Starting phenix.real_space_refine on Mon Jun 16 22:37:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6btm_7286/06_2025/6btm_7286.cif Found real_map, /net/cci-nas-00/data/ceres_data/6btm_7286/06_2025/6btm_7286.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/6btm_7286/06_2025/6btm_7286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6btm_7286/06_2025/6btm_7286.map" model { file = "/net/cci-nas-00/data/ceres_data/6btm_7286/06_2025/6btm_7286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6btm_7286/06_2025/6btm_7286.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= 0.005 sd= 0.117 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 Fe 13 7.16 5 S 109 5.16 5 C 12324 2.51 5 N 3102 2.21 5 O 3386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18934 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1737 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 7208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7208 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 31, 'TRANS': 916} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3697 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 436} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1363 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1263 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 153} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3300 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'E87': 1, 'F3S': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'E87': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7839 SG CYS B 879 55.855 63.976 77.010 1.00112.21 S ATOM 7687 SG CYS B 859 51.556 64.610 81.973 1.00106.17 S ATOM 7886 SG CYS B 885 52.353 59.128 78.996 1.00110.43 S ATOM 7658 SG CYS B 855 46.065 58.003 78.453 1.00111.33 S ATOM 7913 SG CYS B 889 47.380 52.106 76.760 1.00111.86 S ATOM 7597 SG CYS B 847 45.421 56.143 72.566 1.00110.05 S ATOM 7622 SG CYS B 850 41.188 54.019 77.047 1.00112.98 S Time building chain proxies: 10.31, per 1000 atoms: 0.54 Number of scatterers: 18934 At special positions: 0 Unit cell: (107.8, 125.4, 163.9, 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) Fe 13 26.01 S 109 16.00 O 3386 8.00 N 3102 7.00 C 12324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 769 " - pdb=" SG CYS B 971 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 965 " distance=2.03 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 additional links: simple=2, symmetry=0 Simple link: pdb=" N GLU B 71 " - pdb=" C E87 B1103 " Simple link: pdb=" N HIS E 21 " - pdb=" C E87 E 202 " Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1101 " pdb="FE3 F3S B1101 " - pdb=" SG CYS B 859 " pdb="FE4 F3S B1101 " - pdb=" SG CYS B 885 " pdb="FE1 F3S B1101 " - pdb=" SG CYS B 879 " pdb=" SF4 B1102 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 855 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 847 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 889 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 850 " Number of angles added : 21 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4384 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 15 sheets defined 50.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 224 through 244 removed outlier: 4.383A pdb=" N TYR A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.757A pdb=" N HIS A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.667A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 297' Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.526A pdb=" N GLN A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.535A pdb=" N HIS A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.501A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 160 through 179 Processing helix chain 'B' and resid 191 through 205 Processing helix chain 'B' and resid 218 through 230 removed outlier: 3.528A pdb=" N VAL B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.930A pdb=" N GLY B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 300 through 316 removed outlier: 4.199A pdb=" N GLN B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 342 removed outlier: 3.753A pdb=" N GLU B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 369 Processing helix chain 'B' and resid 385 through 399 removed outlier: 3.614A pdb=" N ALA B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.612A pdb=" N VAL B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 497 through 505 Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.684A pdb=" N HIS B 569 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA B 570 " --> pdb=" O GLY B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 570' Processing helix chain 'B' and resid 572 through 578 Processing helix chain 'B' and resid 594 through 602 removed outlier: 4.118A pdb=" N LYS B 600 " --> pdb=" O ALA B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 674 removed outlier: 4.733A pdb=" N LYS B 671 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN B 672 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 717 Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 767 through 777 removed outlier: 4.421A pdb=" N ILE B 771 " --> pdb=" O GLY B 767 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 773 " --> pdb=" O CYS B 769 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 777 " --> pdb=" O CYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.871A pdb=" N ARG B 814 " --> pdb=" O GLY B 810 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS B 815 " --> pdb=" O ASP B 811 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 938 through 949 removed outlier: 4.741A pdb=" N ALA B 944 " --> pdb=" O GLN B 940 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 947 " --> pdb=" O GLN B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 993 removed outlier: 3.927A pdb=" N GLU B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 36 through 64 Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.545A pdb=" N ALA C 110 " --> pdb=" O TRP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 removed outlier: 3.689A pdb=" N THR C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 136 through 144 removed outlier: 5.077A pdb=" N TYR C 141 " --> pdb=" O TRP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 182 removed outlier: 3.526A pdb=" N GLY C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.767A pdb=" N MET C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 Processing helix chain 'C' and resid 213 through 248 Proline residue: C 233 - end of helix removed outlier: 3.724A pdb=" N HIS C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 4.247A pdb=" N VAL C 264 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 325 Processing helix chain 'C' and resid 327 through 339 Processing helix chain 'C' and resid 342 through 356 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.706A pdb=" N MET C 360 " --> pdb=" O PRO C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 368 through 394 removed outlier: 3.893A pdb=" N ASN C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 394 " --> pdb=" O ILE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 410 through 432 removed outlier: 3.660A pdb=" N ILE C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 453 through 460 Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 52 through 79 removed outlier: 4.124A pdb=" N LEU D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 60 " --> pdb=" O CYS D 56 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP D 79 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 124 removed outlier: 3.958A pdb=" N GLU D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 152 through 161 Processing helix chain 'E' and resid 78 through 85 removed outlier: 3.694A pdb=" N ASN E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.743A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 108 removed outlier: 3.583A pdb=" N GLU E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 151 removed outlier: 3.537A pdb=" N HIS E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 removed outlier: 4.003A pdb=" N ASN E 160 " --> pdb=" O SER E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 181 removed outlier: 3.756A pdb=" N TYR E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.927A pdb=" N LEU F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 134 removed outlier: 3.627A pdb=" N HIS F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N HIS F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS F 105 " --> pdb=" O GLN F 101 " (cutoff:3.500A) Proline residue: F 106 - end of helix removed outlier: 3.986A pdb=" N LEU F 110 " --> pdb=" O PRO F 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE F 127 " --> pdb=" O GLY F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 142 through 150 Processing helix chain 'F' and resid 152 through 169 removed outlier: 4.811A pdb=" N ILE F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 197 through 202 Processing helix chain 'F' and resid 202 through 233 removed outlier: 3.712A pdb=" N PHE F 213 " --> pdb=" O ARG F 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 266 removed outlier: 3.529A pdb=" N TRP F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 270 Processing helix chain 'F' and resid 278 through 304 removed outlier: 4.783A pdb=" N SER F 289 " --> pdb=" O SER F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 342 removed outlier: 3.679A pdb=" N ILE F 340 " --> pdb=" O GLN F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 357 removed outlier: 3.915A pdb=" N ARG F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 370 removed outlier: 4.072A pdb=" N VAL F 367 " --> pdb=" O PHE F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 376 removed outlier: 3.628A pdb=" N LEU F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 Processing helix chain 'F' and resid 386 through 414 Proline residue: F 411 - end of helix Processing helix chain 'F' and resid 415 through 418 removed outlier: 3.522A pdb=" N TRP F 418 " --> pdb=" O GLY F 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 415 through 418' Processing helix chain 'F' and resid 421 through 443 removed outlier: 3.749A pdb=" N SER F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 446 No H-bonds generated for 'chain 'F' and resid 444 through 446' Processing helix chain 'F' and resid 455 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.910A pdb=" N ALA A 337 " --> pdb=" O ASP A 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 100 removed outlier: 8.260A pdb=" N ASN B 107 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN B 122 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 109 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE B 120 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 111 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 158 removed outlier: 6.727A pdb=" N SER B 431 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA B 449 " --> pdb=" O SER B 431 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 433 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 182 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL B 211 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 184 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 298 removed outlier: 6.647A pdb=" N HIS B 279 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL B 297 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN B 281 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 245 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE B 282 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER B 247 " --> pdb=" O PHE B 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 633 removed outlier: 5.891A pdb=" N VAL B 591 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 605 through 607 Processing sheet with id=AA9, first strand: chain 'B' and resid 605 through 607 removed outlier: 4.011A pdb=" N LEU B 613 " --> pdb=" O PHE B 690 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 617 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY B 686 " --> pdb=" O TYR B 617 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR B 619 " --> pdb=" O ALA B 684 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA B 684 " --> pdb=" O THR B 619 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR B 621 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA B 682 " --> pdb=" O THR B 621 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 727 through 729 Processing sheet with id=AB2, first strand: chain 'B' and resid 977 through 980 removed outlier: 3.891A pdb=" N GLY B 979 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 755 " --> pdb=" O GLY B 979 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 797 through 798 Processing sheet with id=AB4, first strand: chain 'B' and resid 864 through 865 Processing sheet with id=AB5, first strand: chain 'B' and resid 895 through 896 Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 34 removed outlier: 4.585A pdb=" N LYS D 4 " --> pdb=" O VAL D 149 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2277 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: 5.95 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.75: 19271 1.75 - 2.34: 207 2.34 - 2.92: 0 2.92 - 3.51: 0 3.51 - 4.09: 3 Bond restraints: 19481 Sorted by residual: bond pdb=" S4 F3S B1101 " pdb="FE1 F3S B1101 " ideal model delta sigma weight residual 2.233 4.091 -1.858 2.00e-02 2.50e+03 8.63e+03 bond pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " ideal model delta sigma weight residual 2.258 3.858 -1.600 2.00e-02 2.50e+03 6.40e+03 bond pdb=" S2 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 2.300 3.681 -1.381 2.00e-02 2.50e+03 4.77e+03 bond pdb=" C E87 B1103 " pdb=" O E87 B1103 " ideal model delta sigma weight residual 1.426 1.245 0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" C E87 E 202 " pdb=" O E87 E 202 " ideal model delta sigma weight residual 1.426 1.248 0.178 2.00e-02 2.50e+03 7.92e+01 ... (remaining 19476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.65: 26526 10.65 - 21.30: 9 21.30 - 31.95: 3 31.95 - 42.60: 5 42.60 - 53.25: 2 Bond angle restraints: 26545 Sorted by residual: angle pdb=" S3 F3S B1101 " pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " ideal model delta sigma weight residual 112.59 59.34 53.25 3.00e+00 1.11e-01 3.15e+02 angle pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " pdb=" S3 F3S B1101 " ideal model delta sigma weight residual 114.75 63.49 51.26 3.00e+00 1.11e-01 2.92e+02 angle pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " pdb=" S2 F3S B1101 " ideal model delta sigma weight residual 103.63 65.83 37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 74.86 37.55 37.31 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S2 F3S B1101 " pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " ideal model delta sigma weight residual 102.84 66.13 36.71 3.00e+00 1.11e-01 1.50e+02 ... (remaining 26540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 11079 34.18 - 68.35: 108 68.35 - 102.53: 23 102.53 - 136.70: 2 136.70 - 170.88: 4 Dihedral angle restraints: 11216 sinusoidal: 4375 harmonic: 6841 Sorted by residual: dihedral pdb=" CB CYS B 769 " pdb=" SG CYS B 769 " pdb=" SG CYS B 971 " pdb=" CB CYS B 971 " ideal model delta sinusoidal sigma weight residual 93.00 155.84 -62.84 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA VAL B 880 " pdb=" C VAL B 880 " pdb=" N GLY B 881 " pdb=" CA GLY B 881 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLU E 41 " pdb=" C GLU E 41 " pdb=" N PRO E 42 " pdb=" CA PRO E 42 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 11213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.775: 2868 3.775 - 7.550: 0 7.550 - 11.325: 0 11.325 - 15.100: 0 15.100 - 18.875: 1 Chirality restraints: 2869 Sorted by residual: chirality pdb=" S2 F3S B1101 " pdb="FE1 F3S B1101 " pdb="FE3 F3S B1101 " pdb="FE4 F3S B1101 " both_signs ideal model delta sigma weight residual False 10.77 -8.11 18.88 2.00e-01 2.50e+01 8.91e+03 chirality pdb="FE4 SF4 B1102 " pdb=" S1 SF4 B1102 " pdb=" S2 SF4 B1102 " pdb=" S3 SF4 B1102 " both_signs ideal model delta sigma weight residual False 10.55 11.06 -0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA4 E87 B1103 " pdb=" CA2 E87 B1103 " pdb=" CA6 E87 B1103 " pdb=" O21 E87 B1103 " both_signs ideal model delta sigma weight residual False 2.12 2.59 -0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 2866 not shown) Planarity restraints: 3320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N E87 E 202 " -0.393 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" CA E87 E 202 " 0.283 2.00e-02 2.50e+03 pdb=" C1 E87 E 202 " -0.079 2.00e-02 2.50e+03 pdb=" C2 E87 E 202 " 0.188 2.00e-02 2.50e+03 pdb=" O2 E87 E 202 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N E87 B1103 " -0.280 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" CA E87 B1103 " 0.208 2.00e-02 2.50e+03 pdb=" C1 E87 B1103 " -0.058 2.00e-02 2.50e+03 pdb=" C2 E87 B1103 " 0.149 2.00e-02 2.50e+03 pdb=" O2 E87 B1103 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A1004 " -0.035 2.00e-02 2.50e+03 7.29e-02 1.19e+02 pdb=" C2C HEC A1004 " 0.195 2.00e-02 2.50e+03 pdb=" C3C HEC A1004 " -0.021 2.00e-02 2.50e+03 pdb=" C4C HEC A1004 " 0.016 2.00e-02 2.50e+03 pdb=" CAC HEC A1004 " -0.067 2.00e-02 2.50e+03 pdb=" CHC HEC A1004 " -0.045 2.00e-02 2.50e+03 pdb=" CHD HEC A1004 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC A1004 " -0.030 2.00e-02 2.50e+03 pdb=" NC HEC A1004 " -0.020 2.00e-02 2.50e+03 ... (remaining 3317 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 63 2.57 - 3.15: 15777 3.15 - 3.74: 28426 3.74 - 4.32: 41570 4.32 - 4.90: 65851 Nonbonded interactions: 151687 Sorted by model distance: nonbonded pdb=" NE2 HIS A 400 " pdb="FE HEC A1003 " model vdw 1.991 3.080 nonbonded pdb=" NE2 HIS A 265 " pdb="FE HEC A1000 " model vdw 1.992 3.080 nonbonded pdb=" NE2 HIS A 361 " pdb="FE HEC A1002 " model vdw 1.996 3.080 nonbonded pdb=" NE2 HIS A 262 " pdb="FE HEC A1001 " model vdw 1.999 3.080 nonbonded pdb=" S1 F3S B1101 " pdb="FE1 F3S B1101 " model vdw 2.181 2.688 ... (remaining 151682 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: 0.010 Normalize map: mean=0, sd=1: 0.660 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: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 45.450 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.022 1.858 19510 Z= 1.124 Angle : 1.469 53.253 26576 Z= 0.778 Chirality : 0.357 18.875 2869 Planarity : 0.009 0.235 3318 Dihedral : 11.990 170.878 6820 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.15 % Allowed : 1.42 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.53 (0.16), residues: 2347 helix: -1.28 (0.14), residues: 1125 sheet: -0.68 (0.46), residues: 128 loop : -2.20 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP C 163 HIS 0.020 0.003 HIS A 361 PHE 0.073 0.005 PHE A 356 TYR 0.103 0.005 TYR B 884 ARG 0.017 0.001 ARG B 878 Details of bonding type rmsd link_TRANS : bond 0.00503 ( 2) link_TRANS : angle 1.20009 ( 6) hydrogen bonds : bond 0.22488 ( 796) hydrogen bonds : angle 7.58102 ( 2277) metal coordination : bond 0.10220 ( 7) metal coordination : angle 13.87219 ( 21) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.94533 ( 4) covalent geometry : bond 0.02209 (19481) covalent geometry : angle 1.41667 (26545) Misc. bond : bond 0.10355 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 498 time to evaluate : 2.147 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7604 (mmp) cc_final: 0.7252 (mmm) REVERT: A 270 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8788 (mm-30) REVERT: A 272 ASN cc_start: 0.9165 (t0) cc_final: 0.8934 (t0) REVERT: A 322 ILE cc_start: 0.8255 (tt) cc_final: 0.8026 (tt) REVERT: A 355 ASP cc_start: 0.8428 (p0) cc_final: 0.7928 (t70) REVERT: A 362 SER cc_start: 0.9161 (p) cc_final: 0.8551 (p) REVERT: B 121 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6398 (mt-10) REVERT: B 255 ASP cc_start: 0.8035 (m-30) cc_final: 0.7794 (p0) REVERT: B 381 ILE cc_start: 0.8689 (mm) cc_final: 0.8470 (pt) REVERT: B 606 GLU cc_start: 0.7158 (tp30) cc_final: 0.6818 (tt0) REVERT: B 607 ILE cc_start: 0.9034 (mt) cc_final: 0.8778 (tp) REVERT: B 653 LYS cc_start: 0.8013 (mttt) cc_final: 0.7700 (mttm) REVERT: B 868 ARG cc_start: 0.8134 (mpt-90) cc_final: 0.7078 (mmt180) REVERT: C 5 TYR cc_start: 0.6942 (m-80) cc_final: 0.6501 (m-80) REVERT: C 109 MET cc_start: 0.8757 (mmt) cc_final: 0.8139 (mmm) REVERT: C 208 PHE cc_start: 0.7981 (m-10) cc_final: 0.7754 (m-80) REVERT: C 284 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8124 (mtpt) REVERT: C 442 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7501 (mt-10) REVERT: D 32 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6795 (mm-30) REVERT: D 163 THR cc_start: 0.7680 (m) cc_final: 0.7227 (t) REVERT: E 93 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8581 (mp0) REVERT: E 163 SER cc_start: 0.8722 (p) cc_final: 0.7943 (p) REVERT: F 96 ASN cc_start: 0.7294 (m-40) cc_final: 0.7035 (t0) REVERT: F 317 ASP cc_start: 0.7751 (t70) cc_final: 0.7379 (t70) REVERT: F 419 PHE cc_start: 0.6914 (p90) cc_final: 0.6547 (t80) outliers start: 3 outliers final: 0 residues processed: 499 average time/residue: 0.3001 time to fit residues: 228.3009 Evaluate side-chains 253 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 0.0970 chunk 119 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 183 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS B 761 ASN ** B 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN B 872 ASN C 91 HIS D 142 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101521 restraints weight = 35744.635| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.54 r_work: 0.3236 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.321 19510 Z= 0.156 Angle : 1.166 90.323 26576 Z= 0.402 Chirality : 0.052 1.373 2869 Planarity : 0.004 0.051 3318 Dihedral : 11.328 141.296 2672 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 2.74 % Allowed : 7.91 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.17), residues: 2347 helix: 0.11 (0.15), residues: 1125 sheet: -0.25 (0.44), residues: 150 loop : -2.06 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 206 HIS 0.007 0.001 HIS F 316 PHE 0.031 0.001 PHE C 269 TYR 0.016 0.001 TYR B 413 ARG 0.003 0.000 ARG F 355 Details of bonding type rmsd link_TRANS : bond 0.00101 ( 2) link_TRANS : angle 2.08355 ( 6) hydrogen bonds : bond 0.07050 ( 796) hydrogen bonds : angle 4.98894 ( 2277) metal coordination : bond 0.01626 ( 7) metal coordination : angle 26.25386 ( 21) SS BOND : bond 0.00663 ( 2) SS BOND : angle 1.81422 ( 4) covalent geometry : bond 0.00321 (19481) covalent geometry : angle 0.90208 (26545) Misc. bond : bond 0.13058 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7640 (mmp) cc_final: 0.7285 (mmm) REVERT: A 295 MET cc_start: 0.8966 (mmm) cc_final: 0.8670 (mmm) REVERT: A 355 ASP cc_start: 0.8435 (p0) cc_final: 0.8113 (t0) REVERT: A 393 MET cc_start: 0.8137 (tpt) cc_final: 0.7474 (tpt) REVERT: A 398 ASP cc_start: 0.8795 (t0) cc_final: 0.8588 (t0) REVERT: A 402 LYS cc_start: 0.8659 (mtmp) cc_final: 0.8385 (mtmt) REVERT: B 121 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7070 (mt-10) REVERT: B 299 MET cc_start: 0.7657 (mtp) cc_final: 0.7182 (ttm) REVERT: B 381 ILE cc_start: 0.9034 (mm) cc_final: 0.8782 (pt) REVERT: B 756 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 848 GLN cc_start: 0.8264 (pm20) cc_final: 0.8044 (pm20) REVERT: B 868 ARG cc_start: 0.8354 (mpt-90) cc_final: 0.7547 (mmt180) REVERT: C 5 TYR cc_start: 0.6961 (m-80) cc_final: 0.6676 (m-80) REVERT: C 94 THR cc_start: 0.9267 (m) cc_final: 0.9022 (t) REVERT: C 109 MET cc_start: 0.9048 (mmt) cc_final: 0.8476 (mmm) REVERT: C 284 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8339 (tttt) REVERT: C 386 GLU cc_start: 0.8552 (tp30) cc_final: 0.8051 (tt0) REVERT: C 442 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7265 (mt-10) REVERT: D 21 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8162 (mmtm) REVERT: D 24 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7831 (mmm-85) REVERT: E 93 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8725 (mp0) REVERT: E 166 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8249 (mt-10) REVERT: F 96 ASN cc_start: 0.7661 (m-40) cc_final: 0.7331 (t0) REVERT: F 317 ASP cc_start: 0.7532 (t70) cc_final: 0.7102 (t0) REVERT: F 413 THR cc_start: 0.9232 (m) cc_final: 0.8982 (p) REVERT: F 419 PHE cc_start: 0.7116 (p90) cc_final: 0.6403 (t80) REVERT: F 452 ARG cc_start: 0.8779 (ptm-80) cc_final: 0.8459 (ptm-80) outliers start: 54 outliers final: 35 residues processed: 342 average time/residue: 0.2711 time to fit residues: 149.3102 Evaluate side-chains 276 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 361 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 26 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 849 HIS C 91 HIS C 239 HIS D 29 HIS D 133 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 370 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099338 restraints weight = 36093.549| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.47 r_work: 0.3224 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 19510 Z= 0.146 Angle : 1.030 83.287 26576 Z= 0.369 Chirality : 0.052 1.456 2869 Planarity : 0.004 0.047 3318 Dihedral : 10.839 137.507 2672 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 2.69 % Allowed : 10.59 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2347 helix: 0.62 (0.16), residues: 1118 sheet: 0.37 (0.45), residues: 149 loop : -1.96 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 206 HIS 0.005 0.001 HIS F 316 PHE 0.026 0.001 PHE C 269 TYR 0.015 0.001 TYR B 884 ARG 0.004 0.000 ARG B 894 Details of bonding type rmsd link_TRANS : bond 0.00132 ( 2) link_TRANS : angle 2.15378 ( 6) hydrogen bonds : bond 0.05607 ( 796) hydrogen bonds : angle 4.46180 ( 2277) metal coordination : bond 0.00597 ( 7) metal coordination : angle 20.48986 ( 21) SS BOND : bond 0.01130 ( 2) SS BOND : angle 1.77400 ( 4) covalent geometry : bond 0.00322 (19481) covalent geometry : angle 0.85325 (26545) Misc. bond : bond 0.07470 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7574 (mmp) cc_final: 0.7213 (mmm) REVERT: A 300 ASN cc_start: 0.7971 (p0) cc_final: 0.7581 (p0) REVERT: A 398 ASP cc_start: 0.8940 (t0) cc_final: 0.8712 (t0) REVERT: A 424 TYR cc_start: 0.7787 (m-10) cc_final: 0.7584 (m-10) REVERT: B 121 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7467 (mt-10) REVERT: B 159 SER cc_start: 0.8852 (t) cc_final: 0.8290 (p) REVERT: B 299 MET cc_start: 0.7615 (mtp) cc_final: 0.7286 (ttm) REVERT: B 564 MET cc_start: 0.8556 (mmm) cc_final: 0.8244 (tpt) REVERT: B 756 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8715 (tt) REVERT: B 868 ARG cc_start: 0.8553 (mpt-90) cc_final: 0.7724 (mmt180) REVERT: C 109 MET cc_start: 0.9032 (mmt) cc_final: 0.8484 (mmm) REVERT: C 284 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8376 (tttt) REVERT: C 315 TYR cc_start: 0.8772 (m-10) cc_final: 0.8527 (m-10) REVERT: C 383 MET cc_start: 0.8371 (tpp) cc_final: 0.8005 (mmm) REVERT: C 386 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: C 442 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7357 (mt-10) REVERT: D 21 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8122 (mmtm) REVERT: D 24 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.7842 (mmm-85) REVERT: D 76 MET cc_start: 0.9023 (mmm) cc_final: 0.8691 (mmt) REVERT: E 93 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8685 (mp0) REVERT: E 166 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8344 (mp0) REVERT: F 96 ASN cc_start: 0.7749 (m-40) cc_final: 0.7490 (t0) REVERT: F 404 ASP cc_start: 0.8888 (t0) cc_final: 0.8618 (t0) REVERT: F 452 ARG cc_start: 0.8831 (ptm-80) cc_final: 0.8592 (ptm-80) outliers start: 53 outliers final: 36 residues processed: 291 average time/residue: 0.2771 time to fit residues: 129.3261 Evaluate side-chains 248 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 361 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 228 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 HIS ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 HIS ** B 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 125 GLN C 239 HIS C 440 GLN D 78 HIS E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089650 restraints weight = 36790.774| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.40 r_work: 0.3033 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.235 19510 Z= 0.267 Angle : 1.101 81.401 26576 Z= 0.419 Chirality : 0.056 1.541 2869 Planarity : 0.005 0.044 3318 Dihedral : 10.881 140.158 2672 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.82 % Favored : 93.14 % Rotamer: Outliers : 3.80 % Allowed : 10.90 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2347 helix: 0.61 (0.16), residues: 1128 sheet: 0.19 (0.43), residues: 154 loop : -2.18 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 179 HIS 0.009 0.002 HIS A 443 PHE 0.027 0.002 PHE C 269 TYR 0.020 0.002 TYR B 884 ARG 0.004 0.001 ARG B 894 Details of bonding type rmsd link_TRANS : bond 0.00114 ( 2) link_TRANS : angle 2.23406 ( 6) hydrogen bonds : bond 0.07022 ( 796) hydrogen bonds : angle 4.68145 ( 2277) metal coordination : bond 0.01211 ( 7) metal coordination : angle 20.02835 ( 21) SS BOND : bond 0.00672 ( 2) SS BOND : angle 1.88870 ( 4) covalent geometry : bond 0.00642 (19481) covalent geometry : angle 0.94587 (26545) Misc. bond : bond 0.10425 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 212 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7515 (mmp) cc_final: 0.7282 (mmm) REVERT: A 288 ILE cc_start: 0.9070 (mm) cc_final: 0.8789 (mm) REVERT: A 300 ASN cc_start: 0.8306 (p0) cc_final: 0.7857 (p0) REVERT: A 424 TYR cc_start: 0.7919 (m-10) cc_final: 0.7642 (m-10) REVERT: B 108 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9045 (pp) REVERT: B 121 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8148 (mt-10) REVERT: B 494 THR cc_start: 0.9020 (m) cc_final: 0.8813 (p) REVERT: B 868 ARG cc_start: 0.8995 (mpt-90) cc_final: 0.7993 (mmt180) REVERT: B 997 MET cc_start: 0.8637 (tpp) cc_final: 0.8243 (tmm) REVERT: C 109 MET cc_start: 0.9130 (mmt) cc_final: 0.8603 (mmm) REVERT: C 284 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8470 (tttt) REVERT: C 315 TYR cc_start: 0.8930 (m-10) cc_final: 0.8639 (m-10) REVERT: C 386 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: C 442 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 24 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8098 (mmm-85) REVERT: E 93 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8740 (mp0) REVERT: E 102 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8868 (mm-30) REVERT: E 166 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8547 (mp0) REVERT: F 317 ASP cc_start: 0.8013 (t70) cc_final: 0.7309 (t70) REVERT: F 355 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8699 (mtt90) REVERT: F 404 ASP cc_start: 0.9024 (t0) cc_final: 0.8635 (t0) REVERT: F 424 GLU cc_start: 0.8096 (mp0) cc_final: 0.7537 (mp0) outliers start: 75 outliers final: 51 residues processed: 269 average time/residue: 0.2754 time to fit residues: 116.8833 Evaluate side-chains 245 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 427 SER Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 161 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.090664 restraints weight = 36573.020| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.41 r_work: 0.3023 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 19510 Z= 0.190 Angle : 1.016 81.524 26576 Z= 0.378 Chirality : 0.054 1.552 2869 Planarity : 0.004 0.045 3318 Dihedral : 10.573 139.428 2672 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 3.29 % Allowed : 11.56 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2347 helix: 0.76 (0.16), residues: 1132 sheet: 0.38 (0.45), residues: 144 loop : -2.13 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 206 HIS 0.019 0.001 HIS C 239 PHE 0.022 0.002 PHE C 269 TYR 0.015 0.002 TYR B 413 ARG 0.004 0.000 ARG F 355 Details of bonding type rmsd link_TRANS : bond 0.00104 ( 2) link_TRANS : angle 2.25723 ( 6) hydrogen bonds : bond 0.06210 ( 796) hydrogen bonds : angle 4.46841 ( 2277) metal coordination : bond 0.00919 ( 7) metal coordination : angle 18.28554 ( 21) SS BOND : bond 0.00584 ( 2) SS BOND : angle 1.70592 ( 4) covalent geometry : bond 0.00449 (19481) covalent geometry : angle 0.87547 (26545) Misc. bond : bond 0.09305 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.7515 (mmp) cc_final: 0.7302 (mmm) REVERT: A 288 ILE cc_start: 0.9122 (mm) cc_final: 0.8840 (mm) REVERT: A 300 ASN cc_start: 0.8486 (p0) cc_final: 0.8025 (p0) REVERT: A 385 MET cc_start: 0.9067 (tpt) cc_final: 0.8838 (tpt) REVERT: B 114 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: B 121 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8068 (mt-10) REVERT: B 187 ASN cc_start: 0.9087 (p0) cc_final: 0.8841 (p0) REVERT: B 494 THR cc_start: 0.9068 (m) cc_final: 0.8817 (p) REVERT: B 868 ARG cc_start: 0.9039 (mpt-90) cc_final: 0.8096 (mmt180) REVERT: B 997 MET cc_start: 0.8603 (tpp) cc_final: 0.8200 (tmm) REVERT: C 109 MET cc_start: 0.9075 (mmt) cc_final: 0.8638 (mmt) REVERT: C 284 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8470 (tttt) REVERT: C 315 TYR cc_start: 0.8875 (m-10) cc_final: 0.8643 (m-10) REVERT: C 328 GLU cc_start: 0.7340 (tp30) cc_final: 0.7066 (tp30) REVERT: C 386 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 448 LYS cc_start: 0.8579 (pttp) cc_final: 0.8311 (mtmm) REVERT: D 24 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7913 (mmm-85) REVERT: E 93 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8723 (mp0) REVERT: E 102 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8934 (mm-30) REVERT: E 166 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8584 (mp0) REVERT: F 317 ASP cc_start: 0.7815 (t70) cc_final: 0.7074 (t0) REVERT: F 355 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8671 (mtt90) REVERT: F 404 ASP cc_start: 0.9020 (t0) cc_final: 0.8646 (t0) outliers start: 65 outliers final: 52 residues processed: 253 average time/residue: 0.3110 time to fit residues: 126.6834 Evaluate side-chains 244 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 207 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089259 restraints weight = 36789.003| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.40 r_work: 0.3107 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.274 19510 Z= 0.220 Angle : 1.037 81.607 26576 Z= 0.390 Chirality : 0.054 1.536 2869 Planarity : 0.004 0.045 3318 Dihedral : 10.229 139.312 2672 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.76 % Rotamer: Outliers : 4.16 % Allowed : 11.61 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2347 helix: 0.84 (0.16), residues: 1124 sheet: 0.10 (0.44), residues: 154 loop : -2.16 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 206 HIS 0.006 0.001 HIS C 396 PHE 0.027 0.002 PHE C 320 TYR 0.030 0.002 TYR F 200 ARG 0.004 0.000 ARG F 355 Details of bonding type rmsd link_TRANS : bond 0.00131 ( 2) link_TRANS : angle 2.33829 ( 6) hydrogen bonds : bond 0.06390 ( 796) hydrogen bonds : angle 4.48632 ( 2277) metal coordination : bond 0.01097 ( 7) metal coordination : angle 18.53446 ( 21) SS BOND : bond 0.00505 ( 2) SS BOND : angle 1.12284 ( 4) covalent geometry : bond 0.00526 (19481) covalent geometry : angle 0.89681 (26545) Misc. bond : bond 0.09875 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 197 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9144 (mm) cc_final: 0.8876 (mm) REVERT: A 385 MET cc_start: 0.9083 (tpt) cc_final: 0.8859 (tpt) REVERT: A 427 GLU cc_start: 0.7828 (pp20) cc_final: 0.7587 (pp20) REVERT: B 108 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8965 (pp) REVERT: B 121 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8168 (mt-10) REVERT: B 187 ASN cc_start: 0.9089 (p0) cc_final: 0.8880 (p0) REVERT: B 517 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7421 (mmmt) REVERT: B 736 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8399 (mm-30) REVERT: B 868 ARG cc_start: 0.8986 (mpt-90) cc_final: 0.8110 (mmt180) REVERT: B 997 MET cc_start: 0.8650 (tpp) cc_final: 0.8333 (tmm) REVERT: C 109 MET cc_start: 0.9088 (mmt) cc_final: 0.8692 (mmt) REVERT: C 284 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8500 (tttt) REVERT: C 315 TYR cc_start: 0.8895 (m-10) cc_final: 0.8689 (m-10) REVERT: C 328 GLU cc_start: 0.7444 (tp30) cc_final: 0.7145 (tp30) REVERT: C 386 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: C 442 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8026 (mm-30) REVERT: C 448 LYS cc_start: 0.8635 (pttp) cc_final: 0.8433 (mtmm) REVERT: D 141 ASP cc_start: 0.7503 (t0) cc_final: 0.7189 (t0) REVERT: E 93 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8685 (mp0) REVERT: E 102 GLU cc_start: 0.9227 (mm-30) cc_final: 0.9000 (mm-30) REVERT: E 166 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8593 (mp0) REVERT: F 4 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6749 (t80) REVERT: F 317 ASP cc_start: 0.7826 (t70) cc_final: 0.7096 (t0) REVERT: F 355 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8748 (mtt90) REVERT: F 404 ASP cc_start: 0.8998 (t0) cc_final: 0.8739 (t0) outliers start: 82 outliers final: 58 residues processed: 258 average time/residue: 0.2941 time to fit residues: 123.2833 Evaluate side-chains 247 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 133 HIS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 427 SER Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 94 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 184 optimal weight: 0.0970 chunk 163 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 GLN B 755 ASN B 848 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN F 357 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095465 restraints weight = 35543.496| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.41 r_work: 0.3169 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 19510 Z= 0.126 Angle : 0.925 82.452 26576 Z= 0.347 Chirality : 0.051 1.500 2869 Planarity : 0.004 0.042 3318 Dihedral : 9.751 140.227 2672 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 2.99 % Allowed : 13.38 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2347 helix: 1.17 (0.16), residues: 1121 sheet: 0.47 (0.45), residues: 147 loop : -1.87 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.007 0.001 HIS C 396 PHE 0.020 0.001 PHE C 320 TYR 0.028 0.001 TYR F 200 ARG 0.004 0.000 ARG F 355 Details of bonding type rmsd link_TRANS : bond 0.00050 ( 2) link_TRANS : angle 2.31153 ( 6) hydrogen bonds : bond 0.04715 ( 796) hydrogen bonds : angle 4.20166 ( 2277) metal coordination : bond 0.00261 ( 7) metal coordination : angle 14.81894 ( 21) SS BOND : bond 0.00342 ( 2) SS BOND : angle 0.98071 ( 4) covalent geometry : bond 0.00268 (19481) covalent geometry : angle 0.82514 (26545) Misc. bond : bond 0.07944 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9102 (mm) cc_final: 0.8830 (mm) REVERT: B 108 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8963 (pp) REVERT: B 121 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8038 (mt-10) REVERT: B 159 SER cc_start: 0.9107 (t) cc_final: 0.8619 (p) REVERT: B 187 ASN cc_start: 0.8976 (p0) cc_final: 0.8751 (p0) REVERT: B 517 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7389 (mmmt) REVERT: B 755 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8300 (m-40) REVERT: B 868 ARG cc_start: 0.8972 (mpt-90) cc_final: 0.8025 (mmt180) REVERT: B 997 MET cc_start: 0.8384 (tpp) cc_final: 0.8038 (tmm) REVERT: C 5 TYR cc_start: 0.7455 (m-80) cc_final: 0.7115 (m-10) REVERT: C 109 MET cc_start: 0.9028 (mmt) cc_final: 0.8663 (mmt) REVERT: C 284 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8390 (tttt) REVERT: C 315 TYR cc_start: 0.8777 (m-10) cc_final: 0.8546 (m-10) REVERT: C 328 GLU cc_start: 0.7158 (tp30) cc_final: 0.6791 (tp30) REVERT: C 383 MET cc_start: 0.8558 (tpp) cc_final: 0.8177 (mmp) REVERT: C 386 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: C 442 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7822 (mm-30) REVERT: D 150 ASN cc_start: 0.8465 (m-40) cc_final: 0.8047 (p0) REVERT: D 151 ASP cc_start: 0.8152 (p0) cc_final: 0.7692 (p0) REVERT: E 93 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8681 (mp0) REVERT: E 102 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8941 (mm-30) REVERT: E 166 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8600 (mp0) REVERT: F 174 ILE cc_start: 0.9390 (mt) cc_final: 0.9098 (mt) REVERT: F 368 VAL cc_start: 0.8894 (p) cc_final: 0.8661 (p) REVERT: F 404 ASP cc_start: 0.8938 (t0) cc_final: 0.8693 (t0) outliers start: 59 outliers final: 41 residues processed: 272 average time/residue: 0.3686 time to fit residues: 161.2700 Evaluate side-chains 249 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 138 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 755 ASN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 132 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094136 restraints weight = 36336.111| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.45 r_work: 0.3175 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.232 19510 Z= 0.161 Angle : 0.956 81.851 26576 Z= 0.360 Chirality : 0.052 1.528 2869 Planarity : 0.004 0.043 3318 Dihedral : 9.665 139.824 2672 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 3.19 % Allowed : 13.99 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2347 helix: 1.21 (0.16), residues: 1119 sheet: 0.29 (0.45), residues: 149 loop : -1.83 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 395 HIS 0.008 0.001 HIS B 849 PHE 0.022 0.001 PHE F 286 TYR 0.026 0.001 TYR F 200 ARG 0.003 0.000 ARG F 209 Details of bonding type rmsd link_TRANS : bond 0.00079 ( 2) link_TRANS : angle 2.36127 ( 6) hydrogen bonds : bond 0.05191 ( 796) hydrogen bonds : angle 4.21331 ( 2277) metal coordination : bond 0.00700 ( 7) metal coordination : angle 15.71970 ( 21) SS BOND : bond 0.00591 ( 2) SS BOND : angle 1.32329 ( 4) covalent geometry : bond 0.00376 (19481) covalent geometry : angle 0.84728 (26545) Misc. bond : bond 0.07800 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 2.043 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9092 (mm) cc_final: 0.8814 (mm) REVERT: B 108 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8965 (pp) REVERT: B 121 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8141 (mt-10) REVERT: B 517 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7410 (mmmt) REVERT: B 755 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8200 (m110) REVERT: B 868 ARG cc_start: 0.8993 (mpt-90) cc_final: 0.8075 (mmt180) REVERT: B 997 MET cc_start: 0.8418 (tpp) cc_final: 0.8125 (tmm) REVERT: C 5 TYR cc_start: 0.7455 (m-80) cc_final: 0.7186 (m-10) REVERT: C 109 MET cc_start: 0.9047 (mmt) cc_final: 0.8682 (mmt) REVERT: C 284 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8469 (tttt) REVERT: C 328 GLU cc_start: 0.7230 (tp30) cc_final: 0.6878 (tp30) REVERT: C 386 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: C 442 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7941 (mm-30) REVERT: D 141 ASP cc_start: 0.7537 (t0) cc_final: 0.7207 (t0) REVERT: E 93 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8679 (mp0) REVERT: E 166 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8573 (mp0) REVERT: F 404 ASP cc_start: 0.8940 (t0) cc_final: 0.8733 (t0) REVERT: F 410 MET cc_start: 0.9109 (mmt) cc_final: 0.8508 (mmt) outliers start: 63 outliers final: 53 residues processed: 244 average time/residue: 0.3240 time to fit residues: 130.0594 Evaluate side-chains 252 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 174 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 97 optimal weight: 0.0270 chunk 27 optimal weight: 0.0170 chunk 46 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097987 restraints weight = 35682.793| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.48 r_work: 0.3199 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.224 19510 Z= 0.122 Angle : 0.919 82.528 26576 Z= 0.345 Chirality : 0.050 1.489 2869 Planarity : 0.004 0.041 3318 Dihedral : 9.486 140.611 2672 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 2.89 % Allowed : 14.39 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2347 helix: 1.41 (0.16), residues: 1111 sheet: 0.38 (0.46), residues: 142 loop : -1.69 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 395 HIS 0.006 0.001 HIS C 396 PHE 0.023 0.001 PHE F 286 TYR 0.024 0.001 TYR E 35 ARG 0.003 0.000 ARG F 209 Details of bonding type rmsd link_TRANS : bond 0.00044 ( 2) link_TRANS : angle 2.34742 ( 6) hydrogen bonds : bond 0.04469 ( 796) hydrogen bonds : angle 4.11177 ( 2277) metal coordination : bond 0.00239 ( 7) metal coordination : angle 14.56425 ( 21) SS BOND : bond 0.00413 ( 2) SS BOND : angle 0.93293 ( 4) covalent geometry : bond 0.00260 (19481) covalent geometry : angle 0.82196 (26545) Misc. bond : bond 0.07693 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9004 (mm) cc_final: 0.8741 (mm) REVERT: B 108 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8907 (pp) REVERT: B 121 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7808 (mt-10) REVERT: B 159 SER cc_start: 0.9055 (t) cc_final: 0.8645 (p) REVERT: B 187 ASN cc_start: 0.8861 (p0) cc_final: 0.8607 (p0) REVERT: B 517 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7195 (mmmt) REVERT: B 736 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 868 ARG cc_start: 0.8820 (mpt-90) cc_final: 0.7967 (mmt180) REVERT: B 997 MET cc_start: 0.8169 (tpp) cc_final: 0.7862 (tmm) REVERT: C 5 TYR cc_start: 0.7227 (m-80) cc_final: 0.6955 (m-10) REVERT: C 57 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8592 (tt) REVERT: C 109 MET cc_start: 0.8918 (mmt) cc_final: 0.8601 (mmt) REVERT: C 284 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8401 (tttt) REVERT: C 328 GLU cc_start: 0.6949 (tp30) cc_final: 0.6570 (tp30) REVERT: C 383 MET cc_start: 0.8520 (tpp) cc_final: 0.8089 (mmm) REVERT: C 386 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: D 150 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8171 (p0) REVERT: D 151 ASP cc_start: 0.8139 (p0) cc_final: 0.7776 (p0) REVERT: E 81 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8778 (mp) REVERT: E 93 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8628 (mp0) REVERT: E 166 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8342 (mp0) REVERT: F 410 MET cc_start: 0.9005 (mmt) cc_final: 0.8423 (mmt) outliers start: 57 outliers final: 42 residues processed: 258 average time/residue: 0.3163 time to fit residues: 131.3393 Evaluate side-chains 250 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 204 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 42 optimal weight: 0.0060 chunk 67 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094716 restraints weight = 36230.927| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.45 r_work: 0.3120 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.219 19510 Z= 0.158 Angle : 0.958 81.863 26576 Z= 0.361 Chirality : 0.053 1.524 2869 Planarity : 0.004 0.042 3318 Dihedral : 9.443 139.896 2672 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.48 % Allowed : 14.90 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2347 helix: 1.45 (0.16), residues: 1106 sheet: 0.30 (0.46), residues: 142 loop : -1.71 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 395 HIS 0.006 0.001 HIS C 396 PHE 0.023 0.001 PHE F 286 TYR 0.025 0.001 TYR A 237 ARG 0.003 0.000 ARG F 209 Details of bonding type rmsd link_TRANS : bond 0.00086 ( 2) link_TRANS : angle 2.35989 ( 6) hydrogen bonds : bond 0.05082 ( 796) hydrogen bonds : angle 4.16040 ( 2277) metal coordination : bond 0.00696 ( 7) metal coordination : angle 15.57094 ( 21) SS BOND : bond 0.00595 ( 2) SS BOND : angle 1.14966 ( 4) covalent geometry : bond 0.00366 (19481) covalent geometry : angle 0.85192 (26545) Misc. bond : bond 0.08086 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 2.262 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9101 (mm) cc_final: 0.8804 (mm) REVERT: B 108 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8966 (pp) REVERT: B 121 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8391 (mt-10) REVERT: B 187 ASN cc_start: 0.8953 (p0) cc_final: 0.8702 (p0) REVERT: B 517 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7354 (mmmt) REVERT: B 736 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 868 ARG cc_start: 0.9022 (mpt-90) cc_final: 0.8069 (mmt180) REVERT: B 997 MET cc_start: 0.8455 (tpp) cc_final: 0.8152 (tmm) REVERT: C 57 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8656 (tt) REVERT: C 109 MET cc_start: 0.9047 (mmt) cc_final: 0.8673 (mmt) REVERT: C 284 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8470 (tttt) REVERT: C 328 GLU cc_start: 0.7311 (tp30) cc_final: 0.6914 (tp30) REVERT: C 349 MET cc_start: 0.8804 (tmm) cc_final: 0.8331 (tmm) REVERT: C 386 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 442 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7918 (mm-30) REVERT: D 141 ASP cc_start: 0.7703 (t0) cc_final: 0.7470 (t0) REVERT: E 81 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8756 (mp) REVERT: E 93 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8678 (mp0) REVERT: E 166 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8572 (mp0) REVERT: F 410 MET cc_start: 0.9079 (mmt) cc_final: 0.8463 (mmt) outliers start: 49 outliers final: 41 residues processed: 237 average time/residue: 0.2840 time to fit residues: 108.8459 Evaluate side-chains 243 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.9488 > 50: distance: 8 - 14: 22.065 distance: 14 - 15: 15.364 distance: 15 - 16: 27.287 distance: 15 - 18: 8.541 distance: 16 - 17: 41.957 distance: 16 - 22: 30.191 distance: 18 - 19: 28.891 distance: 19 - 20: 16.650 distance: 20 - 21: 23.731 distance: 22 - 23: 29.273 distance: 23 - 24: 24.375 distance: 24 - 25: 39.641 distance: 24 - 26: 33.205 distance: 26 - 27: 23.852 distance: 27 - 28: 13.873 distance: 27 - 30: 23.775 distance: 28 - 29: 11.246 distance: 28 - 37: 13.930 distance: 30 - 31: 14.001 distance: 31 - 32: 11.025 distance: 32 - 33: 13.805 distance: 33 - 34: 5.040 distance: 34 - 35: 5.026 distance: 34 - 36: 9.336 distance: 37 - 38: 4.636 distance: 38 - 39: 13.132 distance: 39 - 40: 22.338 distance: 39 - 41: 6.458 distance: 41 - 42: 15.851 distance: 42 - 43: 10.349 distance: 42 - 45: 4.549 distance: 43 - 44: 7.185 distance: 43 - 49: 15.358 distance: 45 - 46: 23.574 distance: 46 - 47: 18.566 distance: 46 - 48: 6.780 distance: 49 - 50: 18.178 distance: 50 - 51: 6.575 distance: 50 - 53: 8.247 distance: 51 - 52: 11.770 distance: 51 - 57: 12.398 distance: 53 - 54: 13.288 distance: 53 - 55: 12.051 distance: 54 - 56: 13.061 distance: 57 - 58: 10.076 distance: 58 - 59: 12.957 distance: 58 - 61: 7.987 distance: 59 - 60: 12.685 distance: 59 - 65: 6.444 distance: 61 - 62: 13.583 distance: 61 - 63: 13.792 distance: 62 - 64: 13.856 distance: 65 - 66: 8.929 distance: 66 - 67: 7.454 distance: 66 - 69: 7.194 distance: 67 - 68: 12.708 distance: 67 - 74: 23.755 distance: 69 - 70: 10.715 distance: 70 - 71: 7.893 distance: 71 - 72: 16.667 distance: 72 - 73: 19.094 distance: 74 - 75: 21.938 distance: 75 - 76: 24.914 distance: 75 - 78: 16.408 distance: 76 - 83: 25.839 distance: 78 - 79: 33.839 distance: 79 - 80: 11.387 distance: 80 - 81: 31.666 distance: 80 - 82: 22.611 distance: 83 - 84: 22.153 distance: 84 - 85: 23.886 distance: 84 - 87: 16.237 distance: 85 - 86: 16.588 distance: 85 - 90: 24.303 distance: 87 - 88: 25.457 distance: 87 - 89: 24.126