Starting phenix.real_space_refine on Thu Mar 5 04:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3g_13791/03_2026/7q3g_13791.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3g_13791/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7q3g_13791/03_2026/7q3g_13791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3g_13791/03_2026/7q3g_13791.map" model { file = "/net/cci-nas-00/data/ceres_data/7q3g_13791/03_2026/7q3g_13791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3g_13791/03_2026/7q3g_13791.cif" } 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-dev-5986/lib/python3.9/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: 4.11, 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: 1.19 Conformation dependent library (CDL) restraints added in 859.7 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: 0.65 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: 3.33 Time building geometry restraints manager: 1.66 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: 0.01 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: 1.650 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.070 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 covalent geometry : bond 0.00412 (19985) covalent geometry : angle 0.63930 (27240) hydrogen bonds : bond 0.13211 ( 921) hydrogen bonds : angle 5.98773 ( 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 : 0.623 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: 0.7723 (tp) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1432 time to fit residues: 56.1991 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 : 0.681 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 597 GLN ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 GLN D 233 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.058511 restraints weight = 69096.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060266 restraints weight = 33982.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.061344 restraints weight = 21951.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062052 restraints weight = 16683.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062442 restraints weight = 14134.313| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1816 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= 0.169 Angle : 0.605 12.098 27240 Z= 0.304 Chirality : 0.043 0.153 3175 Planarity : 0.004 0.051 3505 Dihedral : 4.282 19.270 2735 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.95 % Allowed : 11.69 % Favored : 87.36 % 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: -0.45 (0.20), residues: 640 loop : -1.77 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 468 TYR 0.012 0.002 TYR B 441 PHE 0.019 0.001 PHE B 561 TRP 0.004 0.001 TRP C 407 HIS 0.004 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00379 (19985) covalent geometry : angle 0.60512 (27240) hydrogen bonds : bond 0.03506 ( 921) hydrogen bonds : angle 4.93736 ( 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 214 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.710 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 479 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7454 (mp0) REVERT: A 581 ILE cc_start: 0.9405 (mm) cc_final: 0.9095 (mt) REVERT: E 520 LEU cc_start: 0.9609 (tp) cc_final: 0.9398 (mm) REVERT: D 337 ASP cc_start: 0.7962 (t0) cc_final: 0.7750 (t0) REVERT: D 350 SER cc_start: 0.9191 (m) cc_final: 0.8714 (p) REVERT: C 453 ASP cc_start: 0.8227 (m-30) cc_final: 0.7997 (m-30) REVERT: B 439 LEU cc_start: 0.9307 (tp) cc_final: 0.8763 (tp) REVERT: B 581 ILE cc_start: 0.9394 (mm) cc_final: 0.9098 (mt) outliers start: 19 outliers final: 13 residues processed: 203 average time/residue: 0.1234 time to fit residues: 39.3011 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 : 0.632 ------------------------------------------------------------------------------- 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: 9.9990 chunk 208 optimal weight: 50.0000 chunk 110 optimal weight: 0.0470 chunk 20 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 2.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 233 HIS C 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.084813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058053 restraints weight = 68454.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.059776 restraints weight = 34124.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060794 restraints weight = 22123.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061394 restraints weight = 17050.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061820 restraints weight = 14656.102| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19985 Z= 0.144 Angle : 0.578 12.185 27240 Z= 0.289 Chirality : 0.043 0.158 3175 Planarity : 0.003 0.047 3505 Dihedral : 4.083 19.046 2735 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.95 % Allowed : 14.53 % Favored : 84.53 % 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: -0.51 (0.17), residues: 2515 helix: 1.87 (0.20), residues: 685 sheet: -0.36 (0.20), residues: 640 loop : -1.71 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 384 TYR 0.015 0.002 TYR D 624 PHE 0.026 0.001 PHE D 561 TRP 0.006 0.000 TRP C 407 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00320 (19985) covalent geometry : angle 0.57818 (27240) hydrogen bonds : bond 0.03357 ( 921) hydrogen bonds : angle 4.71203 ( 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 199 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 ILE cc_start: 0.9393 (mm) cc_final: 0.9104 (mt) REVERT: E 581 ILE cc_start: 0.9373 (mm) cc_final: 0.9085 (mt) REVERT: D 337 ASP cc_start: 0.7954 (t0) cc_final: 0.7738 (t0) REVERT: D 350 SER cc_start: 0.9161 (m) cc_final: 0.8749 (p) REVERT: D 389 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8444 (tm-30) REVERT: D 515 LEU cc_start: 0.8441 (pt) cc_final: 0.8224 (pp) REVERT: D 520 LEU cc_start: 0.9591 (tp) cc_final: 0.9380 (mm) REVERT: D 581 ILE cc_start: 0.9408 (mm) cc_final: 0.9075 (mt) REVERT: C 453 ASP cc_start: 0.8161 (m-30) cc_final: 0.7935 (m-30) REVERT: C 581 ILE cc_start: 0.9302 (mm) cc_final: 0.9036 (mt) REVERT: B 439 LEU cc_start: 0.9324 (tp) cc_final: 0.8826 (tp) REVERT: B 581 ILE cc_start: 0.9373 (mm) cc_final: 0.9125 (mt) outliers start: 19 outliers final: 16 residues processed: 190 average time/residue: 0.1207 time to fit residues: 36.4790 Evaluate side-chains 173 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 562 THR Chi-restraints excluded: chain A residue 622 LEU 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 622 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain B residue 413 ILE 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: 3.9990 chunk 25 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 163 optimal weight: 0.0970 chunk 11 optimal weight: 30.0000 chunk 217 optimal weight: 40.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.084244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057417 restraints weight = 69340.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059102 restraints weight = 34331.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060141 restraints weight = 22188.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.060819 restraints weight = 17009.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.061191 restraints weight = 14493.844| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19985 Z= 0.144 Angle : 0.569 12.194 27240 Z= 0.284 Chirality : 0.042 0.149 3175 Planarity : 0.003 0.043 3505 Dihedral : 4.014 18.646 2735 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.94 % Allowed : 15.92 % Favored : 82.14 % 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: -0.40 (0.17), residues: 2515 helix: 1.93 (0.20), residues: 685 sheet: -0.35 (0.19), residues: 660 loop : -1.59 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 406 TYR 0.013 0.002 TYR A 627 PHE 0.026 0.001 PHE D 561 TRP 0.007 0.000 TRP E 407 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00321 (19985) covalent geometry : angle 0.56946 (27240) hydrogen bonds : bond 0.03255 ( 921) hydrogen bonds : angle 4.58936 ( 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 212 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 ILE cc_start: 0.9377 (mm) cc_final: 0.9120 (mt) REVERT: E 581 ILE cc_start: 0.9374 (mm) cc_final: 0.9123 (mt) REVERT: D 337 ASP cc_start: 0.7995 (t0) cc_final: 0.7789 (t0) REVERT: D 350 SER cc_start: 0.9197 (m) cc_final: 0.8753 (p) REVERT: D 390 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8702 (pt) REVERT: D 515 LEU cc_start: 0.8457 (pt) cc_final: 0.8254 (pp) REVERT: D 581 ILE cc_start: 0.9408 (mm) cc_final: 0.9108 (mt) REVERT: C 453 ASP cc_start: 0.8196 (m-30) cc_final: 0.7954 (m-30) REVERT: C 581 ILE cc_start: 0.9350 (mm) cc_final: 0.9121 (mt) REVERT: B 581 ILE cc_start: 0.9370 (mm) cc_final: 0.9136 (mt) outliers start: 39 outliers final: 27 residues processed: 199 average time/residue: 0.1211 time to fit residues: 38.7181 Evaluate side-chains 183 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE 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 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 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 304 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 304 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 330 VAL 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: 9.9990 chunk 98 optimal weight: 2.9990 chunk 168 optimal weight: 50.0000 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 30.0000 chunk 204 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 chunk 175 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 74 ASN B 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.082635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055655 restraints weight = 69764.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057267 restraints weight = 34831.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058328 restraints weight = 22801.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059012 restraints weight = 17460.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.059260 restraints weight = 14833.285| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19985 Z= 0.207 Angle : 0.593 11.353 27240 Z= 0.302 Chirality : 0.043 0.158 3175 Planarity : 0.003 0.043 3505 Dihedral : 4.198 18.997 2735 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.24 % Allowed : 17.26 % Favored : 80.50 % 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: -0.40 (0.16), residues: 2515 helix: 1.87 (0.20), residues: 685 sheet: -0.34 (0.19), residues: 660 loop : -1.55 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 406 TYR 0.017 0.002 TYR B 441 PHE 0.026 0.002 PHE C 232 TRP 0.009 0.001 TRP C 407 HIS 0.005 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00460 (19985) covalent geometry : angle 0.59314 (27240) hydrogen bonds : bond 0.03491 ( 921) hydrogen bonds : angle 4.70361 ( 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 195 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7885 (mp0) cc_final: 0.7322 (mp0) REVERT: A 581 ILE cc_start: 0.9389 (mm) cc_final: 0.9155 (mt) REVERT: E 581 ILE cc_start: 0.9410 (mm) cc_final: 0.9186 (mt) REVERT: D 350 SER cc_start: 0.9248 (m) cc_final: 0.8831 (p) REVERT: D 581 ILE cc_start: 0.9416 (mm) cc_final: 0.9105 (mt) REVERT: C 581 ILE cc_start: 0.9408 (mm) cc_final: 0.9204 (mt) REVERT: B 74 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8715 (p0) REVERT: B 439 LEU cc_start: 0.9208 (tp) cc_final: 0.8854 (tp) REVERT: B 581 ILE cc_start: 0.9382 (mm) cc_final: 0.9176 (mt) outliers start: 45 outliers final: 33 residues processed: 186 average time/residue: 0.1160 time to fit residues: 34.8605 Evaluate side-chains 177 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 575 VAL 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 575 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 304 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 74 ASN Chi-restraints excluded: chain B residue 284 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 161 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN E 348 ASN E 464 ASN D 348 ASN C 348 ASN B 74 ASN B 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.086161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060386 restraints weight = 67317.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.062292 restraints weight = 29290.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063498 restraints weight = 17759.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.064236 restraints weight = 13161.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064670 restraints weight = 10990.947| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19985 Z= 0.099 Angle : 0.567 13.722 27240 Z= 0.279 Chirality : 0.042 0.164 3175 Planarity : 0.003 0.042 3505 Dihedral : 3.874 17.803 2735 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.34 % Allowed : 19.15 % 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: -0.27 (0.17), residues: 2515 helix: 1.92 (0.19), residues: 685 sheet: -0.24 (0.19), residues: 660 loop : -1.46 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.010 0.001 TYR A 620 PHE 0.022 0.001 PHE D 561 TRP 0.006 0.001 TRP D 407 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00206 (19985) covalent geometry : angle 0.56688 (27240) hydrogen bonds : bond 0.03051 ( 921) hydrogen bonds : angle 4.43516 ( 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 199 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7839 (mp0) cc_final: 0.7377 (mp0) REVERT: E 581 ILE cc_start: 0.9284 (mm) cc_final: 0.9082 (mt) REVERT: D 350 SER cc_start: 0.9183 (m) cc_final: 0.8798 (p) REVERT: D 581 ILE cc_start: 0.9317 (mm) cc_final: 0.9075 (mt) REVERT: C 453 ASP cc_start: 0.8324 (m-30) cc_final: 0.8088 (m-30) REVERT: B 439 LEU cc_start: 0.9182 (tp) cc_final: 0.8878 (tp) outliers start: 27 outliers final: 15 residues processed: 195 average time/residue: 0.1174 time to fit residues: 37.3911 Evaluate side-chains 161 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 E residue 284 VAL Chi-restraints excluded: chain E residue 413 ILE 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 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 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: 50.0000 chunk 235 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 242 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 103 optimal weight: 0.0170 chunk 107 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 92 optimal weight: 0.0670 chunk 54 optimal weight: 7.9990 overall best weight: 3.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.084500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.058294 restraints weight = 68893.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060166 restraints weight = 30410.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061329 restraints weight = 18751.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062039 restraints weight = 13908.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.062382 restraints weight = 11665.073| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19985 Z= 0.173 Angle : 0.584 12.337 27240 Z= 0.295 Chirality : 0.042 0.157 3175 Planarity : 0.003 0.041 3505 Dihedral : 3.999 18.123 2735 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.64 % Allowed : 19.50 % Favored : 78.86 % 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: -0.25 (0.17), residues: 2515 helix: 1.98 (0.20), residues: 685 sheet: -0.24 (0.19), residues: 660 loop : -1.46 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.015 0.002 TYR B 441 PHE 0.020 0.001 PHE D 561 TRP 0.007 0.001 TRP C 407 HIS 0.003 0.001 HIS E 233 Details of bonding type rmsd covalent geometry : bond 0.00388 (19985) covalent geometry : angle 0.58385 (27240) hydrogen bonds : bond 0.03289 ( 921) hydrogen bonds : angle 4.50965 ( 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 176 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7892 (mp0) cc_final: 0.7456 (mp0) REVERT: E 581 ILE cc_start: 0.9348 (mm) cc_final: 0.9140 (mt) REVERT: D 350 SER cc_start: 0.9251 (m) cc_final: 0.8846 (p) REVERT: D 581 ILE cc_start: 0.9350 (mm) cc_final: 0.9098 (mt) REVERT: C 460 MET cc_start: 0.8697 (tpp) cc_final: 0.8374 (mmm) REVERT: B 439 LEU cc_start: 0.9257 (tp) cc_final: 0.8928 (tp) outliers start: 33 outliers final: 23 residues processed: 172 average time/residue: 0.1036 time to fit residues: 29.4768 Evaluate side-chains 164 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 D residue 562 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 180 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.085158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059213 restraints weight = 68154.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061099 restraints weight = 29943.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.062273 restraints weight = 18320.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062887 restraints weight = 13640.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063371 restraints weight = 11602.282| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19985 Z= 0.131 Angle : 0.573 12.944 27240 Z= 0.286 Chirality : 0.042 0.159 3175 Planarity : 0.003 0.041 3505 Dihedral : 3.922 17.744 2735 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.19 % Allowed : 19.75 % Favored : 79.05 % 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: -0.20 (0.17), residues: 2515 helix: 1.98 (0.19), residues: 685 sheet: -0.25 (0.19), residues: 660 loop : -1.38 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 139 TYR 0.012 0.001 TYR B 441 PHE 0.019 0.001 PHE C 561 TRP 0.006 0.001 TRP D 407 HIS 0.002 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00291 (19985) covalent geometry : angle 0.57272 (27240) hydrogen bonds : bond 0.03141 ( 921) hydrogen bonds : angle 4.40709 ( 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 170 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7841 (mp0) cc_final: 0.7433 (mp0) REVERT: A 515 LEU cc_start: 0.8712 (pt) cc_final: 0.8449 (pp) REVERT: E 581 ILE cc_start: 0.9327 (mm) cc_final: 0.9126 (mt) REVERT: D 350 SER cc_start: 0.9238 (m) cc_final: 0.8826 (p) REVERT: D 581 ILE cc_start: 0.9331 (mm) cc_final: 0.9097 (mt) REVERT: B 439 LEU cc_start: 0.9246 (tp) cc_final: 0.8927 (tp) outliers start: 24 outliers final: 20 residues processed: 169 average time/residue: 0.1128 time to fit residues: 31.1878 Evaluate side-chains 159 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 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 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 350 SER 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: 8.9990 chunk 180 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 59 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS C 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.082983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055983 restraints weight = 68894.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057771 restraints weight = 31322.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058895 restraints weight = 19666.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059595 restraints weight = 14744.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059966 restraints weight = 12435.114| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19985 Z= 0.286 Angle : 0.643 11.097 27240 Z= 0.331 Chirality : 0.044 0.174 3175 Planarity : 0.004 0.042 3505 Dihedral : 4.335 18.735 2735 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.44 % Allowed : 19.90 % Favored : 78.66 % 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: -0.36 (0.17), residues: 2515 helix: 1.89 (0.20), residues: 680 sheet: -0.35 (0.19), residues: 660 loop : -1.49 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 139 TYR 0.021 0.002 TYR B 441 PHE 0.032 0.002 PHE C 561 TRP 0.009 0.001 TRP C 407 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00638 (19985) covalent geometry : angle 0.64340 (27240) hydrogen bonds : bond 0.03656 ( 921) hydrogen bonds : angle 4.77647 ( 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 169 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7931 (mp0) cc_final: 0.7699 (mp0) REVERT: D 350 SER cc_start: 0.9278 (m) cc_final: 0.8893 (p) REVERT: D 581 ILE cc_start: 0.9386 (mm) cc_final: 0.9184 (mt) REVERT: B 439 LEU cc_start: 0.9271 (tp) cc_final: 0.8878 (tp) outliers start: 29 outliers final: 24 residues processed: 166 average time/residue: 0.1115 time to fit residues: 30.0378 Evaluate side-chains 160 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 E residue 533 SER Chi-restraints excluded: chain E residue 562 THR 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 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 304 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 Chi-restraints excluded: chain B residue 562 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 137 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 212 optimal weight: 40.0000 chunk 144 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 209 optimal weight: 30.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3695 r_free = 0.3695 target = 0.084090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057324 restraints weight = 69598.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058980 restraints weight = 34527.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060038 restraints weight = 22434.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060733 restraints weight = 17161.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061072 restraints weight = 14543.623| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19985 Z= 0.112 Angle : 0.585 13.195 27240 Z= 0.291 Chirality : 0.042 0.160 3175 Planarity : 0.003 0.042 3505 Dihedral : 3.996 17.976 2735 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.85 % Allowed : 20.70 % 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: -0.20 (0.17), residues: 2515 helix: 1.84 (0.20), residues: 690 sheet: -0.29 (0.19), residues: 660 loop : -1.25 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.010 0.001 TYR C 624 PHE 0.033 0.001 PHE D 559 TRP 0.007 0.001 TRP D 407 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00243 (19985) covalent geometry : angle 0.58541 (27240) hydrogen bonds : bond 0.03235 ( 921) hydrogen bonds : angle 4.47022 ( 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 164 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7768 (mp0) cc_final: 0.7432 (mp0) REVERT: D 350 SER cc_start: 0.9153 (m) cc_final: 0.8809 (p) REVERT: D 581 ILE cc_start: 0.9369 (mm) cc_final: 0.9136 (mt) REVERT: C 453 ASP cc_start: 0.8166 (m-30) cc_final: 0.7947 (m-30) REVERT: B 439 LEU cc_start: 0.9215 (tp) cc_final: 0.8910 (tp) outliers start: 17 outliers final: 17 residues processed: 163 average time/residue: 0.1097 time to fit residues: 29.6154 Evaluate side-chains 156 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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 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 B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 158 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 119 optimal weight: 50.0000 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.082842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055876 restraints weight = 70407.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.057543 restraints weight = 35057.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058576 restraints weight = 22742.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059251 restraints weight = 17481.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059612 restraints weight = 14937.876| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19985 Z= 0.180 Angle : 0.598 12.027 27240 Z= 0.302 Chirality : 0.043 0.159 3175 Planarity : 0.003 0.051 3505 Dihedral : 4.062 18.431 2735 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.19 % Allowed : 20.55 % Favored : 78.26 % 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: -0.21 (0.17), residues: 2515 helix: 1.91 (0.20), residues: 685 sheet: -0.31 (0.19), residues: 660 loop : -1.28 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.016 0.002 TYR B 441 PHE 0.029 0.001 PHE C 561 TRP 0.007 0.001 TRP D 407 HIS 0.002 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00403 (19985) covalent geometry : angle 0.59833 (27240) hydrogen bonds : bond 0.03334 ( 921) hydrogen bonds : angle 4.52606 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.07 seconds wall clock time: 51 minutes 50.81 seconds (3110.81 seconds total)