Starting phenix.real_space_refine on Tue Aug 26 11:34:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkd_19275/08_2025/8rkd_19275_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkd_19275/08_2025/8rkd_19275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rkd_19275/08_2025/8rkd_19275_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkd_19275/08_2025/8rkd_19275_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rkd_19275/08_2025/8rkd_19275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkd_19275/08_2025/8rkd_19275.map" } resolution = 3.8 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= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 2 5.21 5 S 106 5.16 5 C 11496 2.51 5 N 3430 2.21 5 O 3568 1.98 5 H 17582 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 36198 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 5838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 5838 Classifications: {'peptide': 411} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 6061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6061 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6084 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 5838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 5838 Classifications: {'peptide': 411} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 6061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6061 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6084 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.99, per 1000 atoms: 0.19 Number of scatterers: 36198 At special positions: 0 Unit cell: (147.4, 137.5, 95.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 106 16.00 P 14 15.00 Mg 2 11.99 O 3568 8.00 N 3430 7.00 C 11496 6.00 H 17582 1.00 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: 3.43 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 22 sheets defined 44.2% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'E' and resid 81 through 97 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.909A pdb=" N ARG E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.357A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 263 through 273 Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 337 through 346 removed outlier: 4.252A pdb=" N ASN E 344 " --> pdb=" O ASP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 372 removed outlier: 3.597A pdb=" N LEU E 366 " --> pdb=" O GLU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.709A pdb=" N GLY E 400 " --> pdb=" O MET E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 488 Processing helix chain 'E' and resid 489 through 502 removed outlier: 3.512A pdb=" N ASP E 498 " --> pdb=" O ALA E 494 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA E 499 " --> pdb=" O GLU E 495 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU E 501 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA E 502 " --> pdb=" O ASP E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 102 Processing helix chain 'F' and resid 106 through 125 Processing helix chain 'F' and resid 130 through 147 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 156 removed outlier: 4.136A pdb=" N ALA F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 200 Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 260 through 274 removed outlier: 6.508A pdb=" N VAL F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU F 267 " --> pdb=" O GLY F 263 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 337 through 346 removed outlier: 3.680A pdb=" N ASN F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 removed outlier: 3.956A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 399 Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 479 through 484 removed outlier: 4.412A pdb=" N ARG F 483 " --> pdb=" O ARG F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 Processing helix chain 'A' and resid 81 through 97 removed outlier: 4.630A pdb=" N LYS A 86 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 106 through 125 removed outlier: 4.154A pdb=" N GLU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.755A pdb=" N ALA A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.726A pdb=" N ALA A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.678A pdb=" N ALA A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.620A pdb=" N LEU A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 4.144A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.669A pdb=" N GLY A 400 " --> pdb=" O MET A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 106 through 125 removed outlier: 4.004A pdb=" N ARG B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.365A pdb=" N LEU B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 337 through 346 removed outlier: 4.251A pdb=" N ASN B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.613A pdb=" N LEU B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.693A pdb=" N GLY B 400 " --> pdb=" O MET B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 489 through 502 removed outlier: 3.503A pdb=" N ASP B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 502 " --> pdb=" O ASP B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 106 through 125 Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 156 removed outlier: 4.128A pdb=" N ALA C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 260 through 274 removed outlier: 6.498A pdb=" N VAL C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 337 through 346 removed outlier: 3.764A pdb=" N ASN C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 3.964A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 399 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 479 through 484 removed outlier: 4.438A pdb=" N ARG C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'D' and resid 81 through 97 removed outlier: 4.706A pdb=" N LYS D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 106 through 125 removed outlier: 4.136A pdb=" N GLU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 157 removed outlier: 3.749A pdb=" N ALA D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 removed outlier: 3.722A pdb=" N ALA D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.670A pdb=" N ALA D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 346 removed outlier: 3.622A pdb=" N LEU D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.146A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 removed outlier: 3.670A pdb=" N GLY D 400 " --> pdb=" O MET D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 499 Processing sheet with id=AA1, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.674A pdb=" N ARG E 170 " --> pdb=" O ASN E 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU E 174 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP E 162 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 378 through 380 removed outlier: 3.603A pdb=" N GLY E 379 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 436 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 448 " --> pdb=" O VAL E 440 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 320 through 324 removed outlier: 5.995A pdb=" N VAL E 304 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU E 323 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR E 306 " --> pdb=" O LEU E 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 354 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 178 through 181 removed outlier: 3.991A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 320 through 322 removed outlier: 4.054A pdb=" N THR F 380 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY F 379 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR F 437 " --> pdb=" O ILE F 420 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 422 " --> pdb=" O HIS F 435 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS F 435 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'F' and resid 453 through 460 removed outlier: 3.679A pdb=" N VAL F 454 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL F 467 " --> pdb=" O THR F 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 182 removed outlier: 4.775A pdb=" N VAL A 171 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 277 through 281 removed outlier: 3.751A pdb=" N HIS A 435 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 424 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE A 433 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR A 434 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 454 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 436 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 448 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU A 442 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.926A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 305 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 456 through 460 removed outlier: 7.070A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.678A pdb=" N ARG B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 174 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.609A pdb=" N GLY B 379 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 436 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 448 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.018A pdb=" N VAL B 304 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU B 323 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR B 306 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.001A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 320 through 322 removed outlier: 6.553A pdb=" N VAL C 305 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR C 380 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU C 277 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU C 381 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 279 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR C 437 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 422 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS C 435 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AB9, first strand: chain 'C' and resid 453 through 460 removed outlier: 3.721A pdb=" N VAL C 454 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL C 467 " --> pdb=" O THR C 458 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 179 through 181 removed outlier: 4.173A pdb=" N ASP D 162 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 277 through 281 removed outlier: 3.752A pdb=" N HIS D 435 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA D 424 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 433 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR D 434 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL D 454 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE D 436 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL D 448 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU D 442 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.928A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 305 " --> pdb=" O ARG D 352 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 456 through 460 removed outlier: 7.073A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2559 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: 8.94 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17546 1.03 - 1.23: 38 1.23 - 1.42: 7394 1.42 - 1.61: 11280 1.61 - 1.81: 180 Bond restraints: 36438 Sorted by residual: bond pdb=" N ASP A 80 " pdb=" H1 ASP A 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ASP D 80 " pdb=" H1 ASP D 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASP E 80 " pdb=" H1 ASP E 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASP F 80 " pdb=" H1 ASP F 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASP B 80 " pdb=" H1 ASP B 80 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 36433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.31: 65642 10.31 - 20.62: 6 20.62 - 30.93: 12 30.93 - 41.24: 0 41.24 - 51.55: 12 Bond angle restraints: 65672 Sorted by residual: angle pdb=" C GLU E 312 " pdb=" N LEU E 313 " pdb=" H LEU E 313 " ideal model delta sigma weight residual 123.66 72.11 51.55 3.00e+00 1.11e-01 2.95e+02 angle pdb=" C GLU B 312 " pdb=" N LEU B 313 " pdb=" H LEU B 313 " ideal model delta sigma weight residual 123.68 72.15 51.53 3.00e+00 1.11e-01 2.95e+02 angle pdb=" CA LEU B 313 " pdb=" N LEU B 313 " pdb=" H LEU B 313 " ideal model delta sigma weight residual 113.38 62.98 50.40 3.00e+00 1.11e-01 2.82e+02 angle pdb=" CA LEU E 313 " pdb=" N LEU E 313 " pdb=" H LEU E 313 " ideal model delta sigma weight residual 113.36 63.03 50.33 3.00e+00 1.11e-01 2.81e+02 angle pdb=" C LYS B 242 " pdb=" N PHE B 243 " pdb=" H PHE B 243 " ideal model delta sigma weight residual 124.17 74.54 49.63 3.00e+00 1.11e-01 2.74e+02 ... (remaining 65667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 16269 22.22 - 44.45: 619 44.45 - 66.67: 254 66.67 - 88.90: 48 88.90 - 111.12: 6 Dihedral angle restraints: 17196 sinusoidal: 9498 harmonic: 7698 Sorted by residual: dihedral pdb=" CA HIS C 435 " pdb=" C HIS C 435 " pdb=" N ILE C 436 " pdb=" CA ILE C 436 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA HIS F 435 " pdb=" C HIS F 435 " pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta harmonic sigma weight residual 180.00 153.25 26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" C2' ADP B 702 " pdb=" C1' ADP B 702 " pdb=" N9 ADP B 702 " pdb=" C4 ADP B 702 " ideal model delta sinusoidal sigma weight residual 91.55 -173.20 -95.25 1 2.00e+01 2.50e-03 2.62e+01 ... (remaining 17193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1967 0.029 - 0.058: 578 0.058 - 0.087: 195 0.087 - 0.116: 231 0.116 - 0.145: 69 Chirality restraints: 3040 Sorted by residual: chirality pdb=" CA ILE F 475 " pdb=" N ILE F 475 " pdb=" C ILE F 475 " pdb=" CB ILE F 475 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE A 436 " pdb=" N ILE A 436 " pdb=" C ILE A 436 " pdb=" CB ILE A 436 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE D 436 " pdb=" N ILE D 436 " pdb=" C ILE D 436 " pdb=" CB ILE D 436 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 3037 not shown) Planarity restraints: 5728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 152 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO E 153 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 153 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 153 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 152 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO B 153 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 229 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 230 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.019 5.00e-02 4.00e+02 ... (remaining 5725 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 333 2.05 - 2.69: 55195 2.69 - 3.33: 100282 3.33 - 3.96: 122414 3.96 - 4.60: 192963 Nonbonded interactions: 471187 Sorted by model distance: nonbonded pdb=" H LEU E 313 " pdb=" HA LEU E 313 " model vdw 1.414 1.816 nonbonded pdb=" H LEU B 313 " pdb=" HA LEU B 313 " model vdw 1.415 1.816 nonbonded pdb=" OE1 GLU A 490 " pdb=" H GLU A 490 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU D 490 " pdb=" H GLU D 490 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASP C 208 " pdb=" H SER C 210 " model vdw 1.613 2.450 ... (remaining 471182 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 80 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O )) or resid 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) o \ r (resid 170 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or resid 171 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 188 through \ 243 or (resid 244 through 245 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name CE or name NZ )) or resid 246 through 256 or \ (resid 257 and (name N or name CA or name C or name O or name CB )) or (resid 25 \ 8 and (name N or name CA or name C or name O or name CB or name OG )) or (resid \ 259 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2 or name CD1)) or (resid 260 and (name N or name CA or name C or name O or name \ CB or name OG )) or resid 261 through 281 or resid 287 through 311 or (resid 31 \ 2 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name OE2)) or resid 313 through 425 or resid 433 through 473 or (re \ sid 474 and (name N or name CA or name C or name O )) or resid 475 through 502)) \ selection = (chain 'B' and (resid 80 through 244 or (resid 245 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 246 through 444 or (resid 445 and (name N or name CA or name C or name O or nam \ e CB or name CG or name OD1 or name OD2 or name H or name HA )) or resid 446 thr \ ough 469 or (resid 470 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 471 through \ 502)) selection = (chain 'C' and (resid 80 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O )) or resid 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) o \ r (resid 170 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or resid 171 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 188 through \ 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or ( \ resid 258 and (name N or name CA or name C or name O or name CB or name OG )) or \ (resid 259 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2 or name CD1)) or (resid 260 and (name N or name CA or name C or name O \ or name CB or name OG )) or resid 261 through 281 or resid 287 through 311 or ( \ resid 312 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or resid 313 through 381 or (resid 382 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 383 through 425 or resid 433 through 444 or \ (resid 445 and (name N or name CA or name C or name O or name CB or name CG or n \ ame OD1 or name OD2 or name H or name HA )) or resid 446 through 469 or (resid 4 \ 70 and (name N or name CA or name C or name O or name CB or name CG or name ND1 \ or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 \ or name HD1 or name HD2 or name HE1)) or resid 471 through 502)) selection = (chain 'D' and (resid 80 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O )) or resid 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) o \ r (resid 170 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or resid 171 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 188 through \ 243 or (resid 244 through 245 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name CE or name NZ )) or resid 246 through 256 or \ (resid 257 and (name N or name CA or name C or name O or name CB )) or (resid 25 \ 8 and (name N or name CA or name C or name O or name CB or name OG )) or (resid \ 259 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2 or name CD1)) or (resid 260 and (name N or name CA or name C or name O or name \ CB or name OG )) or resid 261 through 281 or resid 287 through 311 or (resid 31 \ 2 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name OE2)) or resid 313 through 425 or resid 433 through 473 or (re \ sid 474 and (name N or name CA or name C or name O )) or resid 475 through 502)) \ selection = (chain 'E' and (resid 80 through 244 or (resid 245 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 246 through 444 or (resid 445 and (name N or name CA or name C or name O or nam \ e CB or name CG or name OD1 or name OD2 or name H or name HA )) or resid 446 thr \ ough 469 or (resid 470 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 471 through \ 502)) selection = (chain 'F' and (resid 80 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O )) or resid 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) o \ r (resid 170 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or resid 171 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 188 through \ 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or ( \ resid 258 and (name N or name CA or name C or name O or name CB or name OG )) or \ (resid 259 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2 or name CD1)) or (resid 260 and (name N or name CA or name C or name O \ or name CB or name OG )) or resid 261 through 281 or resid 287 through 311 or ( \ resid 312 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or resid 313 through 381 or (resid 382 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 383 through 425 or resid 433 through 444 or \ (resid 445 and (name N or name CA or name C or name O or name CB or name CG or n \ ame OD1 or name OD2 or name H or name HA )) or resid 446 through 469 or (resid 4 \ 70 and (name N or name CA or name C or name O or name CB or name CG or name ND1 \ or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 \ or name HD1 or name HD2 or name HE1)) or resid 471 through 502)) } 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: 2.330 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: 0.160 Extract box with map and model: 0.400 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.340 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 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 : 0.002 0.031 18856 Z= 0.107 Angle : 0.593 19.963 25620 Z= 0.311 Chirality : 0.044 0.145 3040 Planarity : 0.003 0.037 3360 Dihedral : 12.065 111.122 6960 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.81 % Allowed : 3.83 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.18), residues: 2494 helix: 1.30 (0.18), residues: 950 sheet: -1.95 (0.21), residues: 522 loop : -1.16 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 322 TYR 0.007 0.001 TYR E 148 PHE 0.010 0.001 PHE F 172 TRP 0.005 0.001 TRP F 481 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00212 (18856) covalent geometry : angle 0.59301 (25620) hydrogen bonds : bond 0.16194 ( 886) hydrogen bonds : angle 6.24865 ( 2559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 561 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 528 time to evaluate : 0.937 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: 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: 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: E 193 MET cc_start: 0.7847 (tpt) cc_final: 0.7568 (tpt) REVERT: E 307 CYS cc_start: 0.3849 (m) cc_final: 0.3500 (m) REVERT: E 343 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8706 (mtpp) REVERT: F 164 MET cc_start: 0.8372 (mtm) cc_final: 0.7978 (mtm) REVERT: F 210 SER cc_start: 0.8882 (m) cc_final: 0.8600 (t) REVERT: F 254 VAL cc_start: 0.7760 (t) cc_final: 0.7560 (t) REVERT: F 299 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6761 (p0) REVERT: F 317 GLN cc_start: 0.6765 (mp10) cc_final: 0.6395 (mt0) REVERT: F 384 ASN cc_start: 0.7835 (m-40) cc_final: 0.7569 (m110) REVERT: F 395 SER cc_start: 0.8859 (m) cc_final: 0.8611 (t) REVERT: F 480 PHE cc_start: 0.7574 (p90) cc_final: 0.7255 (p90) REVERT: F 493 LEU cc_start: 0.6258 (tp) cc_final: 0.5995 (tt) REVERT: A 330 LEU cc_start: 0.7826 (mt) cc_final: 0.7614 (tp) REVERT: A 348 MET cc_start: 0.8967 (mtp) cc_final: 0.8578 (mtm) REVERT: A 471 ARG cc_start: 0.7968 (ptt180) cc_final: 0.7333 (tpt170) REVERT: B 193 MET cc_start: 0.7935 (tpt) cc_final: 0.7691 (tpt) REVERT: B 307 CYS cc_start: 0.3943 (m) cc_final: 0.3634 (m) REVERT: B 343 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8719 (mtpp) REVERT: C 164 MET cc_start: 0.8275 (mtm) cc_final: 0.7888 (mtm) REVERT: C 210 SER cc_start: 0.8881 (m) cc_final: 0.8592 (t) REVERT: C 292 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (t0) REVERT: C 299 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6842 (p0) REVERT: C 384 ASN cc_start: 0.7830 (m-40) cc_final: 0.7570 (m110) REVERT: C 395 SER cc_start: 0.8864 (m) cc_final: 0.8612 (t) REVERT: C 480 PHE cc_start: 0.7590 (p90) cc_final: 0.7298 (p90) REVERT: C 493 LEU cc_start: 0.6277 (tp) cc_final: 0.5985 (tt) REVERT: D 330 LEU cc_start: 0.7840 (mt) cc_final: 0.7622 (tp) REVERT: D 348 MET cc_start: 0.8976 (mtp) cc_final: 0.8666 (mtm) REVERT: D 471 ARG cc_start: 0.7915 (ptt180) cc_final: 0.7342 (tpt170) outliers start: 33 outliers final: 14 residues processed: 553 average time/residue: 0.3629 time to fit residues: 283.4923 Evaluate side-chains 297 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 278 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 382 HIS Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 382 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.0270 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 ASN A 463 HIS ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN D 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.152650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130276 restraints weight = 82639.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.131651 restraints weight = 63215.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.133202 restraints weight = 53555.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.133997 restraints weight = 34462.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135320 restraints weight = 31983.861| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 18856 Z= 0.152 Angle : 0.651 19.745 25620 Z= 0.335 Chirality : 0.046 0.181 3040 Planarity : 0.005 0.052 3360 Dihedral : 11.179 105.448 2919 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.63 % Allowed : 10.46 % Favored : 86.91 % 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 (0.18), residues: 2494 helix: 1.11 (0.17), residues: 976 sheet: -1.83 (0.22), residues: 532 loop : -1.15 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 359 TYR 0.008 0.001 TYR F 455 PHE 0.007 0.001 PHE F 172 TRP 0.006 0.001 TRP A 481 HIS 0.004 0.001 HIS D 470 Details of bonding type rmsd covalent geometry : bond 0.00345 (18856) covalent geometry : angle 0.65097 (25620) hydrogen bonds : bond 0.04471 ( 886) hydrogen bonds : angle 5.32086 ( 2559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 0.619 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 250 MET cc_start: 0.7299 (tpp) cc_final: 0.7041 (tpt) REVERT: E 367 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7580 (mp) REVERT: F 164 MET cc_start: 0.8177 (mtm) cc_final: 0.7884 (mtm) REVERT: F 299 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7157 (p0) REVERT: F 395 SER cc_start: 0.8573 (m) cc_final: 0.8317 (t) REVERT: F 470 HIS cc_start: 0.5427 (m-70) cc_final: 0.5216 (m-70) REVERT: F 493 LEU cc_start: 0.6627 (tp) cc_final: 0.6308 (tt) REVERT: A 285 SER cc_start: 0.9183 (p) cc_final: 0.8820 (t) REVERT: A 348 MET cc_start: 0.8744 (mtp) cc_final: 0.8358 (mtm) REVERT: B 250 MET cc_start: 0.7448 (tpp) cc_final: 0.7102 (tpt) REVERT: B 367 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7598 (mp) REVERT: C 164 MET cc_start: 0.8117 (mtm) cc_final: 0.7825 (mtm) REVERT: C 299 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7096 (p0) REVERT: C 395 SER cc_start: 0.8569 (m) cc_final: 0.8325 (t) REVERT: C 470 HIS cc_start: 0.5483 (m-70) cc_final: 0.5270 (m-70) REVERT: C 493 LEU cc_start: 0.6630 (tp) cc_final: 0.6333 (tt) REVERT: D 348 MET cc_start: 0.8779 (mtp) cc_final: 0.8482 (mtm) outliers start: 48 outliers final: 32 residues processed: 315 average time/residue: 0.2940 time to fit residues: 142.5184 Evaluate side-chains 270 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 105 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 344 ASN E 371 ASN F 384 ASN A 382 HIS ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN D 382 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.161219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.141025 restraints weight = 79637.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141925 restraints weight = 65533.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143493 restraints weight = 58145.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.144022 restraints weight = 38864.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.144645 restraints weight = 35470.043| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18856 Z= 0.173 Angle : 0.654 19.599 25620 Z= 0.334 Chirality : 0.046 0.145 3040 Planarity : 0.004 0.053 3360 Dihedral : 10.133 105.548 2904 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.12 % Allowed : 11.88 % Favored : 84.99 % 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: -0.83 (0.17), residues: 2494 helix: 1.07 (0.17), residues: 980 sheet: -1.86 (0.21), residues: 540 loop : -1.34 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 170 TYR 0.009 0.001 TYR C 455 PHE 0.021 0.001 PHE C 480 TRP 0.004 0.001 TRP F 481 HIS 0.005 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00388 (18856) covalent geometry : angle 0.65359 (25620) hydrogen bonds : bond 0.03984 ( 886) hydrogen bonds : angle 5.15499 ( 2559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.989 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 367 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7521 (mp) REVERT: F 164 MET cc_start: 0.8111 (mtm) cc_final: 0.7696 (mtt) REVERT: F 299 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7154 (p0) REVERT: F 395 SER cc_start: 0.8357 (m) cc_final: 0.8157 (t) REVERT: F 422 GLN cc_start: 0.8444 (tp40) cc_final: 0.7918 (mm-40) REVERT: F 493 LEU cc_start: 0.6688 (tp) cc_final: 0.6446 (tt) REVERT: A 193 MET cc_start: 0.8067 (mmt) cc_final: 0.7738 (mmt) REVERT: A 285 SER cc_start: 0.9182 (p) cc_final: 0.8893 (t) REVERT: A 294 MET cc_start: 0.8483 (tpp) cc_final: 0.8256 (tpp) REVERT: A 330 LEU cc_start: 0.6897 (tp) cc_final: 0.6668 (tp) REVERT: A 348 MET cc_start: 0.8654 (mtp) cc_final: 0.8377 (mtm) REVERT: B 250 MET cc_start: 0.7260 (tpp) cc_final: 0.6816 (tpt) REVERT: B 367 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7512 (mp) REVERT: B 412 MET cc_start: 0.8670 (ttm) cc_final: 0.8312 (ttm) REVERT: C 164 MET cc_start: 0.8061 (mtm) cc_final: 0.7646 (mtt) REVERT: C 299 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6662 (p0) REVERT: C 422 GLN cc_start: 0.8425 (tp40) cc_final: 0.7897 (mm-40) REVERT: D 285 SER cc_start: 0.9214 (p) cc_final: 0.8870 (t) REVERT: D 294 MET cc_start: 0.8503 (tpp) cc_final: 0.8273 (tpp) REVERT: D 330 LEU cc_start: 0.6916 (tp) cc_final: 0.6667 (tp) REVERT: D 348 MET cc_start: 0.8695 (mtp) cc_final: 0.8462 (mtm) outliers start: 57 outliers final: 42 residues processed: 282 average time/residue: 0.2718 time to fit residues: 118.9006 Evaluate side-chains 265 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 242 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.159800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.139180 restraints weight = 80042.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140716 restraints weight = 69468.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.142409 restraints weight = 56697.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142540 restraints weight = 36977.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143281 restraints weight = 34655.503| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18856 Z= 0.171 Angle : 0.641 19.520 25620 Z= 0.328 Chirality : 0.045 0.152 3040 Planarity : 0.004 0.047 3360 Dihedral : 9.516 106.674 2902 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.18 % Allowed : 12.38 % Favored : 84.45 % 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: -0.90 (0.17), residues: 2494 helix: 1.04 (0.17), residues: 992 sheet: -1.89 (0.22), residues: 530 loop : -1.48 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 170 TYR 0.009 0.001 TYR E 487 PHE 0.021 0.001 PHE C 480 TRP 0.005 0.001 TRP F 481 HIS 0.004 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00383 (18856) covalent geometry : angle 0.64068 (25620) hydrogen bonds : bond 0.03643 ( 886) hydrogen bonds : angle 5.00609 ( 2559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.887 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: 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: E 250 MET cc_start: 0.7082 (tpp) cc_final: 0.6866 (tpt) REVERT: E 367 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7648 (mp) REVERT: F 164 MET cc_start: 0.8095 (mtm) cc_final: 0.7728 (mtt) REVERT: F 299 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.6716 (p0) REVERT: F 395 SER cc_start: 0.8371 (m) cc_final: 0.8160 (t) REVERT: A 285 SER cc_start: 0.9195 (p) cc_final: 0.8888 (t) REVERT: A 294 MET cc_start: 0.8450 (tpp) cc_final: 0.8216 (tpp) REVERT: A 348 MET cc_start: 0.8743 (mtp) cc_final: 0.8473 (mtm) REVERT: B 250 MET cc_start: 0.7278 (tpp) cc_final: 0.6911 (tpt) REVERT: B 367 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7708 (mp) REVERT: B 412 MET cc_start: 0.8697 (ttm) cc_final: 0.8363 (ttm) REVERT: C 164 MET cc_start: 0.8045 (mtm) cc_final: 0.7684 (mtt) REVERT: C 299 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6365 (p0) REVERT: D 285 SER cc_start: 0.9233 (p) cc_final: 0.8853 (t) REVERT: D 294 MET cc_start: 0.8493 (tpp) cc_final: 0.8181 (tpp) REVERT: D 348 MET cc_start: 0.8717 (mtp) cc_final: 0.8481 (mtm) outliers start: 58 outliers final: 46 residues processed: 262 average time/residue: 0.2930 time to fit residues: 119.4317 Evaluate side-chains 258 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 86 optimal weight: 20.0000 chunk 221 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.160275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.140504 restraints weight = 79839.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141579 restraints weight = 64497.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.142969 restraints weight = 57426.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.143244 restraints weight = 38975.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143479 restraints weight = 39133.425| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18856 Z= 0.141 Angle : 0.619 19.536 25620 Z= 0.315 Chirality : 0.045 0.151 3040 Planarity : 0.004 0.045 3360 Dihedral : 8.965 107.463 2898 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.07 % Allowed : 13.20 % Favored : 83.73 % 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 (0.17), residues: 2494 helix: 1.08 (0.17), residues: 1018 sheet: -1.90 (0.22), residues: 536 loop : -1.47 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 352 TYR 0.008 0.001 TYR B 487 PHE 0.023 0.001 PHE C 480 TRP 0.006 0.001 TRP C 481 HIS 0.004 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00317 (18856) covalent geometry : angle 0.61925 (25620) hydrogen bonds : bond 0.03365 ( 886) hydrogen bonds : angle 4.76877 ( 2559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 1.040 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 250 MET cc_start: 0.7104 (tpp) cc_final: 0.6833 (tpt) REVERT: E 367 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7722 (mp) REVERT: F 164 MET cc_start: 0.8070 (mtm) cc_final: 0.7693 (mtt) REVERT: F 299 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6623 (p0) REVERT: F 395 SER cc_start: 0.8295 (m) cc_final: 0.8046 (t) REVERT: F 422 GLN cc_start: 0.8183 (tp40) cc_final: 0.7516 (mm-40) REVERT: A 285 SER cc_start: 0.9169 (p) cc_final: 0.8863 (t) REVERT: A 294 MET cc_start: 0.8424 (tpp) cc_final: 0.8182 (tpp) REVERT: A 348 MET cc_start: 0.8652 (mtp) cc_final: 0.8367 (mtm) REVERT: B 207 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8083 (p) REVERT: B 367 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7666 (mp) REVERT: B 412 MET cc_start: 0.8647 (ttm) cc_final: 0.8324 (ttm) REVERT: C 299 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6977 (p0) REVERT: D 285 SER cc_start: 0.9201 (p) cc_final: 0.8832 (t) REVERT: D 294 MET cc_start: 0.8440 (tpp) cc_final: 0.8201 (tpp) REVERT: D 330 LEU cc_start: 0.7006 (tp) cc_final: 0.6802 (tp) REVERT: D 348 MET cc_start: 0.8672 (mtp) cc_final: 0.8433 (mtm) outliers start: 56 outliers final: 40 residues processed: 260 average time/residue: 0.2886 time to fit residues: 118.4867 Evaluate side-chains 250 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 0.2980 chunk 85 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.158837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138105 restraints weight = 80595.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139284 restraints weight = 72517.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.141080 restraints weight = 57660.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.141101 restraints weight = 39535.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141562 restraints weight = 38732.003| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18856 Z= 0.161 Angle : 0.632 19.373 25620 Z= 0.321 Chirality : 0.045 0.156 3040 Planarity : 0.004 0.044 3360 Dihedral : 8.861 106.560 2898 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.12 % Allowed : 13.80 % Favored : 83.08 % 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: -0.86 (0.17), residues: 2494 helix: 1.09 (0.17), residues: 1018 sheet: -1.90 (0.22), residues: 520 loop : -1.54 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 477 TYR 0.009 0.001 TYR E 487 PHE 0.020 0.001 PHE F 480 TRP 0.006 0.001 TRP F 481 HIS 0.004 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00361 (18856) covalent geometry : angle 0.63163 (25620) hydrogen bonds : bond 0.03356 ( 886) hydrogen bonds : angle 4.74414 ( 2559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 1.076 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 207 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8077 (p) REVERT: E 250 MET cc_start: 0.7162 (tpp) cc_final: 0.6796 (tpt) REVERT: E 367 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7788 (mp) REVERT: F 164 MET cc_start: 0.8101 (mtm) cc_final: 0.7733 (mtt) REVERT: F 299 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7458 (p0) REVERT: F 395 SER cc_start: 0.8342 (m) cc_final: 0.8080 (t) REVERT: A 285 SER cc_start: 0.9152 (p) cc_final: 0.8905 (t) REVERT: A 348 MET cc_start: 0.8712 (mtp) cc_final: 0.8437 (mtm) REVERT: B 207 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 367 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7904 (mp) REVERT: B 370 MET cc_start: 0.7382 (mpp) cc_final: 0.6978 (mpp) REVERT: B 412 MET cc_start: 0.8646 (ttm) cc_final: 0.8338 (ttm) REVERT: C 299 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.6924 (p0) REVERT: D 193 MET cc_start: 0.8240 (mmt) cc_final: 0.7832 (mmt) REVERT: D 285 SER cc_start: 0.9187 (p) cc_final: 0.8845 (t) outliers start: 57 outliers final: 46 residues processed: 258 average time/residue: 0.2678 time to fit residues: 109.9649 Evaluate side-chains 253 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 432 ARG Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 70 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 201 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 87 optimal weight: 0.0570 chunk 168 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 59 optimal weight: 0.3980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 374 HIS ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS C 143 ASN D 202 GLN D 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.161866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141487 restraints weight = 79732.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.144652 restraints weight = 68219.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.145520 restraints weight = 47201.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145575 restraints weight = 30994.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145805 restraints weight = 29466.585| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18856 Z= 0.091 Angle : 0.586 19.539 25620 Z= 0.296 Chirality : 0.045 0.166 3040 Planarity : 0.004 0.042 3360 Dihedral : 8.596 108.752 2896 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.46 % Allowed : 15.12 % Favored : 82.42 % 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: -0.49 (0.18), residues: 2494 helix: 1.38 (0.17), residues: 1018 sheet: -1.76 (0.22), residues: 528 loop : -1.26 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 170 TYR 0.009 0.001 TYR B 487 PHE 0.017 0.001 PHE F 480 TRP 0.008 0.001 TRP F 481 HIS 0.004 0.001 HIS D 470 Details of bonding type rmsd covalent geometry : bond 0.00203 (18856) covalent geometry : angle 0.58592 (25620) hydrogen bonds : bond 0.02924 ( 886) hydrogen bonds : angle 4.39648 ( 2559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.998 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 207 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8024 (p) REVERT: E 367 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7837 (mp) REVERT: F 164 MET cc_start: 0.8063 (mtm) cc_final: 0.7705 (mtt) REVERT: F 299 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7077 (p0) REVERT: F 395 SER cc_start: 0.8291 (m) cc_final: 0.8056 (t) REVERT: F 422 GLN cc_start: 0.8179 (tp40) cc_final: 0.7807 (mm-40) REVERT: A 285 SER cc_start: 0.9102 (p) cc_final: 0.8782 (t) REVERT: A 348 MET cc_start: 0.8664 (mtp) cc_final: 0.8399 (mtm) REVERT: B 207 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 250 MET cc_start: 0.7102 (tpp) cc_final: 0.6777 (tpt) REVERT: B 367 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7800 (mp) REVERT: B 370 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6998 (mpp) REVERT: B 412 MET cc_start: 0.8629 (ttm) cc_final: 0.8356 (ttm) REVERT: C 164 MET cc_start: 0.8035 (mtm) cc_final: 0.7762 (mtt) REVERT: D 285 SER cc_start: 0.9150 (p) cc_final: 0.8784 (t) REVERT: D 348 MET cc_start: 0.8612 (mtp) cc_final: 0.8346 (mtm) outliers start: 45 outliers final: 32 residues processed: 240 average time/residue: 0.2727 time to fit residues: 101.8763 Evaluate side-chains 235 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 432 ARG Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.156969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136388 restraints weight = 80996.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.136835 restraints weight = 69023.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138495 restraints weight = 62499.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.138842 restraints weight = 40978.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139189 restraints weight = 42312.302| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18856 Z= 0.224 Angle : 0.678 19.178 25620 Z= 0.346 Chirality : 0.046 0.143 3040 Planarity : 0.004 0.045 3360 Dihedral : 8.799 106.060 2892 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.25 % Allowed : 15.50 % Favored : 82.26 % 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: -0.87 (0.17), residues: 2494 helix: 1.10 (0.17), residues: 1020 sheet: -1.86 (0.22), residues: 512 loop : -1.60 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 479 TYR 0.012 0.002 TYR E 487 PHE 0.017 0.002 PHE F 480 TRP 0.006 0.001 TRP B 481 HIS 0.007 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00507 (18856) covalent geometry : angle 0.67804 (25620) hydrogen bonds : bond 0.03572 ( 886) hydrogen bonds : angle 4.80095 ( 2559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.657 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: E 207 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7991 (p) REVERT: E 250 MET cc_start: 0.7289 (tpp) cc_final: 0.6968 (tpt) REVERT: E 367 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7940 (mp) REVERT: E 370 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7379 (mpp) REVERT: F 164 MET cc_start: 0.8174 (mtm) cc_final: 0.7788 (mtt) REVERT: F 299 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7184 (p0) REVERT: F 395 SER cc_start: 0.8355 (m) cc_final: 0.8107 (t) REVERT: A 193 MET cc_start: 0.8231 (mmt) cc_final: 0.7894 (mmt) REVERT: B 207 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8194 (p) REVERT: B 250 MET cc_start: 0.7220 (tpp) cc_final: 0.6889 (tpt) REVERT: B 367 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7936 (mp) REVERT: B 412 MET cc_start: 0.8685 (ttm) cc_final: 0.8383 (ttm) REVERT: C 164 MET cc_start: 0.8139 (mtm) cc_final: 0.7830 (mtm) REVERT: D 193 MET cc_start: 0.8228 (mmt) cc_final: 0.7880 (mmt) REVERT: D 285 SER cc_start: 0.9181 (p) cc_final: 0.8920 (t) outliers start: 41 outliers final: 31 residues processed: 230 average time/residue: 0.2952 time to fit residues: 103.1052 Evaluate side-chains 223 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain E residue 432 ARG Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 GLN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.158440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137961 restraints weight = 80728.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139405 restraints weight = 69423.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141041 restraints weight = 57947.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141404 restraints weight = 36554.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141772 restraints weight = 38004.132| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18856 Z= 0.129 Angle : 0.607 19.771 25620 Z= 0.309 Chirality : 0.045 0.142 3040 Planarity : 0.004 0.042 3360 Dihedral : 8.563 109.390 2888 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.81 % Allowed : 16.54 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.70 (0.17), residues: 2494 helix: 1.21 (0.17), residues: 1018 sheet: -1.86 (0.22), residues: 528 loop : -1.41 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 352 TYR 0.009 0.001 TYR F 402 PHE 0.017 0.001 PHE F 480 TRP 0.007 0.001 TRP C 481 HIS 0.005 0.001 HIS F 319 Details of bonding type rmsd covalent geometry : bond 0.00290 (18856) covalent geometry : angle 0.60692 (25620) hydrogen bonds : bond 0.03149 ( 886) hydrogen bonds : angle 4.58572 ( 2559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.973 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: E 207 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7957 (p) REVERT: E 250 MET cc_start: 0.7237 (tpp) cc_final: 0.6913 (tpt) REVERT: E 367 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7817 (mp) REVERT: E 370 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7182 (mpp) REVERT: F 395 SER cc_start: 0.8316 (m) cc_final: 0.8064 (t) REVERT: A 193 MET cc_start: 0.8224 (mmt) cc_final: 0.7772 (mmt) REVERT: A 348 MET cc_start: 0.8632 (mtp) cc_final: 0.8328 (mtm) REVERT: B 207 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 250 MET cc_start: 0.7125 (tpp) cc_final: 0.6840 (tpt) REVERT: B 367 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7799 (mp) REVERT: B 370 MET cc_start: 0.7492 (mpp) cc_final: 0.7285 (mpp) REVERT: B 412 MET cc_start: 0.8637 (ttm) cc_final: 0.8368 (ttm) REVERT: D 285 SER cc_start: 0.9150 (p) cc_final: 0.8843 (t) REVERT: D 348 MET cc_start: 0.8639 (mtp) cc_final: 0.8369 (mtm) outliers start: 33 outliers final: 25 residues processed: 218 average time/residue: 0.2884 time to fit residues: 99.4083 Evaluate side-chains 213 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain E residue 432 ARG Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 15 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 232 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 189 optimal weight: 0.0470 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 463 HIS ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.160688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140413 restraints weight = 80465.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141387 restraints weight = 67463.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143168 restraints weight = 57557.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.143310 restraints weight = 37474.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143576 restraints weight = 40336.139| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18856 Z= 0.097 Angle : 0.583 19.606 25620 Z= 0.296 Chirality : 0.045 0.149 3040 Planarity : 0.004 0.041 3360 Dihedral : 8.220 108.199 2882 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.53 % Allowed : 16.81 % Favored : 81.65 % 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: -0.41 (0.18), residues: 2494 helix: 1.45 (0.17), residues: 1020 sheet: -1.74 (0.22), residues: 524 loop : -1.23 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 352 TYR 0.018 0.001 TYR F 486 PHE 0.017 0.001 PHE E 480 TRP 0.007 0.001 TRP C 481 HIS 0.004 0.001 HIS F 319 Details of bonding type rmsd covalent geometry : bond 0.00223 (18856) covalent geometry : angle 0.58334 (25620) hydrogen bonds : bond 0.02852 ( 886) hydrogen bonds : angle 4.31757 ( 2559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.884 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: E 250 MET cc_start: 0.7166 (tpp) cc_final: 0.6863 (tpt) REVERT: E 367 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7794 (mp) REVERT: E 370 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7141 (mpp) REVERT: F 395 SER cc_start: 0.8281 (m) cc_final: 0.8041 (t) REVERT: F 422 GLN cc_start: 0.8151 (tp40) cc_final: 0.7480 (mm-40) REVERT: A 348 MET cc_start: 0.8611 (mtp) cc_final: 0.8307 (mtm) REVERT: B 250 MET cc_start: 0.7068 (tpp) cc_final: 0.6792 (tpt) REVERT: B 367 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7771 (mp) REVERT: B 370 MET cc_start: 0.7432 (mpp) cc_final: 0.7182 (mpp) REVERT: B 412 MET cc_start: 0.8618 (ttm) cc_final: 0.8361 (ttm) REVERT: D 285 SER cc_start: 0.9142 (p) cc_final: 0.8806 (t) REVERT: D 348 MET cc_start: 0.8618 (mtp) cc_final: 0.8339 (mtm) outliers start: 28 outliers final: 23 residues processed: 215 average time/residue: 0.2857 time to fit residues: 96.9689 Evaluate side-chains 218 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain E residue 432 ARG Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 133 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 184 optimal weight: 0.2980 chunk 160 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.158042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.137407 restraints weight = 80763.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137721 restraints weight = 70202.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139322 restraints weight = 66076.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.140045 restraints weight = 41943.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140228 restraints weight = 38961.026| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18856 Z= 0.155 Angle : 0.617 19.486 25620 Z= 0.314 Chirality : 0.045 0.141 3040 Planarity : 0.004 0.043 3360 Dihedral : 8.341 108.000 2880 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.42 % Allowed : 16.76 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.56 (0.18), residues: 2494 helix: 1.33 (0.17), residues: 1022 sheet: -1.84 (0.22), residues: 532 loop : -1.29 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 352 TYR 0.015 0.002 TYR C 486 PHE 0.015 0.001 PHE C 480 TRP 0.006 0.001 TRP E 481 HIS 0.006 0.001 HIS F 319 Details of bonding type rmsd covalent geometry : bond 0.00347 (18856) covalent geometry : angle 0.61650 (25620) hydrogen bonds : bond 0.03105 ( 886) hydrogen bonds : angle 4.47678 ( 2559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.01 seconds wall clock time: 75 minutes 53.90 seconds (4553.90 seconds total)