Starting phenix.real_space_refine on Wed Nov 19 01:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6btm_7286/11_2025/6btm_7286.cif Found real_map, /net/cci-nas-00/data/ceres_data/6btm_7286/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6btm_7286/11_2025/6btm_7286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6btm_7286/11_2025/6btm_7286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6btm_7286/11_2025/6btm_7286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6btm_7286/11_2025/6btm_7286.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 4.54, per 1000 atoms: 0.24 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: 1.91 Conformation dependent library (CDL) restraints added in 893.7 milliseconds 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: 0.60 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: 3.35 Time building geometry restraints manager: 2.43 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: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.390 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- 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 : 1.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.017 0.001 ARG B 878 TYR 0.103 0.005 TYR B 884 PHE 0.073 0.005 PHE A 356 TRP 0.034 0.006 TRP C 163 HIS 0.020 0.003 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.02209 (19481) covalent geometry : angle 1.41667 (26545) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.94533 ( 4) hydrogen bonds : bond 0.22488 ( 796) hydrogen bonds : angle 7.58102 ( 2277) metal coordination : bond 0.10220 ( 7) metal coordination : angle 13.87219 ( 21) Misc. bond : bond 0.10355 ( 18) link_TRANS : bond 0.00503 ( 2) link_TRANS : angle 1.20009 ( 6) *********************** 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 : 0.690 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: 0.1450 time to fit residues: 111.0633 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 : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN 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 = 0.3546 r_free = 0.3546 target = 0.116104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101504 restraints weight = 35631.688| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.53 r_work: 0.3305 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 19510 Z= 0.155 Angle : 1.179 93.887 26576 Z= 0.405 Chirality : 0.048 0.865 2869 Planarity : 0.004 0.051 3318 Dihedral : 11.291 139.814 2672 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.69 % Allowed : 7.91 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.17), residues: 2347 helix: 0.15 (0.15), residues: 1125 sheet: -0.24 (0.45), residues: 150 loop : -2.06 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.015 0.001 TYR B 454 PHE 0.031 0.001 PHE C 269 TRP 0.016 0.001 TRP F 206 HIS 0.007 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00314 (19481) covalent geometry : angle 0.91668 (26545) SS BOND : bond 0.01196 ( 2) SS BOND : angle 2.14583 ( 4) hydrogen bonds : bond 0.06789 ( 796) hydrogen bonds : angle 4.95228 ( 2277) metal coordination : bond 0.01903 ( 7) metal coordination : angle 26.33478 ( 21) Misc. bond : bond 0.13207 ( 18) link_TRANS : bond 0.00425 ( 2) link_TRANS : angle 2.23624 ( 6) *********************** 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 357 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7736 (mmp) cc_final: 0.7365 (mmm) REVERT: A 300 ASN cc_start: 0.7936 (p0) cc_final: 0.7710 (p0) REVERT: A 355 ASP cc_start: 0.8547 (p0) cc_final: 0.8241 (t0) REVERT: A 393 MET cc_start: 0.8223 (tpt) cc_final: 0.7531 (tpt) REVERT: B 121 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7230 (mt-10) REVERT: B 299 MET cc_start: 0.7817 (mtp) cc_final: 0.7384 (ttm) REVERT: B 381 ILE cc_start: 0.9064 (mm) cc_final: 0.8799 (pt) REVERT: B 607 ILE cc_start: 0.9233 (mt) cc_final: 0.9018 (tt) REVERT: B 756 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8907 (tt) REVERT: B 848 GLN cc_start: 0.8435 (pm20) cc_final: 0.8211 (pm20) REVERT: B 868 ARG cc_start: 0.8438 (mpt-90) cc_final: 0.7600 (mmt180) REVERT: B 884 TYR cc_start: 0.8225 (t80) cc_final: 0.7973 (t80) REVERT: C 5 TYR cc_start: 0.7099 (m-80) cc_final: 0.6796 (m-80) REVERT: C 109 MET cc_start: 0.9090 (mmt) cc_final: 0.8547 (mmm) REVERT: C 208 PHE cc_start: 0.8148 (m-10) cc_final: 0.7947 (m-80) REVERT: C 284 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8368 (tttt) REVERT: C 386 GLU cc_start: 0.8707 (tp30) cc_final: 0.8206 (tt0) REVERT: C 442 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7548 (mt-10) REVERT: D 21 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8212 (mmtm) REVERT: D 24 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7765 (mmm-85) REVERT: E 93 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8770 (mp0) REVERT: E 166 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8504 (mp0) REVERT: F 96 ASN cc_start: 0.7732 (m-40) cc_final: 0.7393 (t0) REVERT: F 317 ASP cc_start: 0.7605 (t70) cc_final: 0.7194 (t0) REVERT: F 413 THR cc_start: 0.9215 (m) cc_final: 0.8973 (p) REVERT: F 419 PHE cc_start: 0.7232 (p90) cc_final: 0.6494 (t80) outliers start: 53 outliers final: 31 residues processed: 340 average time/residue: 0.1236 time to fit residues: 68.2019 Evaluate side-chains 270 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 D residue 117 ILE Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain E residue 88 SER 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 157 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 753 HIS B 849 HIS C 91 HIS C 239 HIS D 133 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 132 GLN F 370 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094016 restraints weight = 35989.516| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.37 r_work: 0.3154 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 19510 Z= 0.165 Angle : 1.048 82.967 26576 Z= 0.379 Chirality : 0.052 1.391 2869 Planarity : 0.004 0.048 3318 Dihedral : 10.833 137.977 2672 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.33 % Rotamer: Outliers : 3.09 % Allowed : 10.39 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2347 helix: 0.65 (0.16), residues: 1117 sheet: 0.31 (0.44), residues: 149 loop : -2.02 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 894 TYR 0.015 0.002 TYR F 200 PHE 0.026 0.002 PHE C 269 TRP 0.015 0.001 TRP F 206 HIS 0.006 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00374 (19481) covalent geometry : angle 0.87137 (26545) SS BOND : bond 0.00749 ( 2) SS BOND : angle 1.66599 ( 4) hydrogen bonds : bond 0.05874 ( 796) hydrogen bonds : angle 4.49376 ( 2277) metal coordination : bond 0.00858 ( 7) metal coordination : angle 20.70400 ( 21) Misc. bond : bond 0.07430 ( 18) link_TRANS : bond 0.00100 ( 2) link_TRANS : angle 2.13091 ( 6) *********************** 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 303 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7805 (mmp) cc_final: 0.7381 (mmm) REVERT: A 300 ASN cc_start: 0.8375 (p0) cc_final: 0.8134 (p0) REVERT: A 424 TYR cc_start: 0.7846 (m-10) cc_final: 0.7610 (m-10) REVERT: B 121 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7842 (mt-10) REVERT: B 159 SER cc_start: 0.8912 (t) cc_final: 0.8282 (p) REVERT: B 756 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8853 (tt) REVERT: B 868 ARG cc_start: 0.8776 (mpt-90) cc_final: 0.7842 (mmt180) REVERT: C 109 MET cc_start: 0.9067 (mmt) cc_final: 0.8522 (mmm) REVERT: C 284 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8419 (tttt) REVERT: C 315 TYR cc_start: 0.8898 (m-10) cc_final: 0.8687 (m-10) REVERT: C 383 MET cc_start: 0.8458 (tpp) cc_final: 0.8040 (mmp) REVERT: C 386 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: C 440 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7789 (mt0) REVERT: C 442 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7561 (mt-10) REVERT: D 21 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8124 (mmtm) REVERT: D 24 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: D 76 MET cc_start: 0.9095 (mmm) cc_final: 0.8821 (mmt) REVERT: E 93 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8734 (mp0) REVERT: E 102 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8771 (mm-30) REVERT: E 166 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8571 (mp0) REVERT: F 16 MET cc_start: 0.8043 (mtp) cc_final: 0.7824 (mtm) REVERT: F 96 ASN cc_start: 0.7865 (m-40) cc_final: 0.7605 (t0) REVERT: F 200 TYR cc_start: 0.8788 (t80) cc_final: 0.8557 (t80) REVERT: F 232 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7926 (t0) REVERT: F 317 ASP cc_start: 0.7502 (t70) cc_final: 0.6973 (t0) REVERT: F 355 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8521 (mtt90) REVERT: F 404 ASP cc_start: 0.9017 (t0) cc_final: 0.8669 (t0) outliers start: 61 outliers final: 37 residues processed: 286 average time/residue: 0.1320 time to fit residues: 60.7973 Evaluate side-chains 255 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 82 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 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 882 THR 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 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 232 ASP 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 355 ARG 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 201 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 HIS B 696 GLN ** B 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 125 GLN C 239 HIS D 78 HIS E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN F 314 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090968 restraints weight = 36642.548| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.42 r_work: 0.3031 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 19510 Z= 0.217 Angle : 1.047 81.708 26576 Z= 0.394 Chirality : 0.054 1.520 2869 Planarity : 0.004 0.044 3318 Dihedral : 10.725 140.209 2672 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 3.90 % Allowed : 10.59 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2347 helix: 0.76 (0.16), residues: 1124 sheet: 0.17 (0.43), residues: 154 loop : -2.09 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 213 TYR 0.017 0.002 TYR A 252 PHE 0.026 0.002 PHE C 269 TRP 0.016 0.001 TRP C 179 HIS 0.007 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00513 (19481) covalent geometry : angle 0.90147 (26545) SS BOND : bond 0.00694 ( 2) SS BOND : angle 1.53444 ( 4) hydrogen bonds : bond 0.06490 ( 796) hydrogen bonds : angle 4.54147 ( 2277) metal coordination : bond 0.01126 ( 7) metal coordination : angle 18.92881 ( 21) Misc. bond : bond 0.09801 ( 18) link_TRANS : bond 0.00112 ( 2) link_TRANS : angle 2.22248 ( 6) *********************** 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 299 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 222 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7496 (mmp) cc_final: 0.7275 (mmm) REVERT: A 288 ILE cc_start: 0.9056 (mm) cc_final: 0.8772 (mm) REVERT: A 385 MET cc_start: 0.9065 (tpt) cc_final: 0.8784 (tpt) REVERT: A 424 TYR cc_start: 0.7879 (m-10) cc_final: 0.7622 (m-10) REVERT: B 121 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8130 (mt-10) REVERT: B 494 THR cc_start: 0.8986 (m) cc_final: 0.8738 (p) REVERT: B 756 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9038 (tt) REVERT: B 868 ARG cc_start: 0.9006 (mpt-90) cc_final: 0.7947 (mmt180) REVERT: C 109 MET cc_start: 0.9088 (mmt) cc_final: 0.8560 (mmm) REVERT: C 284 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8479 (tttt) REVERT: C 328 GLU cc_start: 0.7418 (tp30) cc_final: 0.7094 (tp30) REVERT: C 386 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: C 442 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7612 (mt-10) REVERT: D 24 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.7947 (mmm-85) REVERT: E 93 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8752 (mp0) REVERT: E 102 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8870 (mm-30) REVERT: E 166 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8614 (mp0) REVERT: F 119 LEU cc_start: 0.9149 (mm) cc_final: 0.8876 (mt) REVERT: F 317 ASP cc_start: 0.7845 (t70) cc_final: 0.7188 (t70) REVERT: F 404 ASP cc_start: 0.9024 (t0) cc_final: 0.8645 (t0) REVERT: F 424 GLU cc_start: 0.8122 (mp0) cc_final: 0.7553 (mp0) outliers start: 77 outliers final: 51 residues processed: 274 average time/residue: 0.1340 time to fit residues: 58.6109 Evaluate side-chains 247 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain B residue 99 VAL 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 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 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 60 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 LEU 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 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 40 HIS 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 3 THR 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 327 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 427 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 217 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 118 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 696 GLN B 848 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096405 restraints weight = 35859.660| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.47 r_work: 0.3221 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.236 19510 Z= 0.129 Angle : 0.933 82.121 26576 Z= 0.348 Chirality : 0.051 1.516 2869 Planarity : 0.004 0.042 3318 Dihedral : 10.274 140.224 2672 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 2.94 % Allowed : 11.71 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2347 helix: 1.02 (0.16), residues: 1125 sheet: 0.42 (0.45), residues: 149 loop : -1.99 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 355 TYR 0.011 0.001 TYR F 239 PHE 0.021 0.001 PHE F 286 TRP 0.012 0.001 TRP C 78 HIS 0.021 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00274 (19481) covalent geometry : angle 0.82513 (26545) SS BOND : bond 0.00876 ( 2) SS BOND : angle 1.41801 ( 4) hydrogen bonds : bond 0.05058 ( 796) hydrogen bonds : angle 4.25730 ( 2277) metal coordination : bond 0.00312 ( 7) metal coordination : angle 15.49033 ( 21) Misc. bond : bond 0.07728 ( 18) link_TRANS : bond 0.00019 ( 2) link_TRANS : angle 2.24737 ( 6) *********************** 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 291 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9055 (mm) cc_final: 0.8782 (mm) REVERT: A 424 TYR cc_start: 0.7867 (m-10) cc_final: 0.7647 (m-10) REVERT: A 438 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 108 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9059 (pp) REVERT: B 121 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7913 (mt-10) REVERT: B 159 SER cc_start: 0.8981 (t) cc_final: 0.8432 (p) REVERT: B 187 ASN cc_start: 0.9062 (p0) cc_final: 0.8815 (p0) REVERT: B 564 MET cc_start: 0.8511 (mmm) cc_final: 0.8208 (tpt) REVERT: B 756 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 868 ARG cc_start: 0.8883 (mpt-90) cc_final: 0.7975 (mmt180) REVERT: C 5 TYR cc_start: 0.7434 (m-80) cc_final: 0.7068 (m-10) REVERT: C 109 MET cc_start: 0.9011 (mmt) cc_final: 0.8653 (mmt) REVERT: C 284 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8413 (tttt) REVERT: C 328 GLU cc_start: 0.7262 (tp30) cc_final: 0.6966 (tp30) REVERT: C 383 MET cc_start: 0.8528 (tpp) cc_final: 0.8092 (mmp) REVERT: C 386 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: C 442 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7796 (mm-30) REVERT: D 24 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7956 (mmm-85) REVERT: D 150 ASN cc_start: 0.8143 (m-40) cc_final: 0.7867 (p0) REVERT: D 151 ASP cc_start: 0.7961 (p0) cc_final: 0.7519 (p0) REVERT: E 34 MET cc_start: 0.8529 (mtt) cc_final: 0.8220 (mtt) REVERT: E 93 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8727 (mp0) REVERT: E 166 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8558 (mp0) REVERT: F 404 ASP cc_start: 0.8942 (t0) cc_final: 0.8668 (t0) outliers start: 58 outliers final: 39 residues processed: 275 average time/residue: 0.1369 time to fit residues: 59.9947 Evaluate side-chains 246 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 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 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 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 149 ILE 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 349 VAL Chi-restraints excluded: chain F residue 361 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 140 optimal weight: 0.0980 chunk 131 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 848 GLN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095268 restraints weight = 35758.517| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.46 r_work: 0.3213 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 19510 Z= 0.142 Angle : 0.940 81.960 26576 Z= 0.351 Chirality : 0.052 1.520 2869 Planarity : 0.004 0.041 3318 Dihedral : 9.946 140.275 2672 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 3.09 % Allowed : 12.87 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2347 helix: 1.18 (0.16), residues: 1111 sheet: 0.15 (0.43), residues: 159 loop : -1.88 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 209 TYR 0.026 0.001 TYR F 200 PHE 0.032 0.001 PHE C 269 TRP 0.010 0.001 TRP F 206 HIS 0.008 0.001 HIS B 849 Details of bonding type rmsd covalent geometry : bond 0.00324 (19481) covalent geometry : angle 0.83367 (26545) SS BOND : bond 0.00434 ( 2) SS BOND : angle 0.93778 ( 4) hydrogen bonds : bond 0.05102 ( 796) hydrogen bonds : angle 4.21839 ( 2277) metal coordination : bond 0.00950 ( 7) metal coordination : angle 15.44050 ( 21) Misc. bond : bond 0.07164 ( 18) link_TRANS : bond 0.00058 ( 2) link_TRANS : angle 2.32826 ( 6) *********************** 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 275 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9073 (mm) cc_final: 0.8791 (mm) REVERT: A 424 TYR cc_start: 0.7937 (m-10) cc_final: 0.7689 (m-10) REVERT: A 438 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 108 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8991 (pp) REVERT: B 121 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8088 (mt-10) REVERT: B 159 SER cc_start: 0.9021 (t) cc_final: 0.8474 (p) REVERT: B 187 ASN cc_start: 0.9035 (p0) cc_final: 0.8798 (p0) REVERT: B 517 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7388 (mmmt) REVERT: B 564 MET cc_start: 0.8534 (mmm) cc_final: 0.8269 (tpt) REVERT: B 736 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8294 (mm-30) REVERT: B 756 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8930 (tt) REVERT: B 832 GLU cc_start: 0.8388 (pt0) cc_final: 0.8166 (pt0) REVERT: B 868 ARG cc_start: 0.8896 (mpt-90) cc_final: 0.7985 (mmt180) REVERT: C 109 MET cc_start: 0.9013 (mmt) cc_final: 0.8611 (mmt) REVERT: C 284 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8418 (tttt) REVERT: C 328 GLU cc_start: 0.7306 (tp30) cc_final: 0.6988 (tp30) REVERT: C 383 MET cc_start: 0.8596 (tpp) cc_final: 0.8334 (mmm) REVERT: C 386 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: C 406 MET cc_start: 0.9057 (mmt) cc_final: 0.8799 (mmt) REVERT: D 150 ASN cc_start: 0.8307 (m-40) cc_final: 0.7983 (p0) REVERT: D 151 ASP cc_start: 0.8000 (p0) cc_final: 0.7545 (p0) REVERT: E 93 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8736 (mp0) REVERT: E 166 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8549 (mp0) REVERT: F 4 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6456 (t80) REVERT: F 404 ASP cc_start: 0.8944 (t0) cc_final: 0.8722 (t0) REVERT: F 413 THR cc_start: 0.9178 (m) cc_final: 0.8840 (p) REVERT: F 424 GLU cc_start: 0.8126 (mp0) cc_final: 0.7907 (pm20) outliers start: 61 outliers final: 46 residues processed: 261 average time/residue: 0.1295 time to fit residues: 54.5428 Evaluate side-chains 247 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 597 ASP Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 736 GLU 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 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 58 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 161 LEU 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 40 HIS Chi-restraints excluded: chain D residue 65 ILE 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 4 PHE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 106 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 97 optimal weight: 0.0010 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 GLN B 848 GLN C 91 HIS C 239 HIS ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094578 restraints weight = 36088.808| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.46 r_work: 0.3134 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 19510 Z= 0.149 Angle : 0.946 81.986 26576 Z= 0.353 Chirality : 0.052 1.519 2869 Planarity : 0.004 0.041 3318 Dihedral : 9.757 140.313 2672 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 3.55 % Allowed : 12.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2347 helix: 1.25 (0.16), residues: 1110 sheet: 0.17 (0.43), residues: 152 loop : -1.87 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 209 TYR 0.016 0.001 TYR C 5 PHE 0.030 0.001 PHE C 269 TRP 0.011 0.001 TRP F 206 HIS 0.012 0.001 HIS B 849 Details of bonding type rmsd covalent geometry : bond 0.00341 (19481) covalent geometry : angle 0.83670 (26545) SS BOND : bond 0.00417 ( 2) SS BOND : angle 1.32709 ( 4) hydrogen bonds : bond 0.05153 ( 796) hydrogen bonds : angle 4.19549 ( 2277) metal coordination : bond 0.01226 ( 7) metal coordination : angle 15.66664 ( 21) Misc. bond : bond 0.07316 ( 18) link_TRANS : bond 0.00064 ( 2) link_TRANS : angle 2.34927 ( 6) *********************** 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 270 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9111 (mm) cc_final: 0.8815 (mm) REVERT: A 424 TYR cc_start: 0.7869 (m-10) cc_final: 0.7439 (m-10) REVERT: A 438 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: B 108 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8950 (pp) REVERT: B 121 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8117 (mt-10) REVERT: B 187 ASN cc_start: 0.8971 (p0) cc_final: 0.8764 (p0) REVERT: B 517 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7408 (mmmt) REVERT: B 564 MET cc_start: 0.8718 (mmm) cc_final: 0.8383 (tpt) REVERT: B 756 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8896 (tt) REVERT: B 868 ARG cc_start: 0.8961 (mpt-90) cc_final: 0.7975 (mmt180) REVERT: C 5 TYR cc_start: 0.7558 (m-80) cc_final: 0.7243 (m-10) REVERT: C 109 MET cc_start: 0.9017 (mmt) cc_final: 0.8594 (mmt) REVERT: C 284 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8415 (tttt) REVERT: C 328 GLU cc_start: 0.7330 (tp30) cc_final: 0.6960 (tp30) REVERT: C 386 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: C 406 MET cc_start: 0.9069 (mmt) cc_final: 0.8797 (mmt) REVERT: D 150 ASN cc_start: 0.8417 (m-40) cc_final: 0.8048 (p0) REVERT: D 151 ASP cc_start: 0.7981 (p0) cc_final: 0.7492 (p0) REVERT: E 93 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8679 (mp0) REVERT: E 166 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8596 (mp0) REVERT: F 404 ASP cc_start: 0.8958 (t0) cc_final: 0.8752 (t0) REVERT: F 410 MET cc_start: 0.9043 (mmt) cc_final: 0.8326 (mmt) outliers start: 70 outliers final: 53 residues processed: 251 average time/residue: 0.1339 time to fit residues: 54.3921 Evaluate side-chains 253 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 438 GLU 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 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 756 LEU 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 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 58 ILE Chi-restraints excluded: chain C residue 132 ILE 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 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 C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 117 ILE 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 76 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 264 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 18 optimal weight: 0.3980 chunk 203 optimal weight: 0.9980 chunk 179 optimal weight: 0.4980 chunk 93 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 848 GLN C 91 HIS ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096282 restraints weight = 35872.100| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.46 r_work: 0.3228 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 19510 Z= 0.128 Angle : 0.929 82.281 26576 Z= 0.347 Chirality : 0.051 1.506 2869 Planarity : 0.004 0.042 3318 Dihedral : 9.543 140.600 2672 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 3.14 % Allowed : 13.33 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2347 helix: 1.36 (0.16), residues: 1108 sheet: 0.22 (0.44), residues: 152 loop : -1.74 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 209 TYR 0.023 0.001 TYR A 237 PHE 0.026 0.001 PHE C 269 TRP 0.011 0.001 TRP C 78 HIS 0.013 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00278 (19481) covalent geometry : angle 0.82638 (26545) SS BOND : bond 0.00519 ( 2) SS BOND : angle 1.13960 ( 4) hydrogen bonds : bond 0.04781 ( 796) hydrogen bonds : angle 4.12571 ( 2277) metal coordination : bond 0.00462 ( 7) metal coordination : angle 15.09585 ( 21) Misc. bond : bond 0.07040 ( 18) link_TRANS : bond 0.00025 ( 2) link_TRANS : angle 2.32820 ( 6) *********************** 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 274 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9070 (mm) cc_final: 0.8784 (mm) REVERT: A 438 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: B 108 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8958 (pp) REVERT: B 121 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8121 (mt-10) REVERT: B 159 SER cc_start: 0.9051 (t) cc_final: 0.8539 (p) REVERT: B 517 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7353 (mmmt) REVERT: B 564 MET cc_start: 0.8547 (mmm) cc_final: 0.8280 (tpt) REVERT: B 736 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 756 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8897 (tt) REVERT: B 868 ARG cc_start: 0.8878 (mpt-90) cc_final: 0.7960 (mmt180) REVERT: C 5 TYR cc_start: 0.7477 (m-80) cc_final: 0.7169 (m-10) REVERT: C 109 MET cc_start: 0.8999 (mmt) cc_final: 0.8614 (mmt) REVERT: C 284 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8441 (tttt) REVERT: C 328 GLU cc_start: 0.7275 (tp30) cc_final: 0.6909 (tp30) REVERT: C 386 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: C 406 MET cc_start: 0.9045 (mmt) cc_final: 0.8767 (mmt) REVERT: D 150 ASN cc_start: 0.8349 (m-40) cc_final: 0.8117 (p0) REVERT: D 151 ASP cc_start: 0.8029 (p0) cc_final: 0.7566 (p0) REVERT: E 93 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8686 (mp0) REVERT: E 166 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8560 (mp0) REVERT: F 264 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8509 (t0) REVERT: F 410 MET cc_start: 0.8981 (mmt) cc_final: 0.8231 (mmt) outliers start: 62 outliers final: 52 residues processed: 255 average time/residue: 0.1258 time to fit residues: 52.3797 Evaluate side-chains 257 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 438 GLU 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 756 LEU 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 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 161 LEU 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 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 C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 117 ILE 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 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 259 SER Chi-restraints excluded: chain F residue 264 ASP 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 124 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 848 GLN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095643 restraints weight = 35610.501| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.44 r_work: 0.3222 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 19510 Z= 0.139 Angle : 0.939 82.081 26576 Z= 0.352 Chirality : 0.052 1.518 2869 Planarity : 0.004 0.041 3318 Dihedral : 9.404 140.561 2672 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.99 % Allowed : 13.63 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2347 helix: 1.40 (0.16), residues: 1109 sheet: 0.17 (0.44), residues: 152 loop : -1.73 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 209 TYR 0.023 0.001 TYR A 237 PHE 0.028 0.001 PHE C 269 TRP 0.019 0.001 TRP A 395 HIS 0.010 0.001 HIS B 849 Details of bonding type rmsd covalent geometry : bond 0.00313 (19481) covalent geometry : angle 0.83567 (26545) SS BOND : bond 0.00471 ( 2) SS BOND : angle 1.03711 ( 4) hydrogen bonds : bond 0.04841 ( 796) hydrogen bonds : angle 4.11409 ( 2277) metal coordination : bond 0.00614 ( 7) metal coordination : angle 15.23844 ( 21) Misc. bond : bond 0.07678 ( 18) link_TRANS : bond 0.00054 ( 2) link_TRANS : angle 2.33110 ( 6) *********************** 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 260 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 201 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9072 (mm) cc_final: 0.8783 (mm) REVERT: A 434 MET cc_start: 0.9241 (mmm) cc_final: 0.9030 (mmp) REVERT: A 438 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: B 108 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8957 (pp) REVERT: B 121 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8098 (mt-10) REVERT: B 187 ASN cc_start: 0.8988 (p0) cc_final: 0.8754 (p0) REVERT: B 517 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7390 (mmmt) REVERT: B 736 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 756 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8917 (tt) REVERT: B 830 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8731 (mm-30) REVERT: B 868 ARG cc_start: 0.8861 (mpt-90) cc_final: 0.7964 (mmt180) REVERT: C 5 TYR cc_start: 0.7475 (m-80) cc_final: 0.7171 (m-10) REVERT: C 109 MET cc_start: 0.8995 (mmt) cc_final: 0.8633 (mmt) REVERT: C 284 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8455 (tttt) REVERT: C 328 GLU cc_start: 0.7222 (tp30) cc_final: 0.6853 (tp30) REVERT: C 386 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: C 406 MET cc_start: 0.9045 (mmt) cc_final: 0.8781 (mmt) REVERT: D 141 ASP cc_start: 0.7577 (t0) cc_final: 0.7368 (t0) REVERT: D 150 ASN cc_start: 0.8504 (m-40) cc_final: 0.8203 (p0) REVERT: D 151 ASP cc_start: 0.7982 (p0) cc_final: 0.7531 (p0) REVERT: E 81 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8716 (mp) REVERT: E 93 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8661 (mp0) REVERT: E 166 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8558 (mp0) REVERT: F 264 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8493 (t0) outliers start: 59 outliers final: 50 residues processed: 243 average time/residue: 0.1289 time to fit residues: 50.6688 Evaluate side-chains 250 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 438 GLU 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 756 LEU 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 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 1014 VAL 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 161 LEU 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 286 SER Chi-restraints excluded: chain C residue 289 GLU 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 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 81 LEU 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 259 SER Chi-restraints excluded: chain F residue 264 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 185 optimal weight: 4.9990 chunk 101 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 224 optimal weight: 0.9980 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN C 91 HIS C 239 HIS ** E 33 ASN ** 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 = 0.3439 r_free = 0.3439 target = 0.108806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094145 restraints weight = 36016.009| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.46 r_work: 0.3091 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 19510 Z= 0.171 Angle : 0.974 81.797 26576 Z= 0.367 Chirality : 0.053 1.527 2869 Planarity : 0.004 0.041 3318 Dihedral : 9.406 140.217 2672 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 3.14 % Allowed : 13.53 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2347 helix: 1.39 (0.16), residues: 1100 sheet: 0.24 (0.47), residues: 141 loop : -1.74 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 209 TYR 0.024 0.001 TYR A 237 PHE 0.028 0.001 PHE C 269 TRP 0.015 0.001 TRP A 395 HIS 0.013 0.001 HIS B 849 Details of bonding type rmsd covalent geometry : bond 0.00403 (19481) covalent geometry : angle 0.86044 (26545) SS BOND : bond 0.00548 ( 2) SS BOND : angle 1.16379 ( 4) hydrogen bonds : bond 0.05370 ( 796) hydrogen bonds : angle 4.16939 ( 2277) metal coordination : bond 0.00885 ( 7) metal coordination : angle 16.17669 ( 21) Misc. bond : bond 0.08496 ( 18) link_TRANS : bond 0.00096 ( 2) link_TRANS : angle 2.34397 ( 6) ********************** 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 261 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9109 (mm) cc_final: 0.8810 (mm) REVERT: A 438 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: B 108 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8948 (pp) REVERT: B 121 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8182 (mt-10) REVERT: B 159 SER cc_start: 0.8990 (t) cc_final: 0.8521 (p) REVERT: B 187 ASN cc_start: 0.8934 (p0) cc_final: 0.8688 (p0) REVERT: B 517 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7447 (mmmt) REVERT: B 564 MET cc_start: 0.8244 (tpt) cc_final: 0.8003 (tpt) REVERT: B 736 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8171 (mm-30) REVERT: B 756 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9007 (tt) REVERT: B 868 ARG cc_start: 0.8941 (mpt-90) cc_final: 0.8064 (mmt180) REVERT: B 997 MET cc_start: 0.8553 (tpt) cc_final: 0.8236 (tpt) REVERT: C 109 MET cc_start: 0.9024 (mmt) cc_final: 0.8589 (mmt) REVERT: C 284 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8469 (tttt) REVERT: C 328 GLU cc_start: 0.7347 (tp30) cc_final: 0.6936 (tp30) REVERT: C 386 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: D 76 MET cc_start: 0.9186 (tpt) cc_final: 0.8718 (mmt) REVERT: D 141 ASP cc_start: 0.7656 (t0) cc_final: 0.7400 (t0) REVERT: E 81 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8703 (mp) REVERT: E 93 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8673 (mp0) REVERT: E 166 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8600 (mp0) REVERT: F 368 VAL cc_start: 0.9042 (p) cc_final: 0.8784 (p) REVERT: F 424 GLU cc_start: 0.8054 (pm20) cc_final: 0.7839 (pm20) outliers start: 62 outliers final: 53 residues processed: 246 average time/residue: 0.1281 time to fit residues: 51.0630 Evaluate side-chains 252 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 438 GLU 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 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 756 LEU 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 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 58 ILE Chi-restraints excluded: chain C residue 133 HIS Chi-restraints excluded: chain C residue 161 LEU 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 286 SER Chi-restraints excluded: chain C residue 289 GLU 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 C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 117 ILE 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 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 259 SER Chi-restraints excluded: chain F residue 264 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 226 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 135 optimal weight: 0.0470 chunk 123 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** 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 = 0.3442 r_free = 0.3442 target = 0.108983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094330 restraints weight = 36242.059| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.47 r_work: 0.3094 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.226 19510 Z= 0.160 Angle : 0.968 81.881 26576 Z= 0.363 Chirality : 0.053 1.529 2869 Planarity : 0.004 0.042 3318 Dihedral : 9.384 140.194 2672 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.69 % Rotamer: Outliers : 3.14 % Allowed : 13.53 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2347 helix: 1.41 (0.16), residues: 1107 sheet: 0.23 (0.47), residues: 141 loop : -1.72 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 209 TYR 0.025 0.001 TYR A 237 PHE 0.028 0.001 PHE C 269 TRP 0.015 0.001 TRP A 395 HIS 0.009 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00372 (19481) covalent geometry : angle 0.85458 (26545) SS BOND : bond 0.00606 ( 2) SS BOND : angle 1.09647 ( 4) hydrogen bonds : bond 0.05297 ( 796) hydrogen bonds : angle 4.16150 ( 2277) metal coordination : bond 0.00718 ( 7) metal coordination : angle 16.14194 ( 21) Misc. bond : bond 0.08707 ( 18) link_TRANS : bond 0.00081 ( 2) link_TRANS : angle 2.33643 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.95 seconds wall clock time: 74 minutes 23.26 seconds (4463.26 seconds total)