optimal weight: 0.0770 chunk 37 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS A1055 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.164106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126999 restraints weight = 14501.633| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.78 r_work: 0.3395 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10280 Z= 0.205 Angle : 0.514 7.237 14059 Z= 0.267 Chirality : 0.044 0.144 1669 Planarity : 0.004 0.046 1879 Dihedral : 3.822 24.632 1554 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.50 % Rotamer: Outliers : 2.52 % Allowed : 12.61 % Favored : 84.87 % 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: 0.48 (0.44), residues: 160 sheet: -1.07 (0.22), residues: 555 loop : -1.69 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 223 HIS 0.002 0.001 HIS A 803 PHE 0.015 0.001 PHE A 829 TYR 0.018 0.001 TYR B 282 ARG 0.002 0.000 ARG A 947 *********************** 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 122 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 876 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: A 908 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8160 (t160) REVERT: B 198 GLN cc_start: 0.6324 (tp-100) cc_final: 0.6075 (tp40) REVERT: B 225 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: B 260 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 314 ILE cc_start: 0.8660 (mm) cc_final: 0.8415 (mm) outliers start: 21 outliers final: 15 residues processed: 118 average time/residue: 0.2248 time to fit residues: 38.3728 Evaluate side-chains 115 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 908 ASN 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 225 GLN Chi-restraints excluded: chain B residue 290 ILE 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: 20.0000 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 40.0000 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS B 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.160544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114953 restraints weight = 14469.238| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.26 r_work: 0.3296 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10280 Z= 0.446 Angle : 0.624 8.739 14059 Z= 0.323 Chirality : 0.047 0.170 1669 Planarity : 0.004 0.046 1879 Dihedral : 4.179 26.275 1553 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.12 % Allowed : 13.45 % Favored : 83.43 % 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 (0.22), residues: 1476 helix: 0.55 (0.45), residues: 155 sheet: -1.21 (0.22), residues: 554 loop : -1.86 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 207 HIS 0.004 0.001 HIS A 803 PHE 0.023 0.002 PHE A 876 TYR 0.023 0.002 TYR B 282 ARG 0.005 0.000 ARG B 242 *********************** 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 124 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.102 Fit side-chains REVERT: A 65 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 876 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: A 908 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8052 (t160) REVERT: B 260 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7621 (tm-30) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.2350 time to fit residues: 39.6927 Evaluate side-chains 112 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 908 ASN 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: 2.9990 chunk 56 optimal weight: 50.0000 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 121 optimal weight: 40.0000 chunk 113 optimal weight: 40.0000 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 72 optimal weight: 0.2980 chunk 93 optimal weight: 0.3980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.162770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125093 restraints weight = 14698.966| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.89 r_work: 0.3361 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10280 Z= 0.269 Angle : 0.555 8.028 14059 Z= 0.289 Chirality : 0.045 0.149 1669 Planarity : 0.004 0.045 1879 Dihedral : 4.001 24.840 1553 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.64 % Allowed : 14.77 % Favored : 82.59 % 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: 0.62 (0.45), residues: 155 sheet: -1.17 (0.22), residues: 554 loop : -1.78 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1073 HIS 0.002 0.001 HIS B 233 PHE 0.015 0.002 PHE A 876 TYR 0.023 0.001 TYR B 282 ARG 0.010 0.000 ARG B 242 *********************** 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 120 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.253 Fit side-chains REVERT: A 65 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 876 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: B 198 GLN cc_start: 0.6497 (tp-100) cc_final: 0.6258 (tp40) REVERT: B 260 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7786 (tm-30) outliers start: 22 outliers final: 19 residues processed: 117 average time/residue: 0.2348 time to fit residues: 39.9545 Evaluate side-chains 116 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 40.0000 chunk 29 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 83 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.163074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116682 restraints weight = 14537.555| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.18 r_work: 0.3349 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10280 Z= 0.245 Angle : 0.544 7.711 14059 Z= 0.283 Chirality : 0.045 0.146 1669 Planarity : 0.004 0.045 1879 Dihedral : 3.903 24.319 1553 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.24 % Allowed : 14.89 % Favored : 81.87 % 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: -1.88 (0.22), residues: 1476 helix: 0.72 (0.45), residues: 155 sheet: -1.12 (0.22), residues: 555 loop : -1.74 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 223 HIS 0.011 0.001 HIS A1140 PHE 0.018 0.001 PHE A 876 TYR 0.024 0.001 TYR B 282 ARG 0.010 0.000 ARG B 242 *********************** 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 128 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 1.220 Fit side-chains REVERT: A 65 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 876 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: B 204 LYS cc_start: 0.8274 (mtmm) cc_final: 0.8067 (pttm) REVERT: B 260 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 292 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7804 (t0) outliers start: 27 outliers final: 20 residues processed: 122 average time/residue: 0.2508 time to fit residues: 45.4120 Evaluate side-chains 116 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 62 optimal weight: 50.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.161191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114020 restraints weight = 14586.084| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.48 r_work: 0.3345 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10280 Z= 0.383 Angle : 0.611 7.698 14059 Z= 0.317 Chirality : 0.047 0.148 1669 Planarity : 0.004 0.045 1879 Dihedral : 4.129 25.804 1553 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.36 % Allowed : 15.49 % Favored : 81.15 % 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: -1.98 (0.22), residues: 1476 helix: 0.67 (0.45), residues: 155 sheet: -1.19 (0.22), residues: 555 loop : -1.81 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 224 HIS 0.009 0.001 HIS A1140 PHE 0.023 0.002 PHE A 876 TYR 0.025 0.002 TYR B 282 ARG 0.013 0.000 ARG B 242 *********************** 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 122 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.084 Fit side-chains REVERT: A 65 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 876 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: B 260 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 292 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7798 (t0) outliers start: 28 outliers final: 22 residues processed: 116 average time/residue: 0.2272 time to fit residues: 37.9859 Evaluate side-chains 119 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 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 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: 20.0000 chunk 82 optimal weight: 0.2980 chunk 108 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 50.0000 chunk 74 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.164276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127160 restraints weight = 14545.478| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.76 r_work: 0.3392 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10280 Z= 0.188 Angle : 0.536 8.793 14059 Z= 0.280 Chirality : 0.045 0.148 1669 Planarity : 0.004 0.058 1879 Dihedral : 3.824 23.515 1553 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.40 % Allowed : 16.33 % Favored : 81.27 % 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: -1.81 (0.22), residues: 1476 helix: 0.80 (0.45), residues: 155 sheet: -1.05 (0.23), residues: 544 loop : -1.72 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1073 HIS 0.008 0.001 HIS A1140 PHE 0.015 0.001 PHE A 829 TYR 0.035 0.001 TYR B 221 ARG 0.014 0.000 ARG B 242 ********************** 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 119 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.123 Fit side-chains REVERT: A 65 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 876 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: B 260 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7724 (tm-30) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 0.2266 time to fit residues: 38.5298 Evaluate side-chains 117 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 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 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 94 optimal weight: 1.9990 chunk 120 optimal weight: 40.0000 chunk 91 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 96 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 17 optimal weight: 0.3980 chunk 125 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.164457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127199 restraints weight = 14565.926| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.78 r_work: 0.3391 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10280 Z= 0.210 Angle : 0.537 8.512 14059 Z= 0.279 Chirality : 0.045 0.145 1669 Planarity : 0.004 0.056 1879 Dihedral : 3.786 24.211 1553 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.40 % Allowed : 16.33 % Favored : 81.27 % 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: -1.77 (0.22), residues: 1476 helix: 0.62 (0.44), residues: 160 sheet: -1.04 (0.22), residues: 547 loop : -1.65 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1073 HIS 0.007 0.001 HIS A1140 PHE 0.015 0.001 PHE A 876 TYR 0.032 0.001 TYR B 221 ARG 0.014 0.000 ARG B 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5351.53 seconds wall clock time: 95 minutes 14.72 seconds (5714.72 seconds total)