Starting phenix.real_space_refine on Sat Sep 12 23:36:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3g_13791/09_2026/7q3g_13791.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 40 5.16 5 C 12585 2.51 5 N 3270 2.21 5 O 3670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 6, 'ARG:plan': 6, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 125 Chain: "E" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 6, 'ARG:plan': 6, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 6, 'ARG:plan': 6, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 125 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 6, 'ARG:plan': 6, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 6, 'ARG:plan': 6, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.04, per 1000 atoms: 0.21 Number of scatterers: 19570 At special positions: 0 Unit cell: (137.76, 136.94, 149.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 40 16.00 O 3670 8.00 N 3270 7.00 C 12585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 818.5 milliseconds 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4820 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 31.0% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.550A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.781A pdb=" N ARG A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.756A pdb=" N CYS A 371 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 437 through 441 removed outlier: 4.425A pdb=" N ALA A 440 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.787A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 543 through 564 Processing helix chain 'A' and resid 574 through 604 Processing helix chain 'A' and resid 606 through 637 Proline residue: A 621 - end of helix removed outlier: 3.707A pdb=" N THR A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 98 removed outlier: 3.550A pdb=" N GLY E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'E' and resid 308 through 313 removed outlier: 3.813A pdb=" N ARG E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.459A pdb=" N CYS E 371 " --> pdb=" O SER E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 390 Processing helix chain 'E' and resid 437 through 441 removed outlier: 4.396A pdb=" N ALA E 440 " --> pdb=" O ASP E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 522 removed outlier: 3.755A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 543 through 564 Processing helix chain 'E' and resid 574 through 604 Processing helix chain 'E' and resid 606 through 637 Proline residue: E 621 - end of helix removed outlier: 3.710A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.540A pdb=" N GLY D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 117 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.778A pdb=" N ARG D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.771A pdb=" N CYS D 371 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 390 Processing helix chain 'D' and resid 437 through 441 removed outlier: 4.406A pdb=" N ALA D 440 " --> pdb=" O ASP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 522 removed outlier: 3.715A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 543 through 564 Processing helix chain 'D' and resid 574 through 604 Processing helix chain 'D' and resid 606 through 637 Proline residue: D 621 - end of helix removed outlier: 3.704A pdb=" N THR D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.550A pdb=" N GLY C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 117 Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.784A pdb=" N ARG C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.756A pdb=" N CYS C 371 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 Processing helix chain 'C' and resid 437 through 441 removed outlier: 4.405A pdb=" N ALA C 440 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 522 removed outlier: 3.746A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 removed outlier: 3.542A pdb=" N LEU C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 564 Processing helix chain 'C' and resid 574 through 604 Processing helix chain 'C' and resid 606 through 637 Proline residue: C 621 - end of helix removed outlier: 3.700A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.555A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.798A pdb=" N ARG B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.756A pdb=" N CYS B 371 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 437 through 441 removed outlier: 4.395A pdb=" N ALA B 440 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 522 removed outlier: 3.843A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 543 through 564 Processing helix chain 'B' and resid 574 through 604 Processing helix chain 'B' and resid 606 through 637 Proline residue: B 621 - end of helix removed outlier: 3.703A pdb=" N THR B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 212 removed outlier: 4.070A pdb=" N LEU A 208 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN A 272 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE A 259 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 274 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N LEU A 257 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP A 251 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 260 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 247 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.885A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN A 348 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A 341 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER A 350 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE A 339 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 352 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 360 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU A 329 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 removed outlier: 5.037A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=AA8, first strand: chain 'E' and resid 208 through 212 removed outlier: 4.061A pdb=" N LEU E 208 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN E 272 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE E 259 " --> pdb=" O ASN E 272 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR E 274 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N LEU E 257 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP E 251 " --> pdb=" O PRO E 256 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY E 260 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU E 247 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 376 through 379 removed outlier: 3.896A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN E 348 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY E 341 " --> pdb=" O ASN E 348 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER E 350 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE E 339 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL E 352 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS E 360 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU E 329 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL E 332 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE E 466 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU E 334 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 397 through 398 removed outlier: 5.083A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 70 through 73 Processing sheet with id=AB3, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AB4, first strand: chain 'D' and resid 208 through 212 removed outlier: 4.109A pdb=" N LEU D 208 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN D 272 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE D 259 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 274 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N LEU D 257 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP D 251 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY D 260 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU D 247 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 376 through 379 removed outlier: 3.889A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN D 348 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY D 341 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER D 350 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE D 339 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 352 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS D 360 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU D 329 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 332 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE D 466 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU D 334 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 397 through 398 removed outlier: 5.079A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AB8, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=AB9, first strand: chain 'C' and resid 205 through 212 removed outlier: 3.747A pdb=" N VAL C 304 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 208 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN C 272 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE C 259 " --> pdb=" O ASN C 272 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 274 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N LEU C 257 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP C 251 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C 260 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU C 247 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.882A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS C 360 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU C 329 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 397 through 398 removed outlier: 5.025A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 70 through 73 Processing sheet with id=AC4, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AC5, first strand: chain 'B' and resid 208 through 212 removed outlier: 4.085A pdb=" N LEU B 208 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 272 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 259 " --> pdb=" O ASN B 272 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 274 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N LEU B 257 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 251 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 260 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 247 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.895A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN B 348 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY B 341 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER B 350 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE B 339 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 352 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS B 360 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU B 329 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 397 through 398 removed outlier: 5.036A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6365 1.34 - 1.46: 4256 1.46 - 1.58: 9314 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 19985 Sorted by residual: bond pdb=" CB PRO C 161 " pdb=" CG PRO C 161 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.30e+00 bond pdb=" CG1 ILE D 530 " pdb=" CD1 ILE D 530 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.12e+00 bond pdb=" CG1 ILE C 530 " pdb=" CD1 ILE C 530 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" CG LEU D 553 " pdb=" CD2 LEU D 553 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CG LEU E 553 " pdb=" CD2 LEU E 553 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 ... (remaining 19980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 26407 1.54 - 3.07: 638 3.07 - 4.61: 150 4.61 - 6.15: 30 6.15 - 7.68: 15 Bond angle restraints: 27240 Sorted by residual: angle pdb=" C GLU C 379 " pdb=" N ASP C 380 " pdb=" CA ASP C 380 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLU A 379 " pdb=" N ASP A 380 " pdb=" CA ASP A 380 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C GLU D 379 " pdb=" N ASP D 380 " pdb=" CA ASP D 380 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.57e+00 angle pdb=" C GLU B 379 " pdb=" N ASP B 380 " pdb=" CA ASP B 380 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.31e+00 angle pdb=" C GLU E 379 " pdb=" N ASP E 380 " pdb=" CA ASP E 380 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 ... (remaining 27235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 10543 16.66 - 33.33: 967 33.33 - 49.99: 136 49.99 - 66.65: 23 66.65 - 83.32: 11 Dihedral angle restraints: 11680 sinusoidal: 4225 harmonic: 7455 Sorted by residual: dihedral pdb=" CA GLN D 338 " pdb=" C GLN D 338 " pdb=" N ILE D 339 " pdb=" CA ILE D 339 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLN E 338 " pdb=" C GLN E 338 " pdb=" N ILE E 339 " pdb=" CA ILE E 339 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLN C 338 " pdb=" C GLN C 338 " pdb=" N ILE C 339 " pdb=" CA ILE C 339 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 11677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1900 0.033 - 0.066: 836 0.066 - 0.099: 299 0.099 - 0.132: 114 0.132 - 0.165: 26 Chirality restraints: 3175 Sorted by residual: chirality pdb=" CG LEU B 329 " pdb=" CB LEU B 329 " pdb=" CD1 LEU B 329 " pdb=" CD2 LEU B 329 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CG LEU C 329 " pdb=" CB LEU C 329 " pdb=" CD1 LEU C 329 " pdb=" CD2 LEU C 329 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CB ILE A 413 " pdb=" CA ILE A 413 " pdb=" CG1 ILE A 413 " pdb=" CG2 ILE A 413 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 3172 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 160 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO C 161 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 161 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 161 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 160 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO D 161 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 416 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO D 417 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 417 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 417 " -0.032 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 485 2.69 - 3.25: 19389 3.25 - 3.80: 30327 3.80 - 4.35: 38700 4.35 - 4.90: 64784 Nonbonded interactions: 153685 Sorted by model distance: nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.142 3.040 nonbonded pdb=" OG SER A 533 " pdb=" OD1 ASN A 552 " model vdw 2.145 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.148 3.040 nonbonded pdb=" OG SER C 533 " pdb=" OD1 ASN C 552 " model vdw 2.149 3.040 nonbonded pdb=" OG SER D 533 " pdb=" OD1 ASN D 552 " model vdw 2.161 3.040 ... (remaining 153680 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.690 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 0.057 19985 Z= 0.176 Angle : 0.639 7.682 27240 Z= 0.327 Chirality : 0.045 0.165 3175 Planarity : 0.004 0.076 3505 Dihedral : 13.013 83.316 6860 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.16), residues: 2515 helix: 1.62 (0.20), residues: 670 sheet: -0.59 (0.20), residues: 560 loop : -1.94 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 384 TYR 0.017 0.002 TYR E 441 PHE 0.024 0.002 PHE A 414 TRP 0.005 0.001 TRP E 407 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (19985) covalent geometry : angle 0.63930 / 0.33 (27240) hydrogen bonds : bond 0.13211 / 9.44 ( 921) hydrogen bonds : angle 5.98773 / 4.27 ( 2646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 439 LEU cc_start: 0.8000 (tp) cc_final: 0.7722 (tp) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1545 time to fit residues: 61.6488 Evaluate side-chains 153 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS A 597 GLN ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 GLN D 410 ASN D 597 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS B 233 HIS B 597 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.085285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058524 restraints weight = 69065.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060295 restraints weight = 33966.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061369 restraints weight = 21775.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062080 restraints weight = 16589.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062472 restraints weight = 14081.845| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19985 Z= 0.168 Angle : 0.606 12.099 27240 Z= 0.304 Chirality : 0.043 0.152 3175 Planarity : 0.004 0.051 3505 Dihedral : 4.288 19.333 2735 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.90 % Allowed : 12.04 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2515 helix: 1.79 (0.19), residues: 680 sheet: -0.46 (0.19), residues: 640 loop : -1.78 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 468 TYR 0.013 0.002 TYR B 441 PHE 0.021 0.001 PHE B 561 TRP 0.004 0.001 TRP C 407 HIS 0.004 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (19985) covalent geometry : angle 0.60556 / 0.30 (27240) hydrogen bonds : bond 0.03518 / 2.45 ( 921) hydrogen bonds : angle 4.94565 / 3.51 ( 2646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 ILE cc_start: 0.9409 (mm) cc_final: 0.9099 (mt) REVERT: E 520 LEU cc_start: 0.9611 (tp) cc_final: 0.9401 (mm) REVERT: D 337 ASP cc_start: 0.7969 (t0) cc_final: 0.7747 (t0) REVERT: D 350 SER cc_start: 0.9196 (m) cc_final: 0.8708 (p) REVERT: C 453 ASP cc_start: 0.8236 (m-30) cc_final: 0.8005 (m-30) REVERT: B 580 MET cc_start: 0.8715 (mmm) cc_final: 0.8509 (mmm) REVERT: B 581 ILE cc_start: 0.9399 (mm) cc_final: 0.9100 (mt) outliers start: 18 outliers final: 13 residues processed: 202 average time/residue: 0.1389 time to fit residues: 44.4624 Evaluate side-chains 171 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 137 optimal weight: 10.0000 chunk 208 optimal weight: 50.0000 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 57 optimal weight: 40.0000 chunk 47 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN E 74 ASN D 233 HIS C 206 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN B 74 ASN B 410 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.084257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056949 restraints weight = 68848.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058769 restraints weight = 31167.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059926 restraints weight = 19485.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060653 restraints weight = 14636.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061036 restraints weight = 12301.392| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 19985 Z= 0.287 Angle : 0.645 10.931 27240 Z= 0.333 Chirality : 0.044 0.179 3175 Planarity : 0.004 0.047 3505 Dihedral : 4.510 20.276 2735 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.94 % Allowed : 14.78 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2515 helix: 1.73 (0.20), residues: 685 sheet: -0.52 (0.19), residues: 660 loop : -1.76 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 406 TYR 0.020 0.002 TYR B 441 PHE 0.024 0.002 PHE D 561 TRP 0.006 0.001 TRP E 407 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.29 (19985) covalent geometry : angle 0.64513 / 0.33 (27240) hydrogen bonds : bond 0.03849 / 2.68 ( 921) hydrogen bonds : angle 5.05991 / 3.59 ( 2646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8452 (tp40) cc_final: 0.8236 (tp40) REVERT: A 581 ILE cc_start: 0.9396 (mm) cc_final: 0.9127 (mt) REVERT: E 74 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8883 (p0) REVERT: E 409 GLN cc_start: 0.8429 (tp40) cc_final: 0.8100 (tp40) REVERT: D 350 SER cc_start: 0.9323 (m) cc_final: 0.8896 (p) REVERT: B 74 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8841 (p0) REVERT: B 439 LEU cc_start: 0.9290 (tp) cc_final: 0.9083 (tp) REVERT: B 460 MET cc_start: 0.8833 (mmm) cc_final: 0.8295 (mtm) REVERT: B 580 MET cc_start: 0.8868 (mmm) cc_final: 0.8602 (mmm) REVERT: B 581 ILE cc_start: 0.9425 (mm) cc_final: 0.9173 (mt) outliers start: 39 outliers final: 33 residues processed: 180 average time/residue: 0.1298 time to fit residues: 37.7991 Evaluate side-chains 173 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 97 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 11 optimal weight: 30.0000 chunk 217 optimal weight: 40.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 74 ASN E 464 ASN C 233 HIS B 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.084990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057934 restraints weight = 68000.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059831 restraints weight = 30567.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061006 restraints weight = 18909.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061757 restraints weight = 14183.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.062139 restraints weight = 11932.817| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19985 Z= 0.160 Angle : 0.587 12.489 27240 Z= 0.292 Chirality : 0.043 0.161 3175 Planarity : 0.003 0.044 3505 Dihedral : 4.223 18.469 2735 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.89 % Allowed : 17.06 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2515 helix: 1.87 (0.20), residues: 685 sheet: -0.43 (0.19), residues: 660 loop : -1.62 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 406 TYR 0.014 0.002 TYR B 441 PHE 0.025 0.001 PHE D 561 TRP 0.007 0.001 TRP C 407 HIS 0.004 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (19985) covalent geometry : angle 0.58722 / 0.29 (27240) hydrogen bonds : bond 0.03368 / 2.34 ( 921) hydrogen bonds : angle 4.75129 / 3.37 ( 2646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8470 (tp40) cc_final: 0.8256 (tp40) REVERT: A 479 GLU cc_start: 0.8046 (mp0) cc_final: 0.7631 (mp0) REVERT: A 581 ILE cc_start: 0.9367 (mm) cc_final: 0.9107 (mt) REVERT: E 409 GLN cc_start: 0.8448 (tp40) cc_final: 0.8132 (tp40) REVERT: E 581 ILE cc_start: 0.9338 (mm) cc_final: 0.9088 (mt) REVERT: D 350 SER cc_start: 0.9282 (m) cc_final: 0.8812 (p) REVERT: D 581 ILE cc_start: 0.9376 (mm) cc_final: 0.9060 (mt) REVERT: C 581 ILE cc_start: 0.9310 (mm) cc_final: 0.9104 (mt) REVERT: B 74 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8856 (p0) REVERT: B 439 LEU cc_start: 0.9256 (tp) cc_final: 0.8881 (tp) REVERT: B 580 MET cc_start: 0.8919 (mmm) cc_final: 0.8566 (mmm) REVERT: B 581 ILE cc_start: 0.9391 (mm) cc_final: 0.9167 (mt) outliers start: 38 outliers final: 21 residues processed: 185 average time/residue: 0.1308 time to fit residues: 39.3590 Evaluate side-chains 165 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 562 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 116 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 168 optimal weight: 50.0000 chunk 71 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 chunk 204 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 137 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN C 360 HIS B 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.083739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056631 restraints weight = 68747.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058479 restraints weight = 31009.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059620 restraints weight = 19245.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.060365 restraints weight = 14453.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060734 restraints weight = 12157.041| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19985 Z= 0.230 Angle : 0.610 11.331 27240 Z= 0.310 Chirality : 0.043 0.158 3175 Planarity : 0.003 0.042 3505 Dihedral : 4.330 18.833 2735 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.89 % Allowed : 17.76 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2515 helix: 1.94 (0.20), residues: 680 sheet: -0.37 (0.19), residues: 655 loop : -1.65 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 406 TYR 0.018 0.002 TYR B 441 PHE 0.026 0.002 PHE D 561 TRP 0.005 0.001 TRP D 407 HIS 0.004 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (19985) covalent geometry : angle 0.61001 / 0.31 (27240) hydrogen bonds : bond 0.03591 / 2.50 ( 921) hydrogen bonds : angle 4.82124 / 3.42 ( 2646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8594 (tp40) cc_final: 0.8279 (tp40) REVERT: A 581 ILE cc_start: 0.9390 (mm) cc_final: 0.9159 (mt) REVERT: E 409 GLN cc_start: 0.8526 (tp40) cc_final: 0.8157 (tp40) REVERT: E 581 ILE cc_start: 0.9382 (mm) cc_final: 0.9161 (mt) REVERT: D 350 SER cc_start: 0.9285 (m) cc_final: 0.8856 (p) REVERT: D 581 ILE cc_start: 0.9382 (mm) cc_final: 0.9144 (mt) REVERT: B 439 LEU cc_start: 0.9311 (tp) cc_final: 0.8995 (tp) REVERT: B 580 MET cc_start: 0.8893 (mmm) cc_final: 0.8535 (mmm) REVERT: B 581 ILE cc_start: 0.9425 (mm) cc_final: 0.9206 (mt) outliers start: 38 outliers final: 32 residues processed: 174 average time/residue: 0.1267 time to fit residues: 36.0623 Evaluate side-chains 167 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 161 optimal weight: 0.9980 chunk 123 optimal weight: 0.0570 chunk 179 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN D 348 ASN C 348 ASN B 154 GLN B 348 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.083765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057014 restraints weight = 69283.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058724 restraints weight = 34212.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059768 restraints weight = 21988.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060465 restraints weight = 16858.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060747 restraints weight = 14268.679| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19985 Z= 0.111 Angle : 0.572 13.447 27240 Z= 0.282 Chirality : 0.042 0.154 3175 Planarity : 0.003 0.042 3505 Dihedral : 4.000 17.408 2735 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.44 % Allowed : 19.15 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2515 helix: 1.94 (0.20), residues: 685 sheet: -0.25 (0.19), residues: 655 loop : -1.46 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 139 TYR 0.011 0.001 TYR B 441 PHE 0.021 0.001 PHE D 561 TRP 0.007 0.001 TRP C 407 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (19985) covalent geometry : angle 0.57185 / 0.28 (27240) hydrogen bonds : bond 0.03167 / 2.20 ( 921) hydrogen bonds : angle 4.52944 / 3.21 ( 2646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7924 (mp0) cc_final: 0.7321 (mp0) REVERT: A 515 LEU cc_start: 0.8720 (pt) cc_final: 0.8465 (pp) REVERT: A 581 ILE cc_start: 0.9359 (mm) cc_final: 0.9132 (mt) REVERT: E 409 GLN cc_start: 0.8377 (tp40) cc_final: 0.8166 (tp40) REVERT: E 581 ILE cc_start: 0.9318 (mm) cc_final: 0.9095 (mt) REVERT: D 350 SER cc_start: 0.9148 (m) cc_final: 0.8797 (p) REVERT: D 581 ILE cc_start: 0.9354 (mm) cc_final: 0.9088 (mt) REVERT: B 439 LEU cc_start: 0.9189 (tp) cc_final: 0.8914 (tp) REVERT: B 580 MET cc_start: 0.8819 (mmm) cc_final: 0.8428 (mmm) outliers start: 29 outliers final: 14 residues processed: 194 average time/residue: 0.1263 time to fit residues: 40.4558 Evaluate side-chains 157 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 64 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 107 optimal weight: 50.0000 chunk 115 optimal weight: 40.0000 chunk 142 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.083375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056620 restraints weight = 70128.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.058304 restraints weight = 34711.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.059331 restraints weight = 22409.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060018 restraints weight = 17232.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060357 restraints weight = 14631.959| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19985 Z= 0.136 Angle : 0.576 12.783 27240 Z= 0.288 Chirality : 0.042 0.156 3175 Planarity : 0.003 0.042 3505 Dihedral : 3.973 17.640 2735 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.54 % Allowed : 18.96 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2515 helix: 1.95 (0.20), residues: 685 sheet: -0.22 (0.19), residues: 655 loop : -1.42 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.021 0.001 TYR A 273 PHE 0.030 0.001 PHE A 561 TRP 0.006 0.000 TRP C 407 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (19985) covalent geometry : angle 0.57604 / 0.29 (27240) hydrogen bonds : bond 0.03230 / 2.24 ( 921) hydrogen bonds : angle 4.52889 / 3.21 ( 2646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7929 (mp0) cc_final: 0.7494 (mp0) REVERT: A 515 LEU cc_start: 0.8721 (pt) cc_final: 0.8459 (pp) REVERT: A 581 ILE cc_start: 0.9369 (mm) cc_final: 0.9152 (mt) REVERT: E 409 GLN cc_start: 0.8388 (tp40) cc_final: 0.8158 (tp40) REVERT: E 581 ILE cc_start: 0.9341 (mm) cc_final: 0.9138 (mt) REVERT: D 350 SER cc_start: 0.9168 (m) cc_final: 0.8796 (p) REVERT: D 581 ILE cc_start: 0.9367 (mm) cc_final: 0.9114 (mt) REVERT: B 439 LEU cc_start: 0.9263 (tp) cc_final: 0.8996 (tp) REVERT: B 580 MET cc_start: 0.8798 (mmm) cc_final: 0.8428 (mmm) outliers start: 31 outliers final: 21 residues processed: 175 average time/residue: 0.1250 time to fit residues: 36.1017 Evaluate side-chains 163 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 180 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 212 optimal weight: 0.0070 chunk 215 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.083756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057054 restraints weight = 69860.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058724 restraints weight = 34486.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059740 restraints weight = 22479.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060449 restraints weight = 17208.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060810 restraints weight = 14673.889| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19985 Z= 0.121 Angle : 0.570 13.210 27240 Z= 0.283 Chirality : 0.042 0.156 3175 Planarity : 0.003 0.042 3505 Dihedral : 3.910 17.231 2735 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.34 % Allowed : 19.55 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2515 helix: 1.97 (0.19), residues: 685 sheet: -0.19 (0.19), residues: 655 loop : -1.35 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.018 0.001 TYR A 273 PHE 0.028 0.001 PHE A 561 TRP 0.006 0.001 TRP C 407 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19985) covalent geometry : angle 0.56976 / 0.28 (27240) hydrogen bonds : bond 0.03140 / 2.18 ( 921) hydrogen bonds : angle 4.45768 / 3.16 ( 2646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7833 (mp0) cc_final: 0.7475 (mp0) REVERT: A 515 LEU cc_start: 0.8700 (pt) cc_final: 0.8436 (pp) REVERT: A 581 ILE cc_start: 0.9369 (mm) cc_final: 0.9153 (mt) REVERT: E 409 GLN cc_start: 0.8367 (tp40) cc_final: 0.8155 (tp40) REVERT: D 350 SER cc_start: 0.9159 (m) cc_final: 0.8809 (p) REVERT: D 581 ILE cc_start: 0.9358 (mm) cc_final: 0.9119 (mt) REVERT: C 453 ASP cc_start: 0.8153 (m-30) cc_final: 0.7941 (m-30) REVERT: B 439 LEU cc_start: 0.9269 (tp) cc_final: 0.9011 (tp) REVERT: B 580 MET cc_start: 0.8836 (mmm) cc_final: 0.8382 (mmm) outliers start: 27 outliers final: 21 residues processed: 170 average time/residue: 0.1244 time to fit residues: 35.4401 Evaluate side-chains 158 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 202 optimal weight: 6.9990 chunk 180 optimal weight: 0.2980 chunk 99 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 233 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.4299 > 50:) chunk 150 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 110 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 ASN B 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.081995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055758 restraints weight = 70298.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.057441 restraints weight = 34192.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.058494 restraints weight = 21956.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.059170 restraints weight = 16692.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059409 restraints weight = 14097.360| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19985 Z= 0.218 Angle : 0.606 11.684 27240 Z= 0.309 Chirality : 0.043 0.155 3175 Planarity : 0.003 0.042 3505 Dihedral : 4.185 18.624 2735 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.49 % Allowed : 19.70 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2515 helix: 1.98 (0.20), residues: 680 sheet: -0.23 (0.19), residues: 660 loop : -1.40 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.018 0.002 TYR B 441 PHE 0.027 0.002 PHE A 561 TRP 0.009 0.001 TRP C 407 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (19985) covalent geometry : angle 0.60628 / 0.31 (27240) hydrogen bonds : bond 0.03456 / 2.39 ( 921) hydrogen bonds : angle 4.66580 / 3.31 ( 2646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7792 (mp0) cc_final: 0.7584 (mp0) REVERT: A 515 LEU cc_start: 0.8725 (pt) cc_final: 0.8453 (pp) REVERT: E 409 GLN cc_start: 0.8430 (tp40) cc_final: 0.8123 (tp40) REVERT: D 350 SER cc_start: 0.9194 (m) cc_final: 0.8840 (p) REVERT: C 498 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7312 (mpt-90) REVERT: B 580 MET cc_start: 0.8831 (mmm) cc_final: 0.8416 (mmm) outliers start: 30 outliers final: 26 residues processed: 165 average time/residue: 0.1299 time to fit residues: 35.3332 Evaluate side-chains 159 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 137 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 238 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 15 optimal weight: 0.0270 chunk 1 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 233 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.083696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056946 restraints weight = 69029.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058762 restraints weight = 31084.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059913 restraints weight = 19310.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.060581 restraints weight = 14467.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060937 restraints weight = 12242.629| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19985 Z= 0.194 Angle : 0.602 12.255 27240 Z= 0.304 Chirality : 0.043 0.156 3175 Planarity : 0.003 0.042 3505 Dihedral : 4.163 18.667 2735 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 1.44 % Allowed : 19.85 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2515 helix: 1.82 (0.20), residues: 690 sheet: -0.24 (0.19), residues: 660 loop : -1.35 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 406 TYR 0.016 0.002 TYR A 273 PHE 0.024 0.001 PHE A 561 TRP 0.008 0.001 TRP C 407 HIS 0.003 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (19985) covalent geometry : angle 0.60194 / 0.30 (27240) hydrogen bonds : bond 0.03419 / 2.37 ( 921) hydrogen bonds : angle 4.63457 / 3.29 ( 2646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 515 LEU cc_start: 0.8746 (pt) cc_final: 0.8492 (pp) REVERT: E 409 GLN cc_start: 0.8536 (tp40) cc_final: 0.8116 (tp40) REVERT: D 350 SER cc_start: 0.9255 (m) cc_final: 0.8854 (p) REVERT: C 498 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7484 (mpt-90) REVERT: B 580 MET cc_start: 0.8914 (mmm) cc_final: 0.8459 (mmm) outliers start: 29 outliers final: 24 residues processed: 161 average time/residue: 0.1378 time to fit residues: 36.1551 Evaluate side-chains 153 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 158 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 119 optimal weight: 50.0000 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.0670 chunk 205 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 HIS ** 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 = 0.3691 r_free = 0.3691 target = 0.083896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057237 restraints weight = 70206.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059005 restraints weight = 33410.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060122 restraints weight = 21225.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060830 restraints weight = 16037.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061207 restraints weight = 13496.774| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19985 Z= 0.108 Angle : 0.586 13.798 27240 Z= 0.288 Chirality : 0.042 0.159 3175 Planarity : 0.003 0.060 3505 Dihedral : 3.902 17.980 2735 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 1.19 % Allowed : 20.35 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2515 helix: 1.90 (0.19), residues: 690 sheet: -0.17 (0.20), residues: 655 loop : -1.23 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 139 TYR 0.017 0.001 TYR A 273 PHE 0.022 0.001 PHE A 561 TRP 0.005 0.001 TRP C 407 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (19985) covalent geometry : angle 0.58627 / 0.29 (27240) hydrogen bonds : bond 0.03146 / 2.18 ( 921) hydrogen bonds : angle 4.43160 / 3.14 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.43 seconds wall clock time: 56 minutes 27.23 seconds (3387.23 seconds total)