Starting phenix.real_space_refine on Sun Aug 24 14:00:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6b_49055/08_2025/9n6b_49055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6b_49055/08_2025/9n6b_49055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n6b_49055/08_2025/9n6b_49055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6b_49055/08_2025/9n6b_49055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n6b_49055/08_2025/9n6b_49055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6b_49055/08_2025/9n6b_49055.map" } resolution = 3.09 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= 0.005 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 123 5.49 5 S 34 5.16 5 C 12731 2.51 5 N 3564 2.21 5 O 4033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s 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: 20486 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3929 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 12, 'TRANS': 512} Chain breaks: 2 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASN:plan1': 7, 'GLU:plan': 18, 'ASP:plan': 11, 'ARG:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3765 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 12, 'TRANS': 500} Chain breaks: 2 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 499 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 27, 'HIS:plan': 2, 'ASP:plan': 11, 'TYR:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 238 Chain: "C" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3322 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 10, 'TRANS': 434} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 12, 'ASN:plan1': 6, 'ASP:plan': 13, 'GLN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 158 Chain: "D" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2962 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 9, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 502 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ASN:plan1': 11, 'GLU:plan': 22, 'TYR:plan': 6, 'ASP:plan': 17, 'PHE:plan': 4, 'HIS:plan': 2, 'GLN:plan1': 5, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 287 Chain: "E" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2394 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 295} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 9, 'ASP:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 71 Chain: "F" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1652 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 6, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 4, 'GLU:plan': 13, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 134 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1496 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 872 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna2p': 16, 'rna3p': 24} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16691 SG CYS F 47 75.157 122.205 53.240 1.00 77.40 S ATOM 16714 SG CYS F 50 74.743 120.050 50.151 1.00 75.74 S ATOM 17015 SG CYS F 92 73.848 118.628 53.565 1.00 79.79 S ATOM 17061 SG CYS F 98 77.457 119.197 52.589 1.00 77.68 S Time building chain proxies: 5.01, per 1000 atoms: 0.24 Number of scatterers: 20486 At special positions: 0 Unit cell: (139.539, 156.755, 148.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 34 16.00 P 123 15.00 O 4033 8.00 N 3564 7.00 C 12731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 900.4 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 98 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 92 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 47 " Number of angles added : 6 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4674 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 18 sheets defined 54.5% alpha, 14.9% beta 15 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 6 through 21 removed outlier: 3.631A pdb=" N SER A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 removed outlier: 3.925A pdb=" N LEU A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.584A pdb=" N GLU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 100 removed outlier: 4.112A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.681A pdb=" N ILE A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.758A pdb=" N ILE A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.733A pdb=" N GLU A 214 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 242 removed outlier: 3.907A pdb=" N THR A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 267 removed outlier: 4.028A pdb=" N ILE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 298 removed outlier: 3.520A pdb=" N GLU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.866A pdb=" N PHE A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.524A pdb=" N ILE A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 4.033A pdb=" N GLY A 380 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.740A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 427 No H-bonds generated for 'chain 'A' and resid 426 through 427' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 476 through 491 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.803A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.601A pdb=" N GLU A 519 " --> pdb=" O PRO A 515 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.590A pdb=" N HIS B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 29 removed outlier: 3.604A pdb=" N GLU B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.725A pdb=" N GLN B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.875A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 154 through 171 removed outlier: 3.591A pdb=" N LYS B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.508A pdb=" N PHE B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 262 removed outlier: 4.024A pdb=" N THR B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.792A pdb=" N ASP B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 371 removed outlier: 3.609A pdb=" N LEU B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.838A pdb=" N GLY B 380 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.651A pdb=" N GLN B 399 " --> pdb=" O PRO B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 409 removed outlier: 3.521A pdb=" N ARG B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.762A pdb=" N LEU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 420 through 425' Processing helix chain 'B' and resid 426 through 427 No H-bonds generated for 'chain 'B' and resid 426 through 427' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.514A pdb=" N ALA B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 464 " --> pdb=" O ASN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.945A pdb=" N TRP B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 510 removed outlier: 3.598A pdb=" N LYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 537 removed outlier: 3.529A pdb=" N LEU B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 524 " --> pdb=" O CYS B 520 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 19 Processing helix chain 'C' and resid 23 through 30 removed outlier: 3.658A pdb=" N LEU C 27 " --> pdb=" O ASN C 23 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.599A pdb=" N GLN C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 100 removed outlier: 3.654A pdb=" N ILE C 83 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 171 removed outlier: 3.683A pdb=" N ILE C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 removed outlier: 3.705A pdb=" N ARG C 186 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 187 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 188 " --> pdb=" O ALA C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 188' Processing helix chain 'C' and resid 219 through 241 removed outlier: 4.070A pdb=" N THR C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 263 removed outlier: 3.969A pdb=" N THR C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 294 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 350 through 371 removed outlier: 3.547A pdb=" N ILE C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 380 removed outlier: 3.516A pdb=" N LEU C 379 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 380 " --> pdb=" O PRO C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 380' Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.523A pdb=" N ARG C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 removed outlier: 4.264A pdb=" N LEU C 424 " --> pdb=" O SER C 420 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 425 " --> pdb=" O PRO C 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 420 through 425' Processing helix chain 'C' and resid 426 through 427 No H-bonds generated for 'chain 'C' and resid 426 through 427' Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.671A pdb=" N GLN D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 100 removed outlier: 3.820A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.632A pdb=" N VAL D 113 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 171 removed outlier: 3.560A pdb=" N ILE D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 222 through 240 removed outlier: 3.839A pdb=" N PHE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 264 Processing helix chain 'D' and resid 276 through 291 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 302 through 318 removed outlier: 4.010A pdb=" N PHE D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 371 removed outlier: 3.632A pdb=" N ILE D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.617A pdb=" N LEU D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 14 through 25 removed outlier: 3.611A pdb=" N ASN E 23 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 63 removed outlier: 3.585A pdb=" N ASN E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 80 through 86 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.560A pdb=" N LYS E 105 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.726A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.757A pdb=" N ASN E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 176 removed outlier: 3.546A pdb=" N ASP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP E 173 " --> pdb=" O SER E 169 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 213 removed outlier: 3.543A pdb=" N VAL E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 264 removed outlier: 3.582A pdb=" N LYS E 258 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 264 " --> pdb=" O HIS E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 287 removed outlier: 3.832A pdb=" N ASN E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.580A pdb=" N LYS E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.574A pdb=" N ILE E 302 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 304 " --> pdb=" O GLU E 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 removed outlier: 4.092A pdb=" N LYS F 16 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 12 through 17' Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 28 through 44 removed outlier: 3.509A pdb=" N GLU F 38 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 98 through 103 removed outlier: 3.671A pdb=" N ASP F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 112 Processing helix chain 'F' and resid 119 through 122 Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.529A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG F 151 " --> pdb=" O GLU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.897A pdb=" N GLU F 165 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 189 removed outlier: 3.681A pdb=" N ILE F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 209 removed outlier: 3.609A pdb=" N SER F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.676A pdb=" N GLU F 223 " --> pdb=" O LYS F 219 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG F 225 " --> pdb=" O VAL F 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 64 removed outlier: 6.764A pdb=" N ARG A 59 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 46 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN A 127 " --> pdb=" O ASN A 48 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 50 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP A 125 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 52 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER A 123 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP A 54 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR A 121 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 182 removed outlier: 6.166A pdb=" N LEU A 178 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU A 385 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 180 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 417 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N THR A 70 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 329 removed outlier: 4.253A pdb=" N TRP A 323 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 338 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 64 removed outlier: 6.659A pdb=" N ARG B 59 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 61 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU B 47 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS B 129 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 49 " --> pdb=" O ASN B 127 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 55 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 11.479A pdb=" N TYR B 121 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 137 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 216 through 217 removed outlier: 8.285A pdb=" N PHE B 217 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR B 181 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 387 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR B 70 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ARG B 433 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 71 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU B 435 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B 73 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N GLU B 437 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 328 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 64 removed outlier: 6.703A pdb=" N ARG C 59 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU C 47 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS C 129 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 49 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE C 55 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N TYR C 121 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 137 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.204A pdb=" N LEU C 178 " --> pdb=" O ILE C 383 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU C 385 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 180 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ASP C 387 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR C 182 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C 382 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL C 415 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 384 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR C 417 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE C 386 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR C 70 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR C 418 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE C 72 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ARG C 433 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 71 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU C 435 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL C 73 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N GLU C 437 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 434 " --> pdb=" O SER C 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.644A pdb=" N LEU C 344 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 64 removed outlier: 6.495A pdb=" N ARG D 59 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU D 47 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS D 129 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS D 49 " --> pdb=" O ASN D 127 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE D 55 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 11.238A pdb=" N TYR D 121 " --> pdb=" O PHE D 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 178 through 182 removed outlier: 3.609A pdb=" N THR D 417 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG D 433 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 71 " --> pdb=" O ARG D 433 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU D 435 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL D 73 " --> pdb=" O LEU D 435 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N GLU D 437 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 321 through 329 removed outlier: 4.242A pdb=" N TRP D 323 " --> pdb=" O LYS D 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 35 Processing sheet with id=AB6, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.530A pdb=" N SER E 191 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER E 182 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP E 98 " --> pdb=" O LYS E 222 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS E 222 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 233 through 234 Processing sheet with id=AB8, first strand: chain 'F' and resid 67 through 71 Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 126 979 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4309 1.33 - 1.45: 5144 1.45 - 1.57: 11366 1.57 - 1.69: 241 1.69 - 1.81: 54 Bond restraints: 21114 Sorted by residual: bond pdb=" C ILE C 98 " pdb=" N GLU C 99 " ideal model delta sigma weight residual 1.334 1.437 -0.103 1.23e-02 6.61e+03 6.97e+01 bond pdb=" C THR C 223 " pdb=" N ASP C 224 " ideal model delta sigma weight residual 1.335 1.221 0.114 1.38e-02 5.25e+03 6.81e+01 bond pdb=" C GLU C 99 " pdb=" N LYS C 100 " ideal model delta sigma weight residual 1.332 1.242 0.090 1.25e-02 6.40e+03 5.18e+01 bond pdb=" C ASP C 224 " pdb=" N PHE C 225 " ideal model delta sigma weight residual 1.335 1.413 -0.078 1.30e-02 5.92e+03 3.60e+01 bond pdb=" C LEU A 84 " pdb=" N ASP A 85 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.31e-02 5.83e+03 3.12e+01 ... (remaining 21109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 28820 2.14 - 4.29: 357 4.29 - 6.43: 61 6.43 - 8.57: 12 8.57 - 10.72: 3 Bond angle restraints: 29253 Sorted by residual: angle pdb=" N TYR C 188 " pdb=" CA TYR C 188 " pdb=" C TYR C 188 " ideal model delta sigma weight residual 112.38 101.66 10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" N ILE D 189 " pdb=" CA ILE D 189 " pdb=" C ILE D 189 " ideal model delta sigma weight residual 110.62 103.04 7.58 1.02e+00 9.61e-01 5.53e+01 angle pdb=" O THR C 223 " pdb=" C THR C 223 " pdb=" N ASP C 224 " ideal model delta sigma weight residual 122.12 114.89 7.23 1.06e+00 8.90e-01 4.66e+01 angle pdb=" N GLU D 214 " pdb=" CA GLU D 214 " pdb=" C GLU D 214 " ideal model delta sigma weight residual 110.68 101.31 9.37 1.39e+00 5.18e-01 4.54e+01 angle pdb=" CA THR C 223 " pdb=" C THR C 223 " pdb=" N ASP C 224 " ideal model delta sigma weight residual 117.30 124.57 -7.27 1.16e+00 7.43e-01 3.93e+01 ... (remaining 29248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 11811 35.96 - 71.92: 636 71.92 - 107.89: 24 107.89 - 143.85: 1 143.85 - 179.81: 7 Dihedral angle restraints: 12479 sinusoidal: 5293 harmonic: 7186 Sorted by residual: dihedral pdb=" O4' U I 152 " pdb=" C1' U I 152 " pdb=" N1 U I 152 " pdb=" C2 U I 152 " ideal model delta sinusoidal sigma weight residual 232.00 64.91 167.09 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" O4' U I 147 " pdb=" C1' U I 147 " pdb=" N1 U I 147 " pdb=" C2 U I 147 " ideal model delta sinusoidal sigma weight residual -160.00 -64.32 -95.68 1 1.50e+01 4.44e-03 4.69e+01 dihedral pdb=" CA ASP B 210 " pdb=" C ASP B 210 " pdb=" N VAL B 211 " pdb=" CA VAL B 211 " ideal model delta harmonic sigma weight residual 180.00 -158.50 -21.50 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 12476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2651 0.041 - 0.082: 608 0.082 - 0.123: 209 0.123 - 0.164: 16 0.164 - 0.205: 6 Chirality restraints: 3490 Sorted by residual: chirality pdb=" C3' C I 125 " pdb=" C4' C I 125 " pdb=" O3' C I 125 " pdb=" C2' C I 125 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE D 189 " pdb=" N ILE D 189 " pdb=" C ILE D 189 " pdb=" CB ILE D 189 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" C3' C I 124 " pdb=" C4' C I 124 " pdb=" O3' C I 124 " pdb=" C2' C I 124 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 3487 not shown) Planarity restraints: 3294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 514 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO B 515 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 515 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 515 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 188 " 0.028 2.00e-02 2.50e+03 1.70e-02 5.77e+00 pdb=" CG TYR C 188 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 188 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 188 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 188 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 188 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 188 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 188 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 394 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO B 395 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 395 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 395 " -0.023 5.00e-02 4.00e+02 ... (remaining 3291 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1849 2.74 - 3.28: 19720 3.28 - 3.82: 31230 3.82 - 4.36: 35556 4.36 - 4.90: 60782 Nonbonded interactions: 149137 Sorted by model distance: nonbonded pdb=" CE2 TYR C 188 " pdb=" CD2 TYR D 188 " model vdw 2.204 3.640 nonbonded pdb=" OD1 ASN C 301 " pdb=" N ASN C 302 " model vdw 2.377 3.120 nonbonded pdb=" N TYR C 188 " pdb=" N ILE C 189 " model vdw 2.433 2.560 nonbonded pdb=" OD1 ASP D 75 " pdb=" N ASN D 76 " model vdw 2.473 3.120 nonbonded pdb=" O LYS D 159 " pdb=" OG SER D 162 " model vdw 2.508 3.040 ... (remaining 149132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 14 or (resid 15 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 or (resid 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or na \ me CA or name C or name O or name CB )) or resid 30 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 41 or ( \ resid 42 and (name N or name CA or name C or name O or name CB )) or resid 43 th \ rough 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 through 108 or (resid 109 and (name N or name CA or name C or name O \ or name CB )) or resid 110 through 131 or (resid 132 and (name N or name CA or \ name C or name O or name CB )) or resid 133 through 142 or (resid 143 through 14 \ 4 and (name N or name CA or name C or name O or name CB )) or (resid 145 through \ 151 and (name N or name CA or name C or name O or name CB )) or resid 152 or (r \ esid 153 and (name N or name CA or name C or name O or name CB )) or resid 154 t \ hrough 168 or (resid 169 and (name N or name CA or name C or name O or name CB ) \ ) or resid 170 through 185 or (resid 186 and (name N or name CA or name C or nam \ e O or name CB )) or resid 187 or resid 204 through 206 or (resid 207 through 20 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 209 through \ 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or re \ sid 212 through 220 or (resid 221 and (name N or name CA or name C or name O or \ name CB )) or resid 222 through 238 or (resid 239 through 240 and (name N or nam \ e CA or name C or name O or name CB )) or resid 241 through 267 or resid 273 thr \ ough 307 or (resid 308 and (name N or name CA or name C or name O or name CB )) \ or resid 309 through 342 or (resid 343 and (name N or name CA or name C or name \ O or name CB )) or resid 344 through 438 or (resid 439 through 441 and (name N o \ r name CA or name C or name O or name CB )) or resid 442 through 451 or (resid 4 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 453 through \ 486 or (resid 487 through 488 and (name N or name CA or name C or name O or nam \ e CB )) or resid 489 through 507 or (resid 508 and (name N or name CA or name C \ or name O or name CB )) or resid 509 through 527 or (resid 528 and (name N or na \ me CA or name C or name O or name CB )) or resid 529 through 536)) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 100 or (resid 101 and (name N or name \ CA or name C or name O or name CB )) or resid 102 through 117 or (resid 118 and \ (name N or name CA or name C or name O or name CB )) or resid 119 through 204 or \ (resid 205 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 6 through 212 or (resid 213 through 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 239 or (resid 240 and (name N or name CA o \ r name C or name O or name CB )) or resid 241 through 243 or (resid 244 through \ 277 and (name N or name CA or name C or name O or name CB )) or (resid 278 throu \ gh 303 and (name N or name CA or name C or name O or name CB )) or resid 304 thr \ ough 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) \ or resid 333 through 437 or (resid 438 through 441 and (name N or name CA or nam \ e C or name O or name CB )) or resid 442 through 494 or (resid 495 through 501 a \ nd (name N or name CA or name C or name O or name CB )) or resid 502 through 535 \ or (resid 536 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'C' and ((resid 6 through 40 and (name N or name CA or name C or name O o \ r name CB )) or resid 41 or (resid 42 through 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 98 or (resid 99 and ( \ name N or name CA or name C or name O or name CB )) or resid 100 through 108 or \ (resid 109 through 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 116 or (resid 117 through 118 and (name N or name CA or nam \ e C or name O or name CB )) or resid 119 through 130 or (resid 131 through 132 a \ nd (name N or name CA or name C or name O or name CB )) or resid 133 through 142 \ or (resid 143 through 144 and (name N or name CA or name C or name O or name CB \ )) or (resid 145 through 148 and (name N or name CA or name C or name O or name \ CB )) or resid 149 through 154 or (resid 155 and (name N or name CA or name C o \ r name O or name CB )) or resid 156 through 158 or (resid 159 and (name N or nam \ e CA or name C or name O or name CB )) or resid 160 through 165 or (resid 166 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ through 190 or (resid 205 through 211 and (name N or name CA or name C or name O \ or name CB )) or resid 212 through 214 or (resid 215 through 216 and (name N or \ name CA or name C or name O or name CB )) or resid 217 through 219 or (resid 22 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 221 through \ 234 or (resid 235 through 236 and (name N or name CA or name C or name O or name \ CB )) or resid 237 through 238 or (resid 239 through 264 and (name N or name CA \ or name C or name O or name CB )) or (resid 275 through 303 and (name N or name \ CA or name C or name O or name CB )) or resid 304 through 307 or (resid 308 thr \ ough 309 and (name N or name CA or name C or name O or name CB )) or resid 310 t \ hrough 311 or (resid 312 and (name N or name CA or name C or name O or name CB ) \ ) or resid 313 through 319 or (resid 320 and (name N or name CA or name C or nam \ e O or name CB )) or resid 321 through 333 or (resid 334 and (name N or name CA \ or name C or name O or name CB )) or resid 335 through 344 or (resid 345 and (na \ me N or name CA or name C or name O or name CB )) or resid 346 through 369 or (r \ esid 370 and (name N or name CA or name C or name O or name CB )) or resid 371 t \ hrough 374 or (resid 375 through 376 and (name N or name CA or name C or name O \ or name CB )) or resid 377 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 402 or (resid 403 and (name N \ or name CA or name C or name O or name CB )) or resid 404 through 436 or (resid \ 437 through 441 and (name N or name CA or name C or name O or name CB )) or res \ id 442 through 601)) selection = (chain 'D' and (resid 6 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 109 or (resid 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 117 or (resid 118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 119 through 190 \ or resid 205 through 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 241 or (resid 242 through 277 and (name N \ or name CA or name C or name O or name CB )) or resid 278 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throug \ h 425 or (resid 426 and (name N or name CA or name C or name O or name CB )) or \ resid 427 or (resid 428 through 429 and (name N or name CA or name C or name O o \ r name CB )) or resid 430 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.820 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.004 0.114 21118 Z= 0.230 Angle : 0.614 10.716 29259 Z= 0.390 Chirality : 0.040 0.205 3490 Planarity : 0.003 0.064 3294 Dihedral : 19.435 179.809 7805 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.88 % Allowed : 20.96 % Favored : 77.16 % 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: 0.27 (0.17), residues: 2412 helix: 1.23 (0.16), residues: 1086 sheet: 0.45 (0.27), residues: 367 loop : -1.15 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.038 0.001 TYR C 188 PHE 0.014 0.001 PHE B 529 TRP 0.009 0.001 TRP B 481 HIS 0.010 0.001 HIS A 419 Details of bonding type rmsd covalent geometry : bond 0.00377 (21114) covalent geometry : angle 0.61424 (29253) hydrogen bonds : bond 0.29754 ( 1013) hydrogen bonds : angle 7.39501 ( 2865) metal coordination : bond 0.00450 ( 4) metal coordination : angle 1.24075 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.778 Fit side-chains REVERT: A 363 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 216 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 353 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7960 (mp0) REVERT: C 239 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 102 SER cc_start: 0.7919 (m) cc_final: 0.7705 (p) REVERT: D 163 ILE cc_start: 0.9300 (mt) cc_final: 0.9087 (mp) outliers start: 32 outliers final: 26 residues processed: 123 average time/residue: 0.1113 time to fit residues: 23.4965 Evaluate side-chains 105 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 373 ASN B 531 ASN D 53 HIS F 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.086006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.057048 restraints weight = 60832.719| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.02 r_work: 0.2790 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21118 Z= 0.139 Angle : 0.527 8.304 29259 Z= 0.295 Chirality : 0.041 0.197 3490 Planarity : 0.004 0.061 3294 Dihedral : 19.528 178.844 4194 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.29 % Allowed : 20.08 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2412 helix: 2.09 (0.15), residues: 1152 sheet: 0.74 (0.26), residues: 396 loop : -1.33 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.010 0.001 TYR C 11 PHE 0.016 0.001 PHE A 231 TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00293 (21114) covalent geometry : angle 0.52695 (29253) hydrogen bonds : bond 0.05523 ( 1013) hydrogen bonds : angle 4.48896 ( 2865) metal coordination : bond 0.00247 ( 4) metal coordination : angle 1.49739 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.772 Fit side-chains REVERT: B 216 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8407 (mm-30) REVERT: B 353 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7826 (mp0) REVERT: B 419 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.7722 (t-170) REVERT: D 102 SER cc_start: 0.8306 (m) cc_final: 0.8071 (p) REVERT: F 200 MET cc_start: 0.8122 (tpp) cc_final: 0.7771 (tmm) REVERT: F 204 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8434 (tm-30) outliers start: 39 outliers final: 22 residues processed: 123 average time/residue: 0.1317 time to fit residues: 27.7341 Evaluate side-chains 107 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 183 optimal weight: 0.5980 chunk 227 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 175 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.086292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057268 restraints weight = 61426.398| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.09 r_work: 0.2791 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21118 Z= 0.126 Angle : 0.491 8.901 29259 Z= 0.272 Chirality : 0.040 0.211 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.510 177.829 4162 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.52 % Allowed : 19.32 % Favored : 78.16 % 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: 1.34 (0.17), residues: 2412 helix: 2.47 (0.15), residues: 1149 sheet: 0.76 (0.26), residues: 397 loop : -1.31 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.011 0.001 TYR C 188 PHE 0.011 0.001 PHE A 231 TRP 0.013 0.001 TRP B 481 HIS 0.005 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00276 (21114) covalent geometry : angle 0.49121 (29253) hydrogen bonds : bond 0.04577 ( 1013) hydrogen bonds : angle 4.02216 ( 2865) metal coordination : bond 0.00278 ( 4) metal coordination : angle 1.23190 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.773 Fit side-chains REVERT: B 419 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.7993 (t-170) REVERT: D 102 SER cc_start: 0.8307 (m) cc_final: 0.8088 (p) REVERT: E 19 GLN cc_start: 0.8824 (tp40) cc_final: 0.8377 (tp-100) REVERT: F 111 ASP cc_start: 0.8304 (t0) cc_final: 0.8096 (t0) REVERT: F 187 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7629 (tt) REVERT: F 200 MET cc_start: 0.8075 (tpp) cc_final: 0.7723 (tmm) REVERT: F 204 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8573 (tm-30) outliers start: 43 outliers final: 25 residues processed: 127 average time/residue: 0.1175 time to fit residues: 26.2990 Evaluate side-chains 104 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 79 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS E 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.083096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.054076 restraints weight = 61724.087| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.90 r_work: 0.2709 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21118 Z= 0.257 Angle : 0.594 9.228 29259 Z= 0.329 Chirality : 0.044 0.215 3490 Planarity : 0.004 0.060 3294 Dihedral : 19.718 178.759 4158 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 3.17 % Allowed : 19.55 % Favored : 77.28 % 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: 1.08 (0.17), residues: 2412 helix: 2.42 (0.16), residues: 1143 sheet: 0.50 (0.26), residues: 391 loop : -1.59 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 57 TYR 0.015 0.001 TYR B 333 PHE 0.033 0.002 PHE A 78 TRP 0.013 0.001 TRP B 481 HIS 0.011 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00611 (21114) covalent geometry : angle 0.59293 (29253) hydrogen bonds : bond 0.06293 ( 1013) hydrogen bonds : angle 4.25374 ( 2865) metal coordination : bond 0.00704 ( 4) metal coordination : angle 2.17291 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 76 time to evaluate : 0.762 Fit side-chains REVERT: C 212 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.9039 (m-10) REVERT: D 102 SER cc_start: 0.8255 (m) cc_final: 0.8032 (p) REVERT: E 19 GLN cc_start: 0.8915 (tp40) cc_final: 0.8548 (tp-100) REVERT: E 306 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9179 (mp) REVERT: F 138 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7766 (pt) REVERT: F 204 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8382 (tm-30) outliers start: 54 outliers final: 33 residues processed: 125 average time/residue: 0.1190 time to fit residues: 26.2590 Evaluate side-chains 109 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 171 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 229 optimal weight: 0.4980 chunk 123 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 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 = 0.3643 r_free = 0.3643 target = 0.086354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057257 restraints weight = 61229.457| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.01 r_work: 0.2790 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21118 Z= 0.113 Angle : 0.478 8.280 29259 Z= 0.265 Chirality : 0.040 0.208 3490 Planarity : 0.003 0.059 3294 Dihedral : 19.538 176.919 4157 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 2.29 % Allowed : 20.55 % Favored : 77.16 % 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: 1.37 (0.17), residues: 2412 helix: 2.60 (0.15), residues: 1158 sheet: 0.66 (0.26), residues: 397 loop : -1.46 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.010 0.001 TYR A 26 PHE 0.009 0.001 PHE A 231 TRP 0.011 0.001 TRP D 323 HIS 0.003 0.001 HIS D 394 Details of bonding type rmsd covalent geometry : bond 0.00242 (21114) covalent geometry : angle 0.47796 (29253) hydrogen bonds : bond 0.03786 ( 1013) hydrogen bonds : angle 3.82472 ( 2865) metal coordination : bond 0.00244 ( 4) metal coordination : angle 1.17221 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.536 Fit side-chains REVERT: A 34 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: B 419 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8087 (t-170) REVERT: C 212 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8980 (m-10) REVERT: D 102 SER cc_start: 0.8311 (m) cc_final: 0.8095 (p) REVERT: F 111 ASP cc_start: 0.8255 (t0) cc_final: 0.8046 (t0) REVERT: F 138 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7750 (pt) REVERT: F 204 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8397 (tm-30) outliers start: 39 outliers final: 26 residues processed: 113 average time/residue: 0.1235 time to fit residues: 24.2621 Evaluate side-chains 104 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.055451 restraints weight = 60724.918| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.94 r_work: 0.2759 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21118 Z= 0.146 Angle : 0.500 8.195 29259 Z= 0.277 Chirality : 0.040 0.212 3490 Planarity : 0.003 0.053 3294 Dihedral : 19.526 178.840 4157 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 2.52 % Allowed : 20.85 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.17), residues: 2412 helix: 2.68 (0.15), residues: 1156 sheet: 0.76 (0.26), residues: 391 loop : -1.49 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 219 TYR 0.010 0.001 TYR D 328 PHE 0.011 0.001 PHE A 357 TRP 0.009 0.001 TRP D 323 HIS 0.005 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00334 (21114) covalent geometry : angle 0.49987 (29253) hydrogen bonds : bond 0.04542 ( 1013) hydrogen bonds : angle 3.79992 ( 2865) metal coordination : bond 0.00341 ( 4) metal coordination : angle 1.42679 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 0.514 Fit side-chains REVERT: A 34 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: B 419 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8092 (t-170) REVERT: C 212 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.9039 (m-10) REVERT: D 102 SER cc_start: 0.8278 (m) cc_final: 0.8054 (p) REVERT: F 111 ASP cc_start: 0.8388 (t0) cc_final: 0.8150 (t0) REVERT: F 138 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7821 (pt) REVERT: F 204 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8425 (tm-30) outliers start: 43 outliers final: 32 residues processed: 113 average time/residue: 0.1066 time to fit residues: 20.6842 Evaluate side-chains 108 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 122 optimal weight: 4.9990 chunk 170 optimal weight: 50.0000 chunk 195 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.084164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054456 restraints weight = 62517.653| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.94 r_work: 0.2738 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21118 Z= 0.148 Angle : 0.497 7.969 29259 Z= 0.276 Chirality : 0.041 0.208 3490 Planarity : 0.003 0.054 3294 Dihedral : 19.511 177.902 4157 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 2.58 % Allowed : 20.79 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.17), residues: 2412 helix: 2.72 (0.16), residues: 1151 sheet: 0.73 (0.25), residues: 389 loop : -1.49 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.010 0.001 TYR C 26 PHE 0.012 0.001 PHE E 99 TRP 0.009 0.001 TRP D 323 HIS 0.005 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00340 (21114) covalent geometry : angle 0.49671 (29253) hydrogen bonds : bond 0.04503 ( 1013) hydrogen bonds : angle 3.77998 ( 2865) metal coordination : bond 0.00458 ( 4) metal coordination : angle 1.45293 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 71 time to evaluate : 0.629 Fit side-chains REVERT: A 34 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: B 419 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8133 (t-170) REVERT: C 212 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.9027 (m-10) REVERT: D 53 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7667 (m-70) REVERT: D 102 SER cc_start: 0.8281 (m) cc_final: 0.8073 (p) REVERT: F 111 ASP cc_start: 0.8449 (t0) cc_final: 0.8246 (t0) REVERT: F 138 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7843 (pt) outliers start: 44 outliers final: 33 residues processed: 112 average time/residue: 0.1179 time to fit residues: 22.3227 Evaluate side-chains 107 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 214 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 160 optimal weight: 0.4980 chunk 174 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.082993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053202 restraints weight = 62638.857| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.97 r_work: 0.2704 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21118 Z= 0.208 Angle : 0.547 10.034 29259 Z= 0.303 Chirality : 0.042 0.215 3490 Planarity : 0.004 0.058 3294 Dihedral : 19.585 179.790 4157 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.72 % Favored : 94.24 % Rotamer: Outliers : 2.70 % Allowed : 20.90 % Favored : 76.39 % 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: 1.29 (0.17), residues: 2412 helix: 2.66 (0.16), residues: 1150 sheet: 0.54 (0.25), residues: 392 loop : -1.61 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.014 0.001 TYR A 26 PHE 0.013 0.001 PHE A 45 TRP 0.009 0.001 TRP C 323 HIS 0.007 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00492 (21114) covalent geometry : angle 0.54618 (29253) hydrogen bonds : bond 0.05463 ( 1013) hydrogen bonds : angle 3.92379 ( 2865) metal coordination : bond 0.00563 ( 4) metal coordination : angle 1.86261 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 71 time to evaluate : 0.754 Fit side-chains REVERT: A 34 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: B 419 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.7953 (t-170) REVERT: C 212 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.9077 (m-10) REVERT: C 239 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8587 (tm-30) REVERT: D 53 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: E 228 MET cc_start: 0.9210 (ttm) cc_final: 0.8918 (mtm) REVERT: F 111 ASP cc_start: 0.8443 (t0) cc_final: 0.8233 (t0) REVERT: F 138 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7797 (pt) outliers start: 46 outliers final: 35 residues processed: 114 average time/residue: 0.1122 time to fit residues: 22.1960 Evaluate side-chains 110 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 113 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 173 optimal weight: 40.0000 chunk 192 optimal weight: 0.9980 chunk 81 optimal weight: 0.0670 chunk 250 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.055224 restraints weight = 61900.613| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.88 r_work: 0.2758 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21118 Z= 0.120 Angle : 0.482 10.777 29259 Z= 0.267 Chirality : 0.040 0.209 3490 Planarity : 0.003 0.059 3294 Dihedral : 19.470 177.676 4157 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 2.06 % Allowed : 21.49 % Favored : 76.45 % 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: 1.49 (0.18), residues: 2412 helix: 2.78 (0.16), residues: 1150 sheet: 0.65 (0.25), residues: 397 loop : -1.46 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.013 0.001 TYR D 212 PHE 0.010 0.001 PHE B 45 TRP 0.011 0.001 TRP D 323 HIS 0.004 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00265 (21114) covalent geometry : angle 0.48195 (29253) hydrogen bonds : bond 0.03930 ( 1013) hydrogen bonds : angle 3.70600 ( 2865) metal coordination : bond 0.00328 ( 4) metal coordination : angle 1.10368 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.592 Fit side-chains REVERT: B 419 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8114 (t-170) REVERT: C 212 TYR cc_start: 0.9275 (OUTLIER) cc_final: 0.9021 (m-10) REVERT: F 111 ASP cc_start: 0.8374 (t0) cc_final: 0.8162 (t0) REVERT: F 138 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7716 (pp) outliers start: 35 outliers final: 28 residues processed: 99 average time/residue: 0.1006 time to fit residues: 17.4007 Evaluate side-chains 98 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 112 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 172 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055127 restraints weight = 61850.534| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.92 r_work: 0.2757 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21118 Z= 0.127 Angle : 0.483 11.386 29259 Z= 0.267 Chirality : 0.040 0.211 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.404 178.130 4157 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 2.06 % Allowed : 21.49 % Favored : 76.45 % 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: 1.56 (0.18), residues: 2412 helix: 2.83 (0.15), residues: 1153 sheet: 0.74 (0.25), residues: 395 loop : -1.44 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.016 0.001 TYR D 188 PHE 0.010 0.001 PHE A 357 TRP 0.010 0.001 TRP D 323 HIS 0.004 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00285 (21114) covalent geometry : angle 0.48250 (29253) hydrogen bonds : bond 0.04081 ( 1013) hydrogen bonds : angle 3.64782 ( 2865) metal coordination : bond 0.00288 ( 4) metal coordination : angle 1.22618 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.707 Fit side-chains REVERT: B 419 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8092 (t-170) REVERT: C 212 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.9054 (m-10) REVERT: E 76 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8768 (mm-30) REVERT: F 111 ASP cc_start: 0.8399 (t0) cc_final: 0.8182 (t0) REVERT: F 138 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7762 (pp) outliers start: 35 outliers final: 29 residues processed: 102 average time/residue: 0.1127 time to fit residues: 19.5938 Evaluate side-chains 100 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 204 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.0050 chunk 145 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.085213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.055572 restraints weight = 62148.108| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.01 r_work: 0.2766 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21118 Z= 0.117 Angle : 0.475 11.417 29259 Z= 0.262 Chirality : 0.040 0.209 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.358 177.365 4157 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 2.11 % Allowed : 21.55 % Favored : 76.34 % 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: 1.62 (0.18), residues: 2412 helix: 2.87 (0.15), residues: 1154 sheet: 0.77 (0.25), residues: 396 loop : -1.40 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.012 0.001 TYR D 212 PHE 0.009 0.001 PHE A 357 TRP 0.009 0.001 TRP D 323 HIS 0.003 0.001 HIS D 394 Details of bonding type rmsd covalent geometry : bond 0.00259 (21114) covalent geometry : angle 0.47459 (29253) hydrogen bonds : bond 0.03816 ( 1013) hydrogen bonds : angle 3.60083 ( 2865) metal coordination : bond 0.00234 ( 4) metal coordination : angle 1.05277 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5537.52 seconds wall clock time: 95 minutes 25.53 seconds (5725.53 seconds total)