Starting phenix.real_space_refine on Tue Aug 26 23:08:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n8w_49148/08_2025/9n8w_49148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n8w_49148/08_2025/9n8w_49148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n8w_49148/08_2025/9n8w_49148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n8w_49148/08_2025/9n8w_49148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n8w_49148/08_2025/9n8w_49148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n8w_49148/08_2025/9n8w_49148.map" } resolution = 3.5 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= 0.016 sd= 0.618 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 102 5.16 5 C 26591 2.51 5 N 7176 2.21 5 O 7920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41791 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "B" Number of atoms: 6538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6538 Classifications: {'peptide': 857} Link IDs: {'PTRANS': 45, 'TRANS': 811} Chain: "C" Number of atoms: 6538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6538 Classifications: {'peptide': 857} Link IDs: {'PTRANS': 45, 'TRANS': 811} Chain: "D" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6425 Classifications: {'peptide': 853} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 44, 'TRANS': 808} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "F" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "G" Number of atoms: 6525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6525 Classifications: {'peptide': 855} Link IDs: {'PTRANS': 44, 'TRANS': 810} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 46 SG CYS A 31 55.750 51.705 282.707 1.00 50.10 S ATOM 68 SG CYS A 34 57.330 48.605 284.254 1.00 49.53 S ATOM 203 SG CYS A 51 58.963 51.966 284.670 1.00 56.44 S ATOM 227 SG CYS A 54 58.960 50.277 281.237 1.00 59.27 S ATOM 1662 SG CYS A 233 42.015 56.159 281.084 1.00 55.02 S ATOM 1680 SG CYS A 236 43.152 59.750 281.531 1.00 57.27 S ATOM 1780 SG CYS A 248 40.570 58.260 283.962 1.00 64.71 S ATOM 1804 SG CYS A 251 39.739 58.938 280.229 1.00 67.99 S Time building chain proxies: 8.08, per 1000 atoms: 0.19 Number of scatterers: 41791 At special positions: 0 Unit cell: (116.26, 113.173, 306.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 102 16.00 O 7920 8.00 N 7176 7.00 C 26591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 31 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 54 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 251 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 233 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 236 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 248 " Number of angles added : 12 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9888 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 65 sheets defined 17.9% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 85 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.556A pdb=" N GLY A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 126 through 146 Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.764A pdb=" N LEU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 180 Processing helix chain 'A' and resid 188 through 207 removed outlier: 4.196A pdb=" N PHE A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.734A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 283 removed outlier: 3.972A pdb=" N LEU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 298 through 322 removed outlier: 3.885A pdb=" N ILE A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ALA A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.572A pdb=" N PHE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 361 removed outlier: 3.547A pdb=" N ILE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.622A pdb=" N PHE A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 409 Processing helix chain 'A' and resid 410 through 417 removed outlier: 3.866A pdb=" N LEU A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 Processing helix chain 'B' and resid 25 through 46 removed outlier: 4.331A pdb=" N GLY B 46 " --> pdb=" O TYR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 329 through 332 removed outlier: 3.501A pdb=" N VAL B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 332' Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.530A pdb=" N ARG B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU B 443 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.726A pdb=" N LEU B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 removed outlier: 4.180A pdb=" N SER B 614 " --> pdb=" O GLY B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 632 Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 830 through 834 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 24 through 45 removed outlier: 4.061A pdb=" N PHE C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 329 through 332 removed outlier: 3.501A pdb=" N VAL C 332 " --> pdb=" O PRO C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 332' Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 439 through 446 removed outlier: 3.531A pdb=" N ARG C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU C 443 " --> pdb=" O GLN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.726A pdb=" N LEU C 567 " --> pdb=" O ARG C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 601 Processing helix chain 'C' and resid 610 through 617 removed outlier: 4.179A pdb=" N SER C 614 " --> pdb=" O GLY C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 632 Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 830 through 834 Processing helix chain 'D' and resid 26 through 44 removed outlier: 3.698A pdb=" N ASP D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 329 through 332 removed outlier: 3.502A pdb=" N VAL D 332 " --> pdb=" O PRO D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 332' Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 439 through 446 removed outlier: 3.531A pdb=" N ARG D 442 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU D 443 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 563 through 567 removed outlier: 3.725A pdb=" N LEU D 567 " --> pdb=" O ARG D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 617 removed outlier: 4.180A pdb=" N SER D 614 " --> pdb=" O GLY D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 632 Processing helix chain 'D' and resid 711 through 715 Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 830 through 834 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 329 through 332 removed outlier: 3.501A pdb=" N VAL E 332 " --> pdb=" O PRO E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 332' Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 439 through 446 removed outlier: 3.531A pdb=" N ARG E 442 " --> pdb=" O PRO E 439 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU E 443 " --> pdb=" O GLN E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 507 Processing helix chain 'E' and resid 563 through 567 removed outlier: 3.725A pdb=" N LEU E 567 " --> pdb=" O ARG E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 601 Processing helix chain 'E' and resid 610 through 617 removed outlier: 4.180A pdb=" N SER E 614 " --> pdb=" O GLY E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 632 Processing helix chain 'E' and resid 711 through 715 Processing helix chain 'E' and resid 798 through 802 Processing helix chain 'E' and resid 830 through 834 Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 329 through 332 removed outlier: 3.501A pdb=" N VAL F 332 " --> pdb=" O PRO F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 332' Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 439 through 446 removed outlier: 3.531A pdb=" N ARG F 442 " --> pdb=" O PRO F 439 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU F 443 " --> pdb=" O GLN F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 500 through 507 Processing helix chain 'F' and resid 563 through 567 removed outlier: 3.726A pdb=" N LEU F 567 " --> pdb=" O ARG F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 617 removed outlier: 4.180A pdb=" N SER F 614 " --> pdb=" O GLY F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 632 Processing helix chain 'F' and resid 711 through 715 Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 830 through 834 Processing helix chain 'G' and resid 24 through 44 removed outlier: 3.713A pdb=" N ASP G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 100 Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 273 through 278 Processing helix chain 'G' and resid 329 through 332 removed outlier: 3.501A pdb=" N VAL G 332 " --> pdb=" O PRO G 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 329 through 332' Processing helix chain 'G' and resid 354 through 361 Processing helix chain 'G' and resid 439 through 446 removed outlier: 3.531A pdb=" N ARG G 442 " --> pdb=" O PRO G 439 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU G 443 " --> pdb=" O GLN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 479 Processing helix chain 'G' and resid 500 through 507 Processing helix chain 'G' and resid 563 through 567 removed outlier: 3.726A pdb=" N LEU G 567 " --> pdb=" O ARG G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 601 Processing helix chain 'G' and resid 610 through 617 removed outlier: 4.180A pdb=" N SER G 614 " --> pdb=" O GLY G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 626 through 632 Processing helix chain 'G' and resid 711 through 715 Processing helix chain 'G' and resid 798 through 802 Processing helix chain 'G' and resid 830 through 834 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 7.286A pdb=" N ALA A 49 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 58 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 100 removed outlier: 4.159A pdb=" N ALA A 100 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 89 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 111 removed outlier: 8.208A pdb=" N MET B 134 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG B 67 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.930A pdb=" N VAL B 202 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR B 192 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP B 204 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 178 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE B 253 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR B 180 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 removed outlier: 3.667A pdb=" N VAL B 227 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.516A pdb=" N VAL G 227 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.967A pdb=" N THR B 298 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN B 309 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU B 324 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU B 313 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 315 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS B 320 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 393 through 399 removed outlier: 6.741A pdb=" N THR B 432 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG B 424 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 450 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 451 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N TYR B 495 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B 396 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 497 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 398 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 458 through 461 Processing sheet with id=AB4, first strand: chain 'B' and resid 517 through 521 removed outlier: 6.546A pdb=" N ASP B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL B 546 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 556 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N TYR B 624 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE B 573 " --> pdb=" O TYR B 624 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 587 through 590 removed outlier: 3.604A pdb=" N ALA B 579 " --> pdb=" O ALA C 592 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 581 " --> pdb=" O VAL C 590 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 635 through 641 removed outlier: 7.114A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 696 " --> pdb=" O GLN B 735 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 734 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS B 640 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 749 through 754 removed outlier: 6.922A pdb=" N MET B 789 " --> pdb=" O MET B 779 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET B 779 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 791 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 766 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE B 840 " --> pdb=" O PRO B 765 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 767 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE B 858 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 751 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU B 860 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU B 753 " --> pdb=" O LEU B 860 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 816 through 818 removed outlier: 4.477A pdb=" N ASP B 817 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 824 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 823 " --> pdb=" O PHE G 818 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE G 818 " --> pdb=" O GLY B 823 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 825 " --> pdb=" O LEU G 816 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU G 816 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP G 817 " --> pdb=" O VAL G 824 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL G 824 " --> pdb=" O ASP G 817 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL G 825 " --> pdb=" O LEU F 816 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU F 816 " --> pdb=" O VAL G 825 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP F 817 " --> pdb=" O VAL F 824 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL F 824 " --> pdb=" O ASP F 817 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY F 823 " --> pdb=" O PHE E 818 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL F 825 " --> pdb=" O LEU E 816 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU E 816 " --> pdb=" O VAL F 825 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP E 817 " --> pdb=" O VAL E 824 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL E 824 " --> pdb=" O ASP E 817 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL E 825 " --> pdb=" O LEU D 816 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 816 " --> pdb=" O VAL E 825 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP D 817 " --> pdb=" O VAL D 824 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL D 824 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 823 " --> pdb=" O PHE C 818 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 818 " --> pdb=" O GLY D 823 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D 825 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU C 816 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP C 817 " --> pdb=" O VAL C 824 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL C 824 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL C 825 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 816 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.928A pdb=" N MET C 134 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG C 67 " --> pdb=" O MET C 134 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N PHE C 145 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.931A pdb=" N VAL C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR C 192 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP C 204 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 178 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE C 253 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR C 180 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 227 through 230 removed outlier: 3.636A pdb=" N VAL C 227 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.967A pdb=" N THR C 298 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN C 309 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU C 324 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU C 313 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 322 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU C 315 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS C 320 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 413 removed outlier: 6.624A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 434 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG C 424 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 432 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 450 through 453 Processing sheet with id=AC6, first strand: chain 'C' and resid 458 through 461 Processing sheet with id=AC7, first strand: chain 'C' and resid 517 through 521 removed outlier: 6.546A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL C 532 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE C 605 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 534 " --> pdb=" O PHE C 605 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 635 through 641 removed outlier: 7.113A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE C 696 " --> pdb=" O GLN C 735 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU C 734 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS C 640 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 754 removed outlier: 6.923A pdb=" N MET C 789 " --> pdb=" O MET C 779 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET C 779 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 791 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 766 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE C 840 " --> pdb=" O PRO C 765 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU C 767 " --> pdb=" O PHE C 840 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE C 858 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE C 751 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU C 860 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU C 753 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.132A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.931A pdb=" N VAL D 202 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D 192 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP D 204 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU D 178 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE D 253 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR D 180 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 227 through 230 Processing sheet with id=AD4, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.967A pdb=" N THR D 298 " --> pdb=" O GLN D 309 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN D 309 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU D 324 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU D 313 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR D 322 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU D 315 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS D 320 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 393 through 399 removed outlier: 6.742A pdb=" N THR D 432 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG D 424 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 434 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D 481 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE D 451 " --> pdb=" O TYR D 498 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N TYR D 495 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR D 396 " --> pdb=" O TYR D 495 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU D 497 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR D 398 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 458 through 461 Processing sheet with id=AD7, first strand: chain 'D' and resid 517 through 521 removed outlier: 6.545A pdb=" N ASP D 554 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 546 " --> pdb=" O ASP D 554 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP D 556 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL D 532 " --> pdb=" O ILE D 603 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE D 605 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU D 534 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 587 through 590 removed outlier: 3.540A pdb=" N ALA D 579 " --> pdb=" O ALA E 592 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 581 " --> pdb=" O VAL E 590 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 590 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 635 through 641 removed outlier: 7.113A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE D 696 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU D 734 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS D 640 " --> pdb=" O LEU D 734 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 749 through 754 removed outlier: 6.922A pdb=" N MET D 789 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET D 779 " --> pdb=" O MET D 789 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA D 791 " --> pdb=" O THR D 777 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D 766 " --> pdb=" O VAL D 773 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE D 840 " --> pdb=" O PRO D 765 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU D 767 " --> pdb=" O PHE D 840 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE D 858 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE D 751 " --> pdb=" O PHE D 858 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU D 860 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU D 753 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 106 through 111 removed outlier: 7.606A pdb=" N MET E 134 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG E 67 " --> pdb=" O MET E 134 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N PHE E 145 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.931A pdb=" N VAL E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR E 192 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP E 204 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 178 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE E 253 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR E 180 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 227 through 230 removed outlier: 3.608A pdb=" N VAL E 227 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.967A pdb=" N THR E 298 " --> pdb=" O GLN E 309 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN E 309 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU E 324 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU E 313 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR E 322 " --> pdb=" O LEU E 313 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU E 315 " --> pdb=" O LYS E 320 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS E 320 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 410 through 413 removed outlier: 6.623A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 434 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG E 424 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR E 432 " --> pdb=" O ARG E 424 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 450 through 453 Processing sheet with id=AE8, first strand: chain 'E' and resid 458 through 461 Processing sheet with id=AE9, first strand: chain 'E' and resid 517 through 521 removed outlier: 6.545A pdb=" N ASP E 554 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL E 546 " --> pdb=" O ASP E 554 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP E 556 " --> pdb=" O ILE E 544 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 635 through 641 removed outlier: 7.113A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE E 696 " --> pdb=" O GLN E 735 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU E 734 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS E 640 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 749 through 754 removed outlier: 6.923A pdb=" N MET E 789 " --> pdb=" O MET E 779 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET E 779 " --> pdb=" O MET E 789 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA E 791 " --> pdb=" O THR E 777 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 766 " --> pdb=" O VAL E 773 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE E 840 " --> pdb=" O PRO E 765 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU E 767 " --> pdb=" O PHE E 840 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE E 858 " --> pdb=" O SER E 749 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 751 " --> pdb=" O PHE E 858 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU E 860 " --> pdb=" O ILE E 751 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU E 753 " --> pdb=" O LEU E 860 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 107 through 111 removed outlier: 7.598A pdb=" N MET F 134 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG F 67 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N PHE F 145 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.931A pdb=" N VAL F 202 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR F 192 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP F 204 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 178 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE F 253 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR F 180 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 227 through 230 Processing sheet with id=AF6, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.967A pdb=" N THR F 298 " --> pdb=" O GLN F 309 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN F 309 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU F 324 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU F 313 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR F 322 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU F 315 " --> pdb=" O LYS F 320 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS F 320 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 393 through 399 removed outlier: 6.742A pdb=" N THR F 432 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG F 424 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR F 434 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE F 481 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS F 450 " --> pdb=" O LEU F 484 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE F 451 " --> pdb=" O TYR F 498 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N TYR F 495 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR F 396 " --> pdb=" O TYR F 495 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU F 497 " --> pdb=" O THR F 396 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR F 398 " --> pdb=" O LEU F 497 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 458 through 461 Processing sheet with id=AF9, first strand: chain 'F' and resid 517 through 521 removed outlier: 6.546A pdb=" N ASP F 554 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL F 546 " --> pdb=" O ASP F 554 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP F 556 " --> pdb=" O ILE F 544 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 587 through 590 Processing sheet with id=AG2, first strand: chain 'F' and resid 635 through 641 removed outlier: 7.113A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE F 696 " --> pdb=" O GLN F 735 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU F 734 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS F 640 " --> pdb=" O LEU F 734 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 749 through 754 removed outlier: 6.922A pdb=" N MET F 789 " --> pdb=" O MET F 779 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET F 779 " --> pdb=" O MET F 789 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA F 791 " --> pdb=" O THR F 777 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F 766 " --> pdb=" O VAL F 773 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE F 840 " --> pdb=" O PRO F 765 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU F 767 " --> pdb=" O PHE F 840 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE F 858 " --> pdb=" O SER F 749 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE F 751 " --> pdb=" O PHE F 858 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU F 860 " --> pdb=" O ILE F 751 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU F 753 " --> pdb=" O LEU F 860 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 106 through 111 removed outlier: 7.840A pdb=" N MET G 134 " --> pdb=" O PRO G 65 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG G 67 " --> pdb=" O MET G 134 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL G 66 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS G 91 " --> pdb=" O GLN G 77 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE G 79 " --> pdb=" O GLU G 89 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU G 89 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 161 through 167 removed outlier: 6.931A pdb=" N VAL G 202 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR G 192 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP G 204 " --> pdb=" O TYR G 190 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL G 179 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU G 178 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE G 253 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR G 180 " --> pdb=" O PHE G 253 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE G 221 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 340 through 344 removed outlier: 6.967A pdb=" N THR G 298 " --> pdb=" O GLN G 309 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN G 309 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU G 300 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU G 324 " --> pdb=" O THR G 311 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU G 313 " --> pdb=" O THR G 322 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR G 322 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU G 315 " --> pdb=" O LYS G 320 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS G 320 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE G 377 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS G 284 " --> pdb=" O PHE G 377 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 393 through 399 removed outlier: 6.742A pdb=" N THR G 432 " --> pdb=" O ARG G 424 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG G 424 " --> pdb=" O THR G 432 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR G 434 " --> pdb=" O ILE G 422 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU G 411 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE G 483 " --> pdb=" O PRO G 410 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE G 412 " --> pdb=" O ILE G 483 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE G 451 " --> pdb=" O TYR G 498 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N TYR G 495 " --> pdb=" O THR G 394 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR G 396 " --> pdb=" O TYR G 495 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU G 497 " --> pdb=" O THR G 396 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR G 398 " --> pdb=" O LEU G 497 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 458 through 461 Processing sheet with id=AG9, first strand: chain 'G' and resid 517 through 521 removed outlier: 6.545A pdb=" N ASP G 554 " --> pdb=" O VAL G 546 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL G 546 " --> pdb=" O ASP G 554 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP G 556 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL G 533 " --> pdb=" O VAL G 540 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL G 532 " --> pdb=" O ILE G 603 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE G 605 " --> pdb=" O VAL G 532 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU G 534 " --> pdb=" O PHE G 605 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 635 through 641 removed outlier: 7.113A pdb=" N GLN G 676 " --> pdb=" O LEU G 666 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU G 666 " --> pdb=" O GLN G 676 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS G 678 " --> pdb=" O GLN G 664 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE G 653 " --> pdb=" O ILE G 660 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE G 696 " --> pdb=" O GLN G 735 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N PHE G 732 " --> pdb=" O GLN G 636 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR G 638 " --> pdb=" O PHE G 732 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU G 734 " --> pdb=" O THR G 638 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS G 640 " --> pdb=" O LEU G 734 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 749 through 754 removed outlier: 6.921A pdb=" N MET G 789 " --> pdb=" O MET G 779 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET G 779 " --> pdb=" O MET G 789 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA G 791 " --> pdb=" O THR G 777 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G 766 " --> pdb=" O VAL G 773 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE G 840 " --> pdb=" O PRO G 765 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU G 767 " --> pdb=" O PHE G 840 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE G 808 " --> pdb=" O GLN G 861 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE G 858 " --> pdb=" O SER G 749 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE G 751 " --> pdb=" O PHE G 858 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU G 860 " --> pdb=" O ILE G 751 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU G 753 " --> pdb=" O LEU G 860 " (cutoff:3.500A) 1423 hydrogen bonds defined for protein. 3477 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: 10.90 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10535 1.33 - 1.45: 7471 1.45 - 1.57: 24393 1.57 - 1.69: 0 1.69 - 1.81: 193 Bond restraints: 42592 Sorted by residual: bond pdb=" C GLY E 129 " pdb=" N ASN E 130 " ideal model delta sigma weight residual 1.330 1.502 -0.172 1.38e-02 5.25e+03 1.56e+02 bond pdb=" C GLU F 576 " pdb=" N GLY F 577 " ideal model delta sigma weight residual 1.331 1.494 -0.163 1.46e-02 4.69e+03 1.25e+02 bond pdb=" C PHE G 605 " pdb=" N ASP G 606 " ideal model delta sigma weight residual 1.332 1.473 -0.141 1.37e-02 5.33e+03 1.06e+02 bond pdb=" C GLY B 129 " pdb=" N ASN B 130 " ideal model delta sigma weight residual 1.331 1.452 -0.121 1.33e-02 5.65e+03 8.26e+01 bond pdb=" C GLU D 576 " pdb=" N GLY D 577 " ideal model delta sigma weight residual 1.331 1.211 0.119 1.46e-02 4.69e+03 6.65e+01 ... (remaining 42587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 57392 2.51 - 5.01: 377 5.01 - 7.52: 39 7.52 - 10.02: 10 10.02 - 12.53: 7 Bond angle restraints: 57825 Sorted by residual: angle pdb=" O GLY E 129 " pdb=" C GLY E 129 " pdb=" N ASN E 130 " ideal model delta sigma weight residual 122.77 135.30 -12.53 9.50e-01 1.11e+00 1.74e+02 angle pdb=" CA GLY D 129 " pdb=" C GLY D 129 " pdb=" N ASN D 130 " ideal model delta sigma weight residual 114.88 103.28 11.60 1.20e+00 6.94e-01 9.35e+01 angle pdb=" O GLU C 576 " pdb=" C GLU C 576 " pdb=" N GLY C 577 " ideal model delta sigma weight residual 122.59 110.22 12.37 1.33e+00 5.65e-01 8.65e+01 angle pdb=" O GLY D 129 " pdb=" C GLY D 129 " pdb=" N ASN D 130 " ideal model delta sigma weight residual 122.78 133.73 -10.95 1.18e+00 7.18e-01 8.61e+01 angle pdb=" C GLY D 129 " pdb=" N ASN D 130 " pdb=" CA ASN D 130 " ideal model delta sigma weight residual 120.87 108.46 12.41 1.42e+00 4.96e-01 7.64e+01 ... (remaining 57820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.45: 23855 11.45 - 22.90: 1245 22.90 - 34.35: 380 34.35 - 45.80: 81 45.80 - 57.25: 20 Dihedral angle restraints: 25581 sinusoidal: 10084 harmonic: 15497 Sorted by residual: dihedral pdb=" CA GLU F 576 " pdb=" C GLU F 576 " pdb=" N GLY F 577 " pdb=" CA GLY F 577 " ideal model delta harmonic sigma weight residual 180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLU D 576 " pdb=" C GLU D 576 " pdb=" N GLY D 577 " pdb=" CA GLY D 577 " ideal model delta harmonic sigma weight residual -180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLU B 576 " pdb=" C GLU B 576 " pdb=" N GLY B 577 " pdb=" CA GLY B 577 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 25578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3994 0.028 - 0.056: 1549 0.056 - 0.084: 464 0.084 - 0.112: 451 0.112 - 0.140: 224 Chirality restraints: 6682 Sorted by residual: chirality pdb=" CA ILE D 653 " pdb=" N ILE D 653 " pdb=" C ILE D 653 " pdb=" CB ILE D 653 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE E 653 " pdb=" N ILE E 653 " pdb=" C ILE E 653 " pdb=" CB ILE E 653 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE G 653 " pdb=" N ILE G 653 " pdb=" C ILE G 653 " pdb=" CB ILE G 653 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 6679 not shown) Planarity restraints: 7484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 576 " -0.063 2.00e-02 2.50e+03 1.16e-01 1.35e+02 pdb=" C GLU C 576 " 0.202 2.00e-02 2.50e+03 pdb=" O GLU C 576 " -0.072 2.00e-02 2.50e+03 pdb=" N GLY C 577 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 576 " 0.053 2.00e-02 2.50e+03 1.10e-01 1.20e+02 pdb=" C GLU D 576 " -0.189 2.00e-02 2.50e+03 pdb=" O GLU D 576 " 0.070 2.00e-02 2.50e+03 pdb=" N GLY D 577 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 576 " 0.054 2.00e-02 2.50e+03 1.05e-01 1.11e+02 pdb=" C GLU F 576 " -0.182 2.00e-02 2.50e+03 pdb=" O GLU F 576 " 0.073 2.00e-02 2.50e+03 pdb=" N GLY F 577 " 0.055 2.00e-02 2.50e+03 ... (remaining 7481 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 22197 3.02 - 3.49: 37804 3.49 - 3.96: 65103 3.96 - 4.43: 71520 4.43 - 4.90: 121568 Nonbonded interactions: 318192 Sorted by model distance: nonbonded pdb=" O GLU C 576 " pdb=" CA GLY C 577 " model vdw 2.545 2.752 nonbonded pdb=" O THR F 50 " pdb=" N PHE F 145 " model vdw 2.556 3.120 nonbonded pdb=" CB GLU E 576 " pdb=" N GLY E 577 " model vdw 2.566 2.816 nonbonded pdb=" N SER G 531 " pdb=" OG SER G 531 " model vdw 2.582 2.496 nonbonded pdb=" N SER D 531 " pdb=" OG SER D 531 " model vdw 2.582 2.496 ... (remaining 318187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 46 through 877) selection = (chain 'C' and resid 46 through 877) selection = (chain 'D' and resid 46 through 877) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 46 through 877) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 40.500 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 42600 Z= 0.169 Angle : 0.531 12.527 57837 Z= 0.302 Chirality : 0.044 0.140 6682 Planarity : 0.005 0.116 7484 Dihedral : 8.122 57.249 15693 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 0.82 % Allowed : 3.24 % Favored : 95.94 % 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 aren not related in a simple way. whole: -0.74 (0.11), residues: 5464 helix: -0.02 (0.18), residues: 848 sheet: -0.07 (0.13), residues: 1605 loop : -0.82 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 597 TYR 0.013 0.001 TYR C 131 PHE 0.015 0.001 PHE B 605 TRP 0.007 0.001 TRP F 574 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00258 (42592) covalent geometry : angle 0.53068 (57825) hydrogen bonds : bond 0.16242 ( 1423) hydrogen bonds : angle 6.02721 ( 3477) metal coordination : bond 0.00409 ( 8) metal coordination : angle 1.99823 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1104 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8359 (mmt) cc_final: 0.8096 (mmt) REVERT: B 359 LEU cc_start: 0.9003 (mt) cc_final: 0.8718 (mp) REVERT: B 411 LEU cc_start: 0.8948 (mp) cc_final: 0.8645 (mp) REVERT: B 543 VAL cc_start: 0.6627 (t) cc_final: 0.6060 (t) REVERT: B 642 PHE cc_start: 0.8236 (m-80) cc_final: 0.7900 (m-80) REVERT: B 678 LYS cc_start: 0.8651 (mttt) cc_final: 0.8199 (mmtt) REVERT: B 697 SER cc_start: 0.9152 (t) cc_final: 0.8844 (p) REVERT: B 777 THR cc_start: 0.8951 (m) cc_final: 0.8625 (p) REVERT: C 36 TRP cc_start: 0.8412 (t-100) cc_final: 0.8158 (t-100) REVERT: C 38 ILE cc_start: 0.8717 (mm) cc_final: 0.8466 (mt) REVERT: C 42 TYR cc_start: 0.7428 (t80) cc_final: 0.6783 (t80) REVERT: C 63 ARG cc_start: 0.6343 (ptt90) cc_final: 0.5830 (ptm-80) REVERT: C 145 PHE cc_start: 0.6948 (m-80) cc_final: 0.6674 (m-80) REVERT: C 356 SER cc_start: 0.8478 (m) cc_final: 0.8164 (p) REVERT: C 524 LEU cc_start: 0.8597 (tp) cc_final: 0.8397 (mt) REVERT: C 777 THR cc_start: 0.9045 (m) cc_final: 0.8835 (p) REVERT: C 779 MET cc_start: 0.8453 (mtp) cc_final: 0.8155 (mtt) REVERT: D 297 SER cc_start: 0.8510 (m) cc_final: 0.8270 (t) REVERT: D 355 LEU cc_start: 0.8194 (mp) cc_final: 0.7811 (mp) REVERT: D 456 ARG cc_start: 0.7329 (mtt180) cc_final: 0.5553 (mmp-170) REVERT: D 476 TRP cc_start: 0.5083 (t60) cc_final: 0.4828 (t60) REVERT: E 190 TYR cc_start: 0.8762 (t80) cc_final: 0.8526 (t80) REVERT: E 354 ASN cc_start: 0.7723 (m-40) cc_final: 0.7281 (p0) REVERT: E 452 VAL cc_start: 0.8595 (t) cc_final: 0.8375 (t) REVERT: E 749 SER cc_start: 0.8079 (p) cc_final: 0.7812 (t) REVERT: E 779 MET cc_start: 0.7942 (mtp) cc_final: 0.7571 (mtm) REVERT: F 91 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7961 (mmtt) REVERT: F 246 LEU cc_start: 0.8411 (tt) cc_final: 0.8018 (mt) REVERT: F 355 LEU cc_start: 0.8334 (mp) cc_final: 0.8087 (pt) REVERT: G 40 ASP cc_start: 0.7265 (t0) cc_final: 0.6975 (m-30) REVERT: G 49 VAL cc_start: 0.8979 (t) cc_final: 0.8425 (p) REVERT: G 87 LYS cc_start: 0.7471 (mttm) cc_final: 0.7054 (mmtt) REVERT: G 106 THR cc_start: 0.8415 (m) cc_final: 0.7919 (p) REVERT: G 162 MET cc_start: 0.8777 (tpp) cc_final: 0.8402 (tpp) outliers start: 37 outliers final: 7 residues processed: 1121 average time/residue: 0.2365 time to fit residues: 427.3122 Evaluate side-chains 602 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 595 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 531 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 0.5980 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS A 379 ASN B 43 GLN B 151 GLN B 454 ASN C 174 ASN C 636 GLN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 ASN E 151 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 ASN E 582 GLN F 166 GLN F 174 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 ASN F 528 GLN F 702 GLN F 832 GLN G 43 GLN G 151 GLN G 454 ASN ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103846 restraints weight = 67034.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104182 restraints weight = 39217.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105063 restraints weight = 28990.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.105557 restraints weight = 26177.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.105571 restraints weight = 23259.645| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 42600 Z= 0.274 Angle : 0.656 9.134 57837 Z= 0.339 Chirality : 0.050 0.298 6682 Planarity : 0.005 0.064 7484 Dihedral : 4.547 43.207 5893 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.00 % Allowed : 8.86 % Favored : 88.14 % 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 aren not related in a simple way. whole: -0.67 (0.11), residues: 5464 helix: -0.17 (0.18), residues: 880 sheet: 0.23 (0.13), residues: 1510 loop : -0.85 (0.11), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 30 TYR 0.022 0.002 TYR F 302 PHE 0.025 0.002 PHE B 553 TRP 0.013 0.002 TRP A 84 HIS 0.007 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00659 (42592) covalent geometry : angle 0.65350 (57825) hydrogen bonds : bond 0.04076 ( 1423) hydrogen bonds : angle 5.57596 ( 3477) metal coordination : bond 0.01991 ( 8) metal coordination : angle 4.23922 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 601 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8402 (p0) cc_final: 0.7880 (p0) REVERT: B 92 VAL cc_start: 0.9233 (t) cc_final: 0.8989 (m) REVERT: B 105 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8321 (mt-10) REVERT: B 114 LYS cc_start: 0.7233 (ptpp) cc_final: 0.6778 (mmtt) REVERT: B 297 SER cc_start: 0.9103 (m) cc_final: 0.8783 (t) REVERT: B 591 GLN cc_start: 0.7923 (mt0) cc_final: 0.7376 (mp10) REVERT: B 627 GLU cc_start: 0.7753 (tm-30) cc_final: 0.6868 (tp30) REVERT: B 631 ARG cc_start: 0.9138 (mmt180) cc_final: 0.8799 (mtt-85) REVERT: B 678 LYS cc_start: 0.7991 (mttt) cc_final: 0.7414 (mmtt) REVERT: B 764 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 777 THR cc_start: 0.9116 (m) cc_final: 0.8792 (p) REVERT: C 38 ILE cc_start: 0.8827 (mm) cc_final: 0.8615 (mt) REVERT: C 42 TYR cc_start: 0.7680 (t80) cc_final: 0.7209 (t80) REVERT: C 63 ARG cc_start: 0.6900 (ptt90) cc_final: 0.6385 (ptm-80) REVERT: C 162 MET cc_start: 0.8782 (tpp) cc_final: 0.8452 (tpp) REVERT: C 354 ASN cc_start: 0.8457 (t0) cc_final: 0.8025 (t0) REVERT: C 356 SER cc_start: 0.8372 (m) cc_final: 0.7936 (p) REVERT: C 702 GLN cc_start: 0.8026 (mt0) cc_final: 0.7787 (mm-40) REVERT: D 456 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7088 (mmp-170) REVERT: D 591 GLN cc_start: 0.8166 (mt0) cc_final: 0.7486 (mp10) REVERT: E 107 GLN cc_start: 0.8320 (mt0) cc_final: 0.7996 (mp10) REVERT: E 273 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: E 491 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7841 (tpt) REVERT: E 580 LYS cc_start: 0.7999 (mppt) cc_final: 0.7600 (mmtm) REVERT: E 662 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: E 749 SER cc_start: 0.8399 (p) cc_final: 0.8153 (t) REVERT: E 764 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.9019 (m) REVERT: F 626 SER cc_start: 0.9095 (t) cc_final: 0.8736 (p) REVERT: F 678 LYS cc_start: 0.8576 (mttt) cc_final: 0.8276 (mmtt) REVERT: G 40 ASP cc_start: 0.7322 (t0) cc_final: 0.7082 (m-30) REVERT: G 87 LYS cc_start: 0.7643 (mttm) cc_final: 0.7218 (mmtt) REVERT: G 796 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8720 (ttpp) outliers start: 135 outliers final: 67 residues processed: 707 average time/residue: 0.2314 time to fit residues: 267.6305 Evaluate side-chains 565 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 492 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 527 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 582 GLN Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 662 GLN Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 733 GLU Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 528 GLN Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 751 ILE Chi-restraints excluded: chain F residue 797 ARG Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 796 LYS Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 225 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 512 optimal weight: 10.0000 chunk 251 optimal weight: 0.8980 chunk 467 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 311 optimal weight: 0.6980 chunk 506 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 186 GLN C 664 GLN D 47 ASN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 GLN D 805 ASN E 582 GLN F 702 GLN G 664 GLN G 673 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106479 restraints weight = 66796.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106218 restraints weight = 37337.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106814 restraints weight = 28811.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107258 restraints weight = 26361.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107384 restraints weight = 23533.098| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42600 Z= 0.125 Angle : 0.532 10.273 57837 Z= 0.271 Chirality : 0.046 0.179 6682 Planarity : 0.004 0.056 7484 Dihedral : 4.234 44.071 5891 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.04 % Allowed : 10.95 % Favored : 87.01 % 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 aren not related in a simple way. whole: -0.55 (0.11), residues: 5464 helix: 0.02 (0.18), residues: 869 sheet: 0.29 (0.13), residues: 1548 loop : -0.80 (0.11), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.015 0.001 TYR A 50 PHE 0.017 0.001 PHE G 28 TRP 0.009 0.001 TRP D 222 HIS 0.002 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00288 (42592) covalent geometry : angle 0.53040 (57825) hydrogen bonds : bond 0.03247 ( 1423) hydrogen bonds : angle 5.25531 ( 3477) metal coordination : bond 0.00905 ( 8) metal coordination : angle 2.79768 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 541 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8317 (p0) cc_final: 0.7899 (p0) REVERT: B 114 LYS cc_start: 0.7357 (ptpp) cc_final: 0.6938 (mmtt) REVERT: B 355 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8350 (pt) REVERT: B 411 LEU cc_start: 0.9215 (mp) cc_final: 0.8844 (mp) REVERT: B 542 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6996 (tp30) REVERT: B 553 PHE cc_start: 0.8141 (m-80) cc_final: 0.7888 (m-80) REVERT: B 627 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7224 (tp30) REVERT: B 678 LYS cc_start: 0.7974 (mttt) cc_final: 0.7416 (mmtt) REVERT: B 777 THR cc_start: 0.9111 (m) cc_final: 0.8851 (p) REVERT: B 805 ASN cc_start: 0.8948 (p0) cc_final: 0.8574 (p0) REVERT: C 38 ILE cc_start: 0.8791 (mm) cc_final: 0.8566 (mt) REVERT: C 42 TYR cc_start: 0.7613 (t80) cc_final: 0.7163 (t80) REVERT: C 63 ARG cc_start: 0.6893 (ptt90) cc_final: 0.6515 (ptm-80) REVERT: C 162 MET cc_start: 0.8809 (tpp) cc_final: 0.8399 (tpp) REVERT: C 354 ASN cc_start: 0.8466 (t0) cc_final: 0.8002 (t0) REVERT: C 356 SER cc_start: 0.8415 (m) cc_final: 0.7936 (p) REVERT: C 524 LEU cc_start: 0.8728 (tt) cc_final: 0.8482 (mt) REVERT: C 702 GLN cc_start: 0.8073 (mt0) cc_final: 0.7817 (mm-40) REVERT: D 99 LYS cc_start: 0.8565 (tmmt) cc_final: 0.8315 (tmmt) REVERT: D 456 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7283 (mmp-170) REVERT: D 591 GLN cc_start: 0.8142 (mt0) cc_final: 0.7538 (mp10) REVERT: E 107 GLN cc_start: 0.8290 (mt0) cc_final: 0.8053 (mp10) REVERT: E 273 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: E 491 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7910 (tpt) REVERT: E 580 LYS cc_start: 0.8020 (mppt) cc_final: 0.7716 (mmtm) REVERT: E 748 LEU cc_start: 0.8645 (mt) cc_final: 0.8423 (tp) REVERT: F 54 MET cc_start: 0.8742 (tpp) cc_final: 0.8492 (tpp) REVERT: F 156 LEU cc_start: 0.8883 (mm) cc_final: 0.8634 (mm) REVERT: F 544 ILE cc_start: 0.9242 (mt) cc_final: 0.8899 (mm) REVERT: F 626 SER cc_start: 0.9044 (t) cc_final: 0.8626 (p) REVERT: F 678 LYS cc_start: 0.8531 (mttt) cc_final: 0.8302 (mmtt) REVERT: G 40 ASP cc_start: 0.7257 (t0) cc_final: 0.7046 (m-30) REVERT: G 91 LYS cc_start: 0.8313 (mtpp) cc_final: 0.8041 (mttm) REVERT: G 106 THR cc_start: 0.8757 (m) cc_final: 0.8258 (p) REVERT: G 756 GLU cc_start: 0.8262 (tt0) cc_final: 0.7856 (pt0) REVERT: G 796 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8762 (ttpp) outliers start: 92 outliers final: 62 residues processed: 600 average time/residue: 0.2255 time to fit residues: 221.3401 Evaluate side-chains 545 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 479 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 527 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 582 GLN Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 797 ARG Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 599 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 796 LYS Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 515 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 514 optimal weight: 0.7980 chunk 348 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 384 optimal weight: 7.9990 chunk 343 optimal weight: 0.0870 chunk 365 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 503 optimal weight: 9.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS A 379 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 528 GLN F 702 GLN F 857 HIS G 673 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100985 restraints weight = 66536.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100741 restraints weight = 36540.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101234 restraints weight = 30237.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101635 restraints weight = 27175.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.101836 restraints weight = 24252.712| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 42600 Z= 0.248 Angle : 0.617 10.852 57837 Z= 0.318 Chirality : 0.049 0.216 6682 Planarity : 0.004 0.057 7484 Dihedral : 4.706 38.262 5890 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.98 % Allowed : 10.79 % Favored : 86.23 % 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 aren not related in a simple way. whole: -0.68 (0.11), residues: 5464 helix: -0.23 (0.18), residues: 869 sheet: 0.28 (0.13), residues: 1582 loop : -0.90 (0.11), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 631 TYR 0.016 0.002 TYR A 50 PHE 0.026 0.002 PHE E 605 TRP 0.014 0.001 TRP D 222 HIS 0.005 0.001 HIS E 388 Details of bonding type rmsd covalent geometry : bond 0.00578 (42592) covalent geometry : angle 0.61457 (57825) hydrogen bonds : bond 0.03957 ( 1423) hydrogen bonds : angle 5.51848 ( 3477) metal coordination : bond 0.01811 ( 8) metal coordination : angle 4.03777 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 499 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8443 (p0) cc_final: 0.7884 (p0) REVERT: B 98 MET cc_start: 0.8272 (mmm) cc_final: 0.7857 (mmm) REVERT: B 355 LEU cc_start: 0.8580 (mt) cc_final: 0.8364 (pt) REVERT: B 542 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7403 (tp30) REVERT: B 553 PHE cc_start: 0.8304 (m-80) cc_final: 0.8041 (m-80) REVERT: B 642 PHE cc_start: 0.8297 (m-80) cc_final: 0.8055 (m-80) REVERT: B 678 LYS cc_start: 0.7942 (mttt) cc_final: 0.7349 (mmtt) REVERT: B 764 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8598 (m) REVERT: B 777 THR cc_start: 0.9117 (m) cc_final: 0.8843 (p) REVERT: B 805 ASN cc_start: 0.8974 (p0) cc_final: 0.8497 (p0) REVERT: B 835 ARG cc_start: 0.7579 (ptt90) cc_final: 0.7293 (ptt90) REVERT: C 38 ILE cc_start: 0.8867 (mm) cc_final: 0.8654 (mt) REVERT: C 42 TYR cc_start: 0.7697 (t80) cc_final: 0.7296 (t80) REVERT: C 124 ASP cc_start: 0.8910 (p0) cc_final: 0.8652 (p0) REVERT: C 134 MET cc_start: 0.8751 (ttp) cc_final: 0.8415 (ptm) REVERT: C 142 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8036 (tp-100) REVERT: C 162 MET cc_start: 0.8772 (tpp) cc_final: 0.8466 (tpp) REVERT: C 247 VAL cc_start: 0.8887 (p) cc_final: 0.8638 (t) REVERT: C 354 ASN cc_start: 0.8459 (t0) cc_final: 0.8167 (t0) REVERT: C 524 LEU cc_start: 0.8851 (tt) cc_final: 0.8594 (mt) REVERT: C 702 GLN cc_start: 0.8033 (mt0) cc_final: 0.7822 (mm-40) REVERT: C 743 ARG cc_start: 0.8344 (ptt180) cc_final: 0.7965 (ptt180) REVERT: C 777 THR cc_start: 0.9225 (m) cc_final: 0.8933 (p) REVERT: D 99 LYS cc_start: 0.8507 (tmmt) cc_final: 0.8243 (tmmt) REVERT: D 456 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7237 (mmp-170) REVERT: D 591 GLN cc_start: 0.8149 (mt0) cc_final: 0.7505 (mp10) REVERT: D 792 MET cc_start: 0.9450 (ptp) cc_final: 0.9185 (ptm) REVERT: E 107 GLN cc_start: 0.8305 (mt0) cc_final: 0.7996 (mp10) REVERT: E 580 LYS cc_start: 0.8056 (mppt) cc_final: 0.7814 (mmtm) REVERT: E 662 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: E 764 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.8992 (m) REVERT: F 54 MET cc_start: 0.8753 (tpp) cc_final: 0.8435 (tpp) REVERT: F 156 LEU cc_start: 0.8941 (mm) cc_final: 0.8726 (mm) REVERT: F 626 SER cc_start: 0.9127 (t) cc_final: 0.8712 (p) REVERT: F 678 LYS cc_start: 0.8764 (mttt) cc_final: 0.8399 (mmtt) REVERT: G 40 ASP cc_start: 0.7434 (t0) cc_final: 0.7159 (m-30) REVERT: G 580 LYS cc_start: 0.8342 (mttp) cc_final: 0.8110 (mttm) REVERT: G 756 GLU cc_start: 0.8442 (tt0) cc_final: 0.8016 (pt0) outliers start: 134 outliers final: 94 residues processed: 594 average time/residue: 0.2660 time to fit residues: 259.1033 Evaluate side-chains 551 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 453 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain E residue 527 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 662 GLN Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 733 GLU Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 528 GLN Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 660 ILE Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 797 ARG Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 514 THR Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 202 optimal weight: 4.9990 chunk 416 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 519 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 495 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 GLN G 673 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101259 restraints weight = 67633.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.100985 restraints weight = 36760.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101492 restraints weight = 30638.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.101915 restraints weight = 27354.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102104 restraints weight = 24817.320| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 42600 Z= 0.165 Angle : 0.557 11.199 57837 Z= 0.283 Chirality : 0.046 0.195 6682 Planarity : 0.004 0.046 7484 Dihedral : 4.462 36.009 5889 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.35 % Allowed : 12.59 % Favored : 85.05 % 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 aren not related in a simple way. whole: -0.62 (0.11), residues: 5464 helix: -0.11 (0.18), residues: 851 sheet: 0.35 (0.13), residues: 1563 loop : -0.90 (0.11), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 729 TYR 0.010 0.001 TYR B 131 PHE 0.021 0.001 PHE E 605 TRP 0.012 0.001 TRP D 222 HIS 0.003 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00388 (42592) covalent geometry : angle 0.55466 (57825) hydrogen bonds : bond 0.03373 ( 1423) hydrogen bonds : angle 5.35050 ( 3477) metal coordination : bond 0.01311 ( 8) metal coordination : angle 3.20854 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 485 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8233 (p0) REVERT: A 297 ASP cc_start: 0.8410 (p0) cc_final: 0.7943 (p0) REVERT: B 98 MET cc_start: 0.8255 (mmm) cc_final: 0.7864 (mmm) REVERT: B 114 LYS cc_start: 0.7569 (ptpp) cc_final: 0.6838 (mmtt) REVERT: B 642 PHE cc_start: 0.8244 (m-80) cc_final: 0.8016 (m-80) REVERT: B 678 LYS cc_start: 0.7939 (mttt) cc_final: 0.7357 (mmtt) REVERT: B 764 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8570 (m) REVERT: B 777 THR cc_start: 0.9089 (m) cc_final: 0.8840 (p) REVERT: B 805 ASN cc_start: 0.8983 (p0) cc_final: 0.8647 (p0) REVERT: B 835 ARG cc_start: 0.7621 (ptt90) cc_final: 0.7319 (ptt90) REVERT: C 38 ILE cc_start: 0.8835 (mm) cc_final: 0.8628 (mt) REVERT: C 42 TYR cc_start: 0.7666 (t80) cc_final: 0.7372 (t80) REVERT: C 124 ASP cc_start: 0.8911 (p0) cc_final: 0.8653 (p0) REVERT: C 142 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8010 (tp-100) REVERT: C 247 VAL cc_start: 0.8909 (p) cc_final: 0.8658 (t) REVERT: C 354 ASN cc_start: 0.8454 (t0) cc_final: 0.8189 (t0) REVERT: C 524 LEU cc_start: 0.8826 (tt) cc_final: 0.8614 (mt) REVERT: C 678 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8576 (mmmm) REVERT: C 702 GLN cc_start: 0.8051 (mt0) cc_final: 0.7821 (mm-40) REVERT: C 777 THR cc_start: 0.9196 (m) cc_final: 0.8944 (p) REVERT: D 99 LYS cc_start: 0.8517 (tmmt) cc_final: 0.8262 (tmmt) REVERT: D 108 PHE cc_start: 0.8619 (m-80) cc_final: 0.8371 (m-80) REVERT: D 297 SER cc_start: 0.8806 (m) cc_final: 0.8556 (t) REVERT: D 456 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7270 (mmp-170) REVERT: D 792 MET cc_start: 0.9394 (ptp) cc_final: 0.9165 (ptm) REVERT: E 107 GLN cc_start: 0.8337 (mt0) cc_final: 0.8100 (mp10) REVERT: E 524 LEU cc_start: 0.8959 (mt) cc_final: 0.8278 (tt) REVERT: E 580 LYS cc_start: 0.8112 (mppt) cc_final: 0.7883 (mmtm) REVERT: E 662 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: E 697 SER cc_start: 0.9321 (t) cc_final: 0.8594 (p) REVERT: E 764 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8977 (m) REVERT: F 54 MET cc_start: 0.8769 (tpp) cc_final: 0.8451 (tpp) REVERT: F 347 LYS cc_start: 0.7411 (mppt) cc_final: 0.7097 (mppt) REVERT: F 501 LEU cc_start: 0.9120 (mp) cc_final: 0.8917 (mt) REVERT: F 544 ILE cc_start: 0.9109 (mp) cc_final: 0.8834 (mm) REVERT: F 626 SER cc_start: 0.9106 (t) cc_final: 0.8637 (p) REVERT: F 678 LYS cc_start: 0.8756 (mttt) cc_final: 0.8392 (mmtt) REVERT: F 702 GLN cc_start: 0.7954 (mt0) cc_final: 0.7645 (mm-40) REVERT: G 40 ASP cc_start: 0.7379 (t0) cc_final: 0.7098 (m-30) REVERT: G 580 LYS cc_start: 0.8371 (mttp) cc_final: 0.8147 (mttm) outliers start: 106 outliers final: 87 residues processed: 570 average time/residue: 0.2629 time to fit residues: 246.7825 Evaluate side-chains 551 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 459 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 731 ASP Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain E residue 527 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 662 GLN Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 660 ILE Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 764 THR Chi-restraints excluded: chain F residue 797 ARG Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 168 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 487 optimal weight: 0.0000 chunk 536 optimal weight: 9.9990 chunk 479 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 461 optimal weight: 0.9990 chunk 310 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN D 799 GLN F 151 GLN F 309 GLN G 673 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104283 restraints weight = 67166.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104211 restraints weight = 36269.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104833 restraints weight = 28740.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.105248 restraints weight = 26120.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105363 restraints weight = 23523.434| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 42600 Z= 0.105 Angle : 0.518 10.142 57837 Z= 0.263 Chirality : 0.045 0.177 6682 Planarity : 0.003 0.045 7484 Dihedral : 4.149 30.949 5888 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.11 % Allowed : 13.19 % Favored : 84.70 % 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 aren not related in a simple way. whole: -0.51 (0.11), residues: 5464 helix: 0.04 (0.18), residues: 846 sheet: 0.40 (0.13), residues: 1581 loop : -0.84 (0.11), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 631 TYR 0.021 0.001 TYR F 154 PHE 0.019 0.001 PHE E 605 TRP 0.019 0.001 TRP A 415 HIS 0.003 0.000 HIS B 558 Details of bonding type rmsd covalent geometry : bond 0.00240 (42592) covalent geometry : angle 0.51619 (57825) hydrogen bonds : bond 0.02956 ( 1423) hydrogen bonds : angle 5.13764 ( 3477) metal coordination : bond 0.00655 ( 8) metal coordination : angle 2.75568 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 499 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8517 (tptm) cc_final: 0.8267 (tptm) REVERT: A 60 ASP cc_start: 0.7773 (m-30) cc_final: 0.7303 (m-30) REVERT: A 297 ASP cc_start: 0.8303 (p0) cc_final: 0.7854 (p0) REVERT: B 98 MET cc_start: 0.8233 (mmm) cc_final: 0.7864 (mmm) REVERT: B 114 LYS cc_start: 0.7670 (ptpp) cc_final: 0.6937 (mmtt) REVERT: B 591 GLN cc_start: 0.8010 (mt0) cc_final: 0.7528 (mp10) REVERT: B 642 PHE cc_start: 0.8246 (m-80) cc_final: 0.8035 (m-80) REVERT: B 678 LYS cc_start: 0.7955 (mttt) cc_final: 0.7318 (mmtt) REVERT: B 764 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8439 (m) REVERT: B 805 ASN cc_start: 0.9005 (p0) cc_final: 0.8597 (p0) REVERT: B 835 ARG cc_start: 0.7596 (ptt90) cc_final: 0.7265 (ptt90) REVERT: C 38 ILE cc_start: 0.8834 (mm) cc_final: 0.8592 (mt) REVERT: C 42 TYR cc_start: 0.7664 (t80) cc_final: 0.7144 (t80) REVERT: C 63 ARG cc_start: 0.7375 (ptt90) cc_final: 0.6604 (ptm-80) REVERT: C 124 ASP cc_start: 0.8866 (p0) cc_final: 0.8573 (p0) REVERT: C 138 LYS cc_start: 0.8087 (mttt) cc_final: 0.7842 (mmtm) REVERT: C 247 VAL cc_start: 0.8902 (p) cc_final: 0.8650 (t) REVERT: C 678 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8534 (mmmm) REVERT: C 702 GLN cc_start: 0.8041 (mt0) cc_final: 0.7802 (mm-40) REVERT: C 759 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7821 (t) REVERT: C 777 THR cc_start: 0.9170 (m) cc_final: 0.8825 (p) REVERT: D 99 LYS cc_start: 0.8424 (tmmt) cc_final: 0.8180 (tmmt) REVERT: D 456 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7278 (mmp-170) REVERT: E 107 GLN cc_start: 0.8295 (mt0) cc_final: 0.8074 (mp10) REVERT: E 524 LEU cc_start: 0.9053 (mt) cc_final: 0.8389 (tt) REVERT: E 697 SER cc_start: 0.9314 (t) cc_final: 0.8614 (p) REVERT: E 764 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8885 (m) REVERT: F 54 MET cc_start: 0.8744 (tpp) cc_final: 0.8434 (tpp) REVERT: F 134 MET cc_start: 0.8832 (ttt) cc_final: 0.8532 (ttt) REVERT: F 273 ASP cc_start: 0.7726 (m-30) cc_final: 0.7479 (m-30) REVERT: F 626 SER cc_start: 0.8989 (t) cc_final: 0.8533 (p) REVERT: F 678 LYS cc_start: 0.8733 (mttt) cc_final: 0.8380 (mmtt) REVERT: F 702 GLN cc_start: 0.7963 (mt0) cc_final: 0.7612 (mm-40) REVERT: F 756 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: G 580 LYS cc_start: 0.8317 (mttp) cc_final: 0.8099 (mttm) outliers start: 95 outliers final: 69 residues processed: 570 average time/residue: 0.2630 time to fit residues: 247.4580 Evaluate side-chains 529 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 456 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 731 ASP Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 527 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 660 ILE Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 797 ARG Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 371 optimal weight: 4.9990 chunk 304 optimal weight: 0.6980 chunk 509 optimal weight: 9.9990 chunk 67 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 253 optimal weight: 30.0000 chunk 322 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 446 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102212 restraints weight = 67418.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102223 restraints weight = 36180.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102633 restraints weight = 29880.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103027 restraints weight = 26918.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103235 restraints weight = 24385.652| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 42600 Z= 0.152 Angle : 0.544 11.242 57837 Z= 0.277 Chirality : 0.046 0.191 6682 Planarity : 0.004 0.040 7484 Dihedral : 4.239 30.648 5888 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.51 % Allowed : 13.06 % Favored : 84.43 % 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 aren not related in a simple way. whole: -0.50 (0.11), residues: 5464 helix: 0.01 (0.18), residues: 845 sheet: 0.40 (0.13), residues: 1587 loop : -0.82 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 631 TYR 0.011 0.001 TYR A 28 PHE 0.018 0.001 PHE E 605 TRP 0.008 0.001 TRP D 222 HIS 0.004 0.001 HIS B 558 Details of bonding type rmsd covalent geometry : bond 0.00359 (42592) covalent geometry : angle 0.54189 (57825) hydrogen bonds : bond 0.03223 ( 1423) hydrogen bonds : angle 5.18315 ( 3477) metal coordination : bond 0.00977 ( 8) metal coordination : angle 3.59374 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 468 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.7378 (mtp) cc_final: 0.6495 (ttm) REVERT: A 57 LYS cc_start: 0.8615 (tptm) cc_final: 0.8189 (tptm) REVERT: A 60 ASP cc_start: 0.7685 (m-30) cc_final: 0.7056 (m-30) REVERT: A 101 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 297 ASP cc_start: 0.8381 (p0) cc_final: 0.7918 (p0) REVERT: B 98 MET cc_start: 0.8307 (mmm) cc_final: 0.7934 (mmm) REVERT: B 114 LYS cc_start: 0.7649 (ptpp) cc_final: 0.6888 (mmtt) REVERT: B 678 LYS cc_start: 0.7967 (mttt) cc_final: 0.7332 (mmtt) REVERT: B 764 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8491 (m) REVERT: B 805 ASN cc_start: 0.9007 (p0) cc_final: 0.8590 (p0) REVERT: B 835 ARG cc_start: 0.7615 (ptt90) cc_final: 0.7288 (ptt90) REVERT: C 38 ILE cc_start: 0.8860 (mm) cc_final: 0.8635 (mt) REVERT: C 42 TYR cc_start: 0.7682 (t80) cc_final: 0.7156 (t80) REVERT: C 124 ASP cc_start: 0.8883 (p0) cc_final: 0.8592 (p0) REVERT: C 138 LYS cc_start: 0.8179 (mttt) cc_final: 0.7955 (mmtm) REVERT: C 142 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8046 (tp-100) REVERT: C 247 VAL cc_start: 0.8910 (p) cc_final: 0.8648 (t) REVERT: C 532 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8226 (p) REVERT: C 678 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8554 (mmmm) REVERT: C 702 GLN cc_start: 0.8048 (mt0) cc_final: 0.7827 (mm-40) REVERT: C 742 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8615 (t) REVERT: C 759 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7830 (t) REVERT: C 777 THR cc_start: 0.9190 (m) cc_final: 0.8859 (p) REVERT: D 99 LYS cc_start: 0.8435 (tmmt) cc_final: 0.8170 (tmmt) REVERT: D 456 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7279 (mmp-170) REVERT: E 98 MET cc_start: 0.6662 (mpp) cc_final: 0.5825 (tpt) REVERT: E 107 GLN cc_start: 0.8307 (mt0) cc_final: 0.8095 (mp10) REVERT: E 524 LEU cc_start: 0.9100 (mt) cc_final: 0.8418 (tt) REVERT: E 697 SER cc_start: 0.9321 (t) cc_final: 0.8612 (p) REVERT: E 764 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8921 (m) REVERT: F 54 MET cc_start: 0.8745 (tpp) cc_final: 0.8430 (tpp) REVERT: F 134 MET cc_start: 0.8808 (ttt) cc_final: 0.8565 (ttt) REVERT: F 273 ASP cc_start: 0.7812 (m-30) cc_final: 0.7566 (m-30) REVERT: F 626 SER cc_start: 0.9003 (t) cc_final: 0.8552 (p) REVERT: F 678 LYS cc_start: 0.8765 (mttt) cc_final: 0.8401 (mmtt) REVERT: F 702 GLN cc_start: 0.7961 (mt0) cc_final: 0.7640 (mm-40) REVERT: F 756 GLU cc_start: 0.8544 (tt0) cc_final: 0.8269 (pt0) REVERT: G 580 LYS cc_start: 0.8355 (mttp) cc_final: 0.8147 (mttm) outliers start: 113 outliers final: 87 residues processed: 553 average time/residue: 0.2459 time to fit residues: 224.4697 Evaluate side-chains 548 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 454 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 731 ASP Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 527 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 660 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 797 ARG Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 764 THR Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 52 optimal weight: 2.9990 chunk 355 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 chunk 425 optimal weight: 9.9990 chunk 75 optimal weight: 0.0070 chunk 478 optimal weight: 4.9990 chunk 455 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 395 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN C 107 GLN ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 GLN G 43 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103796 restraints weight = 67644.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103690 restraints weight = 36310.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104267 restraints weight = 29189.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104693 restraints weight = 26533.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.104936 restraints weight = 23809.555| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 42600 Z= 0.099 Angle : 0.519 11.035 57837 Z= 0.262 Chirality : 0.045 0.188 6682 Planarity : 0.003 0.044 7484 Dihedral : 4.015 27.632 5888 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.95 % Allowed : 13.84 % Favored : 84.21 % 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 aren not related in a simple way. whole: -0.44 (0.11), residues: 5464 helix: 0.10 (0.18), residues: 841 sheet: 0.43 (0.13), residues: 1588 loop : -0.77 (0.11), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 631 TYR 0.018 0.001 TYR A 50 PHE 0.022 0.001 PHE C 553 TRP 0.010 0.001 TRP G 868 HIS 0.003 0.000 HIS B 558 Details of bonding type rmsd covalent geometry : bond 0.00227 (42592) covalent geometry : angle 0.51758 (57825) hydrogen bonds : bond 0.02827 ( 1423) hydrogen bonds : angle 5.03416 ( 3477) metal coordination : bond 0.00560 ( 8) metal coordination : angle 2.75404 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 480 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6670 (OUTLIER) cc_final: 0.6419 (t80) REVERT: A 57 LYS cc_start: 0.8457 (tptm) cc_final: 0.8179 (tptm) REVERT: A 59 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7830 (tpp-160) REVERT: A 60 ASP cc_start: 0.7681 (m-30) cc_final: 0.7207 (m-30) REVERT: A 101 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7920 (p0) REVERT: A 213 LEU cc_start: 0.9087 (mp) cc_final: 0.8865 (mp) REVERT: A 297 ASP cc_start: 0.8252 (p0) cc_final: 0.7817 (p0) REVERT: B 98 MET cc_start: 0.8170 (mmm) cc_final: 0.7860 (mmm) REVERT: B 114 LYS cc_start: 0.7590 (ptpp) cc_final: 0.6841 (mmtt) REVERT: B 359 LEU cc_start: 0.9138 (mp) cc_final: 0.8826 (mp) REVERT: B 678 LYS cc_start: 0.7969 (mttt) cc_final: 0.7331 (mmtt) REVERT: B 764 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8406 (m) REVERT: B 805 ASN cc_start: 0.9008 (p0) cc_final: 0.8620 (p0) REVERT: B 835 ARG cc_start: 0.7576 (ptt90) cc_final: 0.7219 (ptt90) REVERT: C 38 ILE cc_start: 0.8806 (mm) cc_final: 0.8587 (mt) REVERT: C 42 TYR cc_start: 0.7649 (t80) cc_final: 0.7109 (t80) REVERT: C 63 ARG cc_start: 0.7484 (ptt90) cc_final: 0.6608 (ptm-80) REVERT: C 78 ASP cc_start: 0.8871 (t0) cc_final: 0.8596 (t70) REVERT: C 124 ASP cc_start: 0.8847 (p0) cc_final: 0.8557 (p0) REVERT: C 247 VAL cc_start: 0.8894 (p) cc_final: 0.8639 (t) REVERT: C 476 TRP cc_start: 0.8062 (t60) cc_final: 0.7845 (t60) REVERT: C 532 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 678 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8564 (mmmm) REVERT: C 702 GLN cc_start: 0.8057 (mt0) cc_final: 0.7831 (mm-40) REVERT: C 756 GLU cc_start: 0.8882 (pt0) cc_final: 0.8457 (pt0) REVERT: C 759 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7821 (t) REVERT: C 777 THR cc_start: 0.9134 (m) cc_final: 0.8868 (p) REVERT: D 99 LYS cc_start: 0.8408 (tmmt) cc_final: 0.8156 (tmmt) REVERT: D 297 SER cc_start: 0.8741 (m) cc_final: 0.8488 (t) REVERT: D 456 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7280 (mmp-170) REVERT: E 98 MET cc_start: 0.6692 (mpp) cc_final: 0.5884 (tpt) REVERT: E 524 LEU cc_start: 0.9063 (mt) cc_final: 0.8439 (tt) REVERT: E 697 SER cc_start: 0.9264 (t) cc_final: 0.8564 (p) REVERT: E 764 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8863 (m) REVERT: F 54 MET cc_start: 0.8758 (tpp) cc_final: 0.8407 (tpp) REVERT: F 273 ASP cc_start: 0.7711 (m-30) cc_final: 0.7468 (m-30) REVERT: F 678 LYS cc_start: 0.8740 (mttt) cc_final: 0.8392 (mmtt) REVERT: F 702 GLN cc_start: 0.7936 (mt0) cc_final: 0.7626 (mm-40) REVERT: F 756 GLU cc_start: 0.8505 (tt0) cc_final: 0.8253 (pt0) REVERT: G 580 LYS cc_start: 0.8303 (mttp) cc_final: 0.8098 (mttm) outliers start: 88 outliers final: 68 residues processed: 545 average time/residue: 0.2624 time to fit residues: 236.0760 Evaluate side-chains 529 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 455 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 731 ASP Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 429 LYS Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 660 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 2 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 537 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 327 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 GLN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS D 799 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101053 restraints weight = 67076.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100932 restraints weight = 36013.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101437 restraints weight = 29155.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101835 restraints weight = 26804.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101980 restraints weight = 23955.451| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 42600 Z= 0.203 Angle : 0.587 11.216 57837 Z= 0.299 Chirality : 0.048 0.276 6682 Planarity : 0.004 0.037 7484 Dihedral : 4.389 31.933 5887 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.18 % Allowed : 13.61 % Favored : 84.21 % 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 aren not related in a simple way. whole: -0.53 (0.11), residues: 5464 helix: 0.04 (0.18), residues: 846 sheet: 0.36 (0.13), residues: 1586 loop : -0.84 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 63 TYR 0.014 0.001 TYR A 50 PHE 0.020 0.002 PHE C 553 TRP 0.009 0.001 TRP D 222 HIS 0.004 0.001 HIS B 558 Details of bonding type rmsd covalent geometry : bond 0.00482 (42592) covalent geometry : angle 0.58466 (57825) hydrogen bonds : bond 0.03498 ( 1423) hydrogen bonds : angle 5.24247 ( 3477) metal coordination : bond 0.01372 ( 8) metal coordination : angle 3.80948 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 481 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7962 (tpp-160) REVERT: A 60 ASP cc_start: 0.7685 (m-30) cc_final: 0.7085 (m-30) REVERT: A 101 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8357 (p0) REVERT: A 297 ASP cc_start: 0.8408 (p0) cc_final: 0.7918 (p0) REVERT: B 98 MET cc_start: 0.8380 (mmm) cc_final: 0.7901 (mmm) REVERT: B 99 LYS cc_start: 0.8093 (tttt) cc_final: 0.7597 (tptt) REVERT: B 114 LYS cc_start: 0.7798 (ptpp) cc_final: 0.6987 (mmtt) REVERT: B 359 LEU cc_start: 0.9153 (mp) cc_final: 0.8844 (mp) REVERT: B 591 GLN cc_start: 0.7979 (mt0) cc_final: 0.7507 (pt0) REVERT: B 678 LYS cc_start: 0.7985 (mttt) cc_final: 0.7346 (mmtt) REVERT: B 764 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 805 ASN cc_start: 0.9025 (p0) cc_final: 0.8613 (p0) REVERT: B 835 ARG cc_start: 0.7625 (ptt90) cc_final: 0.7289 (ptt90) REVERT: C 38 ILE cc_start: 0.8884 (mm) cc_final: 0.8631 (mt) REVERT: C 42 TYR cc_start: 0.7663 (t80) cc_final: 0.7124 (t80) REVERT: C 78 ASP cc_start: 0.8889 (t0) cc_final: 0.8593 (t70) REVERT: C 124 ASP cc_start: 0.8873 (p0) cc_final: 0.8584 (p0) REVERT: C 142 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8067 (tp-100) REVERT: C 247 VAL cc_start: 0.8924 (p) cc_final: 0.8692 (t) REVERT: C 678 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8567 (mmmm) REVERT: C 702 GLN cc_start: 0.7958 (mt0) cc_final: 0.7756 (mm-40) REVERT: C 742 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8642 (t) REVERT: C 756 GLU cc_start: 0.8978 (pt0) cc_final: 0.8613 (pt0) REVERT: C 759 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7915 (t) REVERT: C 777 THR cc_start: 0.9118 (m) cc_final: 0.8890 (p) REVERT: C 792 MET cc_start: 0.8700 (ptt) cc_final: 0.8320 (ptt) REVERT: D 99 LYS cc_start: 0.8443 (tmmt) cc_final: 0.8187 (tmmt) REVERT: D 342 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: D 456 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7205 (mmp-170) REVERT: E 98 MET cc_start: 0.6729 (mpp) cc_final: 0.5917 (tpt) REVERT: E 524 LEU cc_start: 0.9157 (mt) cc_final: 0.8495 (tt) REVERT: E 697 SER cc_start: 0.9327 (t) cc_final: 0.8639 (p) REVERT: E 764 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.8988 (m) REVERT: F 54 MET cc_start: 0.8679 (tpp) cc_final: 0.8328 (tpp) REVERT: F 135 MET cc_start: 0.7428 (tpp) cc_final: 0.7087 (tpp) REVERT: F 273 ASP cc_start: 0.7858 (m-30) cc_final: 0.7616 (m-30) REVERT: F 626 SER cc_start: 0.8965 (t) cc_final: 0.8635 (p) REVERT: F 678 LYS cc_start: 0.8742 (mttt) cc_final: 0.8345 (mmtt) REVERT: F 756 GLU cc_start: 0.8559 (tt0) cc_final: 0.8306 (pt0) REVERT: G 580 LYS cc_start: 0.8346 (mttp) cc_final: 0.8133 (mttm) outliers start: 98 outliers final: 79 residues processed: 554 average time/residue: 0.2644 time to fit residues: 239.9868 Evaluate side-chains 540 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 454 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 660 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 539 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 486 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 236 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 393 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 454 ASN D 799 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104897 restraints weight = 67435.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104899 restraints weight = 35736.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105373 restraints weight = 28994.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105810 restraints weight = 26219.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105983 restraints weight = 23460.984| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42600 Z= 0.112 Angle : 0.546 11.680 57837 Z= 0.275 Chirality : 0.046 0.312 6682 Planarity : 0.003 0.037 7484 Dihedral : 4.132 27.488 5887 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.71 % Allowed : 14.23 % Favored : 84.06 % 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 aren not related in a simple way. whole: -0.45 (0.11), residues: 5464 helix: 0.08 (0.19), residues: 842 sheet: 0.45 (0.13), residues: 1590 loop : -0.80 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 725 TYR 0.014 0.001 TYR A 28 PHE 0.019 0.001 PHE C 553 TRP 0.012 0.001 TRP G 868 HIS 0.004 0.000 HIS B 558 Details of bonding type rmsd covalent geometry : bond 0.00259 (42592) covalent geometry : angle 0.54444 (57825) hydrogen bonds : bond 0.02949 ( 1423) hydrogen bonds : angle 5.08749 ( 3477) metal coordination : bond 0.00800 ( 8) metal coordination : angle 2.81626 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10928 Ramachandran restraints generated. 5464 Oldfield, 0 Emsley, 5464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 478 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8583 (tptm) cc_final: 0.8208 (tptp) REVERT: A 79 LEU cc_start: 0.9147 (tp) cc_final: 0.8915 (tt) REVERT: A 101 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8009 (p0) REVERT: A 213 LEU cc_start: 0.9087 (mp) cc_final: 0.8885 (mp) REVERT: A 297 ASP cc_start: 0.8278 (p0) cc_final: 0.7826 (p0) REVERT: B 98 MET cc_start: 0.8364 (mmm) cc_final: 0.7831 (mmm) REVERT: B 99 LYS cc_start: 0.8081 (tttt) cc_final: 0.7567 (tptt) REVERT: B 114 LYS cc_start: 0.7722 (ptpp) cc_final: 0.6974 (mmtt) REVERT: B 359 LEU cc_start: 0.9151 (mp) cc_final: 0.8863 (mp) REVERT: B 591 GLN cc_start: 0.7973 (mt0) cc_final: 0.7499 (pt0) REVERT: B 678 LYS cc_start: 0.7963 (mttt) cc_final: 0.7293 (mmtt) REVERT: B 764 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8401 (m) REVERT: B 805 ASN cc_start: 0.9014 (p0) cc_final: 0.8649 (p0) REVERT: B 835 ARG cc_start: 0.7594 (ptt90) cc_final: 0.7235 (ptt90) REVERT: C 38 ILE cc_start: 0.8826 (mm) cc_final: 0.8584 (mt) REVERT: C 42 TYR cc_start: 0.7615 (t80) cc_final: 0.7090 (t80) REVERT: C 78 ASP cc_start: 0.8861 (t0) cc_final: 0.8583 (t70) REVERT: C 124 ASP cc_start: 0.8830 (p0) cc_final: 0.8527 (p0) REVERT: C 247 VAL cc_start: 0.8881 (p) cc_final: 0.8655 (t) REVERT: C 678 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8532 (mmmm) REVERT: C 702 GLN cc_start: 0.7963 (mt0) cc_final: 0.7723 (mm-40) REVERT: C 756 GLU cc_start: 0.8953 (pt0) cc_final: 0.8584 (pt0) REVERT: C 759 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7889 (t) REVERT: C 777 THR cc_start: 0.9168 (m) cc_final: 0.8913 (p) REVERT: D 99 LYS cc_start: 0.8409 (tmmt) cc_final: 0.8199 (tmmt) REVERT: D 297 SER cc_start: 0.8785 (m) cc_final: 0.8520 (t) REVERT: D 342 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: D 456 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7236 (mmp-170) REVERT: E 98 MET cc_start: 0.6694 (mpp) cc_final: 0.5917 (tpt) REVERT: E 524 LEU cc_start: 0.9094 (mt) cc_final: 0.8476 (tt) REVERT: E 697 SER cc_start: 0.9289 (t) cc_final: 0.8592 (p) REVERT: E 764 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8909 (m) REVERT: F 54 MET cc_start: 0.8652 (tpp) cc_final: 0.8349 (tpp) REVERT: F 135 MET cc_start: 0.7330 (tpp) cc_final: 0.6961 (tpp) REVERT: F 273 ASP cc_start: 0.7728 (m-30) cc_final: 0.7495 (m-30) REVERT: F 678 LYS cc_start: 0.8724 (mttt) cc_final: 0.8337 (mmtt) REVERT: F 756 GLU cc_start: 0.8525 (tt0) cc_final: 0.8289 (pt0) REVERT: G 867 GLU cc_start: 0.8044 (pm20) cc_final: 0.7782 (pm20) outliers start: 77 outliers final: 64 residues processed: 534 average time/residue: 0.2645 time to fit residues: 231.8340 Evaluate side-chains 525 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 456 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 558 HIS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 672 ARG Chi-restraints excluded: chain D residue 816 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 660 ILE Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 759 SER Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 797 ARG Chi-restraints excluded: chain G residue 810 LEU Chi-restraints excluded: chain G residue 864 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 424 optimal weight: 10.0000 chunk 486 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 387 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 461 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 ASN F 636 GLN ** G 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095229 restraints weight = 68370.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.095654 restraints weight = 37326.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096471 restraints weight = 27234.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.096969 restraints weight = 26611.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.096902 restraints weight = 23158.680| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 42600 Z= 0.408 Angle : 0.753 10.827 57837 Z= 0.385 Chirality : 0.054 0.318 6682 Planarity : 0.005 0.055 7484 Dihedral : 5.118 29.565 5887 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.07 % Allowed : 14.04 % Favored : 83.90 % 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 aren not related in a simple way. whole: -0.84 (0.11), residues: 5464 helix: -0.32 (0.18), residues: 852 sheet: 0.09 (0.13), residues: 1646 loop : -0.98 (0.11), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 63 TYR 0.024 0.002 TYR A 138 PHE 0.029 0.003 PHE F 211 TRP 0.015 0.002 TRP C 222 HIS 0.006 0.002 HIS G 414 Details of bonding type rmsd covalent geometry : bond 0.00970 (42592) covalent geometry : angle 0.74946 (57825) hydrogen bonds : bond 0.04522 ( 1423) hydrogen bonds : angle 5.76058 ( 3477) metal coordination : bond 0.02716 ( 8) metal coordination : angle 4.99187 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7352.64 seconds wall clock time: 127 minutes 39.44 seconds (7659.44 seconds total)