Starting phenix.real_space_refine on Tue May 20 19:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6b_49055/05_2025/9n6b_49055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6b_49055/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9n6b_49055/05_2025/9n6b_49055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6b_49055/05_2025/9n6b_49055.map" model { file = "/net/cci-nas-00/data/ceres_data/9n6b_49055/05_2025/9n6b_49055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6b_49055/05_2025/9n6b_49055.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG: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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 27, 'ARG: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: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 12, '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: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 22, 'ASP:plan': 17} 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, 'GLU:plan': 9, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'ASP:plan': 8, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} 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: 13.29, per 1000 atoms: 0.65 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: 5.26 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 7.53 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: 7.36 Time building geometry restraints manager: 5.93 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 451 or resid 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 451 or resid 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: 0.010 Normalize map: mean=0, sd=1: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.520 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.070 ------------------------------------------------------------------------------- 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 : 3.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), 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 TRP 0.009 0.001 TRP B 481 HIS 0.010 0.001 HIS A 419 PHE 0.014 0.001 PHE B 529 TYR 0.038 0.001 TYR C 188 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.29754 ( 1013) hydrogen bonds : angle 7.39501 ( 2865) metal coordination : bond 0.00450 ( 4) metal coordination : angle 1.24075 ( 6) covalent geometry : bond 0.00377 (21114) covalent geometry : angle 0.61424 (29253) *********************** 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 : 2.186 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: 0.2662 time to fit residues: 55.9946 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 : 2.410 ------------------------------------------------------------------------------- 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 212 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 197 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS F 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.086134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056924 restraints weight = 61233.742| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.96 r_work: 0.2802 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21118 Z= 0.130 Angle : 0.525 8.567 29259 Z= 0.292 Chirality : 0.041 0.197 3490 Planarity : 0.004 0.061 3294 Dihedral : 19.542 178.725 4194 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.35 % Allowed : 19.44 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2412 helix: 2.03 (0.15), residues: 1152 sheet: 0.74 (0.26), residues: 396 loop : -1.32 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS D 53 PHE 0.015 0.001 PHE A 231 TYR 0.010 0.001 TYR C 26 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 1013) hydrogen bonds : angle 4.47367 ( 2865) metal coordination : bond 0.00176 ( 4) metal coordination : angle 1.41752 ( 6) covalent geometry : bond 0.00267 (21114) covalent geometry : angle 0.52506 (29253) *********************** 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 128 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 2.146 Fit side-chains REVERT: B 216 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 353 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7856 (mp0) REVERT: B 419 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7803 (t70) REVERT: D 102 SER cc_start: 0.8296 (m) cc_final: 0.8059 (p) REVERT: F 200 MET cc_start: 0.8131 (tpp) cc_final: 0.7783 (tmm) REVERT: F 204 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8443 (tm-30) outliers start: 40 outliers final: 21 residues processed: 125 average time/residue: 0.2542 time to fit residues: 54.4837 Evaluate side-chains 105 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 227 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.085379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056097 restraints weight = 60702.564| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 4.00 r_work: 0.2771 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21118 Z= 0.146 Angle : 0.508 8.897 29259 Z= 0.282 Chirality : 0.041 0.213 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.533 178.584 4162 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.70 % Allowed : 18.97 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2412 helix: 2.45 (0.16), residues: 1149 sheet: 0.70 (0.26), residues: 397 loop : -1.36 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.004 0.001 HIS D 394 PHE 0.013 0.001 PHE E 99 TYR 0.013 0.001 TYR C 188 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.05106 ( 1013) hydrogen bonds : angle 4.07326 ( 2865) metal coordination : bond 0.00359 ( 4) metal coordination : angle 1.39149 ( 6) covalent geometry : bond 0.00328 (21114) covalent geometry : angle 0.50782 (29253) *********************** 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 135 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 89 time to evaluate : 2.367 Fit side-chains REVERT: B 419 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.7975 (t-170) REVERT: D 102 SER cc_start: 0.8300 (m) cc_final: 0.8077 (p) REVERT: E 19 GLN cc_start: 0.8829 (tp40) cc_final: 0.8386 (tp-100) REVERT: F 204 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8503 (tm-30) outliers start: 46 outliers final: 30 residues processed: 131 average time/residue: 0.2528 time to fit residues: 57.3986 Evaluate side-chains 109 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain A residue 346 ILE 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 424 LEU 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 C residue 447 ILE 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 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 402 ILE 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 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 161 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 226 optimal weight: 0.0670 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.086392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.057322 restraints weight = 61121.906| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.98 r_work: 0.2805 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21118 Z= 0.120 Angle : 0.481 8.825 29259 Z= 0.267 Chirality : 0.040 0.206 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.475 176.865 4160 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 2.41 % Allowed : 19.38 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2412 helix: 2.54 (0.15), residues: 1157 sheet: 0.80 (0.26), residues: 396 loop : -1.37 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 323 HIS 0.004 0.001 HIS A 514 PHE 0.033 0.001 PHE A 78 TYR 0.009 0.001 TYR D 121 ARG 0.001 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 1013) hydrogen bonds : angle 3.86077 ( 2865) metal coordination : bond 0.00249 ( 4) metal coordination : angle 1.18814 ( 6) covalent geometry : bond 0.00264 (21114) covalent geometry : angle 0.48099 (29253) *********************** 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 121 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 2.474 Fit side-chains REVERT: B 419 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8015 (t-170) REVERT: C 212 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.9038 (m-10) REVERT: D 102 SER cc_start: 0.8304 (m) cc_final: 0.8093 (p) REVERT: F 111 ASP cc_start: 0.8334 (t0) cc_final: 0.8113 (t0) REVERT: F 138 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7814 (pt) REVERT: F 204 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8513 (tm-30) outliers start: 41 outliers final: 28 residues processed: 117 average time/residue: 0.2623 time to fit residues: 54.2537 Evaluate side-chains 109 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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 246 THR Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 432 VAL 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 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 402 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 165 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 178 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** E 101 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 = 0.084455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.055406 restraints weight = 61684.495| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.91 r_work: 0.2752 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21118 Z= 0.175 Angle : 0.521 8.969 29259 Z= 0.289 Chirality : 0.041 0.211 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.533 178.887 4158 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 2.70 % Allowed : 19.85 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2412 helix: 2.61 (0.16), residues: 1150 sheet: 0.75 (0.26), residues: 392 loop : -1.45 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 481 HIS 0.006 0.001 HIS A 46 PHE 0.033 0.001 PHE A 78 TYR 0.011 0.001 TYR B 333 ARG 0.003 0.000 ARG E 253 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 1013) hydrogen bonds : angle 3.92932 ( 2865) metal coordination : bond 0.00437 ( 4) metal coordination : angle 1.73933 ( 6) covalent geometry : bond 0.00406 (21114) covalent geometry : angle 0.52009 (29253) *********************** 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 122 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 76 time to evaluate : 2.275 Fit side-chains REVERT: B 419 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8043 (t-170) REVERT: C 212 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.9024 (m-10) REVERT: D 102 SER cc_start: 0.8249 (m) cc_final: 0.8029 (p) REVERT: F 138 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7828 (pt) REVERT: F 204 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8463 (tm-30) outliers start: 46 outliers final: 32 residues processed: 119 average time/residue: 0.2461 time to fit residues: 52.0493 Evaluate side-chains 110 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 2.414 ------------------------------------------------------------------------------- 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 337 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 166 LEU 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 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 402 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 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 239 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.086067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057009 restraints weight = 61100.426| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.96 r_work: 0.2797 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21118 Z= 0.116 Angle : 0.469 7.429 29259 Z= 0.261 Chirality : 0.040 0.207 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.463 177.140 4157 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 2.00 % Allowed : 20.79 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2412 helix: 2.69 (0.15), residues: 1157 sheet: 0.78 (0.26), residues: 399 loop : -1.39 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 323 HIS 0.003 0.001 HIS A 46 PHE 0.035 0.001 PHE A 78 TYR 0.008 0.001 TYR C 26 ARG 0.001 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 1013) hydrogen bonds : angle 3.73791 ( 2865) metal coordination : bond 0.00252 ( 4) metal coordination : angle 1.29805 ( 6) covalent geometry : bond 0.00252 (21114) covalent geometry : angle 0.46917 (29253) *********************** 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 113 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 2.236 Fit side-chains REVERT: A 34 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: B 419 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8073 (t-170) REVERT: C 212 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.9015 (m-10) REVERT: C 239 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8545 (tm-30) REVERT: F 138 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7825 (pt) REVERT: F 204 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8462 (tm-30) outliers start: 34 outliers final: 28 residues processed: 109 average time/residue: 0.2848 time to fit residues: 52.3204 Evaluate side-chains 104 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 2.367 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 337 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 419 HIS 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 232 LEU Chi-restraints excluded: chain D residue 402 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 171 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 173 optimal weight: 40.0000 chunk 45 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 HIS D 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053527 restraints weight = 61360.690| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.91 r_work: 0.2705 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21118 Z= 0.254 Angle : 0.577 7.755 29259 Z= 0.321 Chirality : 0.044 0.217 3490 Planarity : 0.004 0.055 3294 Dihedral : 19.638 179.611 4157 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 2.76 % Allowed : 20.26 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2412 helix: 2.57 (0.16), residues: 1150 sheet: 0.60 (0.26), residues: 393 loop : -1.63 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 323 HIS 0.008 0.001 HIS C 46 PHE 0.036 0.002 PHE A 78 TYR 0.015 0.001 TYR B 333 ARG 0.003 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.06022 ( 1013) hydrogen bonds : angle 4.07137 ( 2865) metal coordination : bond 0.00670 ( 4) metal coordination : angle 2.19628 ( 6) covalent geometry : bond 0.00604 (21114) covalent geometry : angle 0.57610 (29253) *********************** 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 116 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 69 time to evaluate : 2.305 Fit side-chains REVERT: A 34 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: B 419 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.7876 (t-170) REVERT: C 212 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.9045 (m-10) REVERT: F 138 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7777 (pt) outliers start: 47 outliers final: 33 residues processed: 110 average time/residue: 0.2576 time to fit residues: 49.6033 Evaluate side-chains 103 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 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 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 424 LEU Chi-restraints excluded: chain C residue 447 ILE 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 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 402 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 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 228 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 174 optimal weight: 30.0000 chunk 193 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 373 ASN D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.084818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.055148 restraints weight = 62471.959| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.97 r_work: 0.2754 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21118 Z= 0.121 Angle : 0.482 7.713 29259 Z= 0.268 Chirality : 0.040 0.208 3490 Planarity : 0.003 0.055 3294 Dihedral : 19.505 177.701 4157 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 2.00 % Allowed : 21.20 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.17), residues: 2412 helix: 2.74 (0.15), residues: 1151 sheet: 0.69 (0.26), residues: 393 loop : -1.45 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 323 HIS 0.008 0.001 HIS A 419 PHE 0.038 0.001 PHE A 78 TYR 0.013 0.001 TYR A 26 ARG 0.005 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 1013) hydrogen bonds : angle 3.75076 ( 2865) metal coordination : bond 0.00315 ( 4) metal coordination : angle 1.17539 ( 6) covalent geometry : bond 0.00266 (21114) covalent geometry : angle 0.48179 (29253) *********************** 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 104 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 2.115 Fit side-chains REVERT: A 34 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: B 419 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.8088 (t-170) REVERT: C 212 TYR cc_start: 0.9278 (OUTLIER) cc_final: 0.9016 (m-10) REVERT: C 239 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8537 (tm-30) REVERT: D 53 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7634 (m-70) REVERT: F 138 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7784 (pt) outliers start: 34 outliers final: 28 residues processed: 101 average time/residue: 0.2983 time to fit residues: 52.5926 Evaluate side-chains 101 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 2.668 ------------------------------------------------------------------------------- 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 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 246 THR Chi-restraints excluded: chain B residue 373 ASN Chi-restraints excluded: chain B residue 419 HIS 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 53 HIS 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 232 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 247 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.083321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053551 restraints weight = 62540.940| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 4.02 r_work: 0.2712 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21118 Z= 0.193 Angle : 0.531 7.788 29259 Z= 0.295 Chirality : 0.042 0.214 3490 Planarity : 0.004 0.057 3294 Dihedral : 19.538 179.275 4157 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.76 % Favored : 94.20 % Rotamer: Outliers : 2.23 % Allowed : 21.02 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2412 helix: 2.68 (0.15), residues: 1155 sheet: 0.63 (0.26), residues: 392 loop : -1.59 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.007 0.001 HIS A 46 PHE 0.036 0.001 PHE A 78 TYR 0.012 0.001 TYR D 188 ARG 0.005 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.05189 ( 1013) hydrogen bonds : angle 3.87020 ( 2865) metal coordination : bond 0.00457 ( 4) metal coordination : angle 1.73414 ( 6) covalent geometry : bond 0.00453 (21114) covalent geometry : angle 0.53048 (29253) *********************** 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 108 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 70 time to evaluate : 2.342 Fit side-chains REVERT: A 34 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: B 419 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7979 (t-170) REVERT: C 212 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.9044 (m-10) REVERT: C 239 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8592 (tm-30) REVERT: D 53 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7776 (m-70) REVERT: F 138 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7772 (pt) outliers start: 38 outliers final: 31 residues processed: 104 average time/residue: 0.2606 time to fit residues: 47.4915 Evaluate side-chains 105 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 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 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 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 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 232 LEU Chi-restraints excluded: chain D residue 402 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 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 154 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 160 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 422 GLN D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.085066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.055647 restraints weight = 62000.655| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.94 r_work: 0.2766 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21118 Z= 0.112 Angle : 0.474 7.673 29259 Z= 0.263 Chirality : 0.039 0.209 3490 Planarity : 0.003 0.058 3294 Dihedral : 19.439 177.243 4157 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 1.88 % Allowed : 21.55 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2412 helix: 2.83 (0.15), residues: 1150 sheet: 0.71 (0.25), residues: 397 loop : -1.42 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 323 HIS 0.014 0.001 HIS D 53 PHE 0.037 0.001 PHE A 78 TYR 0.015 0.001 TYR A 26 ARG 0.004 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1013) hydrogen bonds : angle 3.66607 ( 2865) metal coordination : bond 0.00220 ( 4) metal coordination : angle 1.13078 ( 6) covalent geometry : bond 0.00242 (21114) covalent geometry : angle 0.47359 (29253) ********************** 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 100 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 2.209 Fit side-chains REVERT: A 34 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: B 419 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8081 (t-170) REVERT: C 212 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.9004 (m-10) REVERT: F 138 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7703 (pp) outliers start: 32 outliers final: 26 residues processed: 97 average time/residue: 0.2615 time to fit residues: 43.6165 Evaluate side-chains 97 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 2.420 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 337 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 419 HIS 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 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 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 1 optimal weight: 2.9990 chunk 219 optimal weight: 0.0270 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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** D 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.055757 restraints weight = 62428.535| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.02 r_work: 0.2772 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21118 Z= 0.112 Angle : 0.472 12.936 29259 Z= 0.260 Chirality : 0.039 0.210 3490 Planarity : 0.003 0.057 3294 Dihedral : 19.373 177.199 4157 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 1.82 % Allowed : 21.61 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2412 helix: 2.89 (0.15), residues: 1152 sheet: 0.79 (0.26), residues: 399 loop : -1.36 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 323 HIS 0.003 0.001 HIS D 394 PHE 0.036 0.001 PHE A 78 TYR 0.007 0.001 TYR C 11 ARG 0.004 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 1013) hydrogen bonds : angle 3.58161 ( 2865) metal coordination : bond 0.00208 ( 4) metal coordination : angle 1.12095 ( 6) covalent geometry : bond 0.00244 (21114) covalent geometry : angle 0.47155 (29253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11000.00 seconds wall clock time: 190 minutes 56.04 seconds (11456.04 seconds total)