Starting phenix.real_space_refine on Sun Jul 5 22:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvq_34136/07_2026/7yvq_34136.map" } resolution = 3.18 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= 0.032 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 21 9.91 5 S 47 5.16 5 C 19238 2.51 5 N 5003 2.21 5 O 6433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30742 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "B" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "D" Number of atoms: 3898 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 497, 3898 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} Chain breaks: 1 Chain: "E" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "F" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "G" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 3776 Chain: "H" Number of atoms: 3349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3346 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 413, 3346 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3414 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 77 residue: pdb=" N AGLY A 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 488 " occ=0.50 residue: pdb=" N ATHR A 489 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 489 " occ=0.50 residue: pdb=" N ALYS A 490 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 490 " occ=0.50 residue: pdb=" N AASN A 491 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 491 " occ=0.50 residue: pdb=" N ASER A 492 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 492 " occ=0.50 residue: pdb=" N ASER A 493 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 493 " occ=0.50 residue: pdb=" N AGLY A 494 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 494 " occ=0.50 residue: pdb=" N AGLN A 495 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 495 " occ=0.50 residue: pdb=" N AILE A 496 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 496 " occ=0.50 residue: pdb=" N AVAL A 497 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 497 " occ=0.50 residue: pdb=" N THR A 498 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR A 498 " occ=0.50 residue: pdb=" N AGLY B 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 488 " occ=0.50 ... (remaining 65 not shown) Time building chain proxies: 11.45, per 1000 atoms: 0.37 Number of scatterers: 30742 At special positions: 0 Unit cell: (189.2, 176.88, 177.76, 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 21 19.99 S 47 16.00 O 6433 8.00 N 5003 7.00 C 19238 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: 2.59 Conformation dependent library (CDL) restraints added in 1.8 seconds 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7338 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 61 sheets defined 20.3% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.665A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.925A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.850A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.607A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.631A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.773A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.973A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.645A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.950A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.957A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.934A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.877A pdb=" N ASP C 505 " --> pdb=" O SER C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.621A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 595 removed outlier: 3.779A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.848A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.807A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 502 through 505 removed outlier: 3.728A pdb=" N ASP D 505 " --> pdb=" O SER D 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 505' Processing helix chain 'D' and resid 506 through 513 removed outlier: 3.554A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.726A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.834A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 290 removed outlier: 3.517A pdb=" N ARG E 290 " --> pdb=" O THR E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.023A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.549A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 595 removed outlier: 4.033A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.582A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.934A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 512 removed outlier: 3.527A pdb=" N ILE F 507 " --> pdb=" O TRP F 503 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 572 through 576 removed outlier: 3.876A pdb=" N VAL F 576 " --> pdb=" O GLU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 593 removed outlier: 3.852A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.559A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.943A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.039A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.674A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.938A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'H' and resid 13 through 31 removed outlier: 3.816A pdb=" N TRP H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS H 30 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 60 through 67 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.925A pdb=" N ASN H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 115 through 127 Processing helix chain 'H' and resid 217 through 229 removed outlier: 3.967A pdb=" N ALA H 226 " --> pdb=" O SER H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 235 removed outlier: 3.897A pdb=" N LYS H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU H 235 " --> pdb=" O TRP H 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 230 through 235' Processing helix chain 'H' and resid 236 through 248 removed outlier: 3.814A pdb=" N MET H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 260 removed outlier: 4.478A pdb=" N ALA H 253 " --> pdb=" O GLY H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 removed outlier: 3.591A pdb=" N ASN H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 283 Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.556A pdb=" N PHE H 349 " --> pdb=" O MET H 346 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA H 350 " --> pdb=" O SER H 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 346 through 350' Processing helix chain 'H' and resid 370 through 372 No H-bonds generated for 'chain 'H' and resid 370 through 372' Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 311 removed outlier: 5.739A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 330 removed outlier: 3.550A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 374 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 328 " --> pdb=" O ALA A 366 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 365 through 382 current: chain 'B' and resid 365 through 370 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 365 through 370 current: chain 'C' and resid 365 through 382 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 365 through 382 current: chain 'D' and resid 365 through 382 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 365 through 382 current: chain 'E' and resid 365 through 376 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 365 through 376 current: chain 'F' and resid 365 through 382 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 365 through 382 current: chain 'G' and resid 366 through 382 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 423 removed outlier: 7.011A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.232A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 618 through 620 current: chain 'A' and resid 705 through 706 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.540A pdb=" N ILE A 656 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 723 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 722 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 689 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB2, first strand: chain 'B' and resid 300 through 311 removed outlier: 6.885A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 403 through 413 removed outlier: 4.982A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.302A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AB7, first strand: chain 'B' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 618 through 620 current: chain 'B' and resid 705 through 706 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.542A pdb=" N GLU B 722 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 724 " --> pdb=" O LYS B 687 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 687 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 684 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 698 " --> pdb=" O ILE B 684 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 694 " --> pdb=" O ILE B 688 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 311 removed outlier: 6.828A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 418 through 423 removed outlier: 7.027A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC4, first strand: chain 'C' and resid 526 through 531 removed outlier: 9.323A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC6, first strand: chain 'C' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 618 through 620 current: chain 'C' and resid 705 through 706 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 693 through 698 removed outlier: 3.974A pdb=" N LYS C 694 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 698 " --> pdb=" O ILE C 684 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC9, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.802A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.919A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 526 through 531 removed outlier: 9.174A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AD5, first strand: chain 'D' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 618 through 620 current: chain 'D' and resid 705 through 706 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 655 through 658 removed outlier: 3.979A pdb=" N ILE D 656 " --> pdb=" O ILE D 723 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 723 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU D 722 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 689 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D 688 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 694 " --> pdb=" O ILE D 688 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD8, first strand: chain 'E' and resid 300 through 311 removed outlier: 6.921A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 403 through 413 removed outlier: 4.841A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AE2, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.125A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AE4, first strand: chain 'E' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 618 through 620 current: chain 'E' and resid 705 through 706 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 694 through 698 removed outlier: 3.548A pdb=" N LYS E 694 " --> pdb=" O ILE E 688 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU E 722 " --> pdb=" O LYS E 689 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE7, first strand: chain 'F' and resid 300 through 311 removed outlier: 5.749A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 403 through 413 removed outlier: 4.949A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 524 through 531 removed outlier: 3.741A pdb=" N GLU F 524 " --> pdb=" O THR F 521 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AF2, first strand: chain 'F' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 618 through 620 current: chain 'F' and resid 705 through 706 No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 655 through 658 removed outlier: 3.896A pdb=" N ILE F 656 " --> pdb=" O ILE F 723 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 723 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 721 " --> pdb=" O ILE F 658 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU F 722 " --> pdb=" O LYS F 689 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AF5, first strand: chain 'G' and resid 300 through 311 removed outlier: 6.803A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.790A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS G 405 " --> pdb=" O AGLY G 485 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N AGLY G 485 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR G 407 " --> pdb=" O AVAL G 483 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N AVAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR G 409 " --> pdb=" O ATHR G 481 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AF8, first strand: chain 'G' and resid 525 through 531 removed outlier: 9.456A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AG1, first strand: chain 'G' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 618 through 620 current: chain 'G' and resid 705 through 706 No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'G' and resid 655 through 658 removed outlier: 3.970A pdb=" N ILE G 688 " --> pdb=" O LYS G 694 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS G 694 " --> pdb=" O ILE G 688 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 684 through 685 Processing sheet with id=AG4, first strand: chain 'H' and resid 89 through 94 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 89 through 94 current: chain 'H' and resid 175 through 195 removed outlier: 6.731A pdb=" N GLU H 204 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE H 190 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS H 202 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG H 192 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR H 200 " --> pdb=" O ARG H 192 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL H 194 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 291 through 297 removed outlier: 6.470A pdb=" N VAL H 355 " --> pdb=" O VAL H 407 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 330 through 333 Processing sheet with id=AG7, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.906A pdb=" N ILE H 337 " --> pdb=" O LEU H 383 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1766 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: 6.24 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 9970 1.34 - 1.49: 8065 1.49 - 1.65: 13138 1.65 - 1.81: 87 Bond restraints: 31261 Sorted by residual: bond pdb=" CG PRO D 629 " pdb=" CD PRO D 629 " ideal model delta sigma weight residual 1.503 1.020 0.483 3.40e-02 8.65e+02 2.02e+02 bond pdb=" N PRO D 629 " pdb=" CD PRO D 629 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" N GLN C 644 " pdb=" CA GLN C 644 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.01e+01 bond pdb=" N ASP E 717 " pdb=" CA ASP E 717 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.10e-02 8.26e+03 9.17e+00 bond pdb=" CA ASP E 717 " pdb=" C ASP E 717 " ideal model delta sigma weight residual 1.521 1.556 -0.034 1.14e-02 7.69e+03 9.10e+00 ... (remaining 31256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 42339 5.44 - 10.87: 20 10.87 - 16.31: 2 16.31 - 21.75: 2 21.75 - 27.18: 1 Bond angle restraints: 42364 Sorted by residual: angle pdb=" N PRO D 629 " pdb=" CD PRO D 629 " pdb=" CG PRO D 629 " ideal model delta sigma weight residual 103.20 76.02 27.18 1.50e+00 4.44e-01 3.28e+02 angle pdb=" CA PRO D 629 " pdb=" CB PRO D 629 " pdb=" CG PRO D 629 " ideal model delta sigma weight residual 104.50 84.49 20.01 1.90e+00 2.77e-01 1.11e+02 angle pdb=" CA PRO D 629 " pdb=" N PRO D 629 " pdb=" CD PRO D 629 " ideal model delta sigma weight residual 112.00 100.79 11.21 1.40e+00 5.10e-01 6.41e+01 angle pdb=" N ASN C 720 " pdb=" CA ASN C 720 " pdb=" C ASN C 720 " ideal model delta sigma weight residual 107.32 119.20 -11.88 1.65e+00 3.67e-01 5.19e+01 angle pdb=" CA PHE F 281 " pdb=" CB PHE F 281 " pdb=" CG PHE F 281 " ideal model delta sigma weight residual 113.80 119.85 -6.05 1.00e+00 1.00e+00 3.66e+01 ... (remaining 42359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17311 17.96 - 35.93: 1382 35.93 - 53.89: 273 53.89 - 71.86: 67 71.86 - 89.82: 31 Dihedral angle restraints: 19064 sinusoidal: 7602 harmonic: 11462 Sorted by residual: dihedral pdb=" N PRO D 629 " pdb=" CG PRO D 629 " pdb=" CD PRO D 629 " pdb=" CB PRO D 629 " ideal model delta sinusoidal sigma weight residual 30.00 78.14 -48.14 1 1.50e+01 4.44e-03 1.42e+01 dihedral pdb=" CA PHE G 566 " pdb=" C PHE G 566 " pdb=" N ASN G 567 " pdb=" CA ASN G 567 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP C 717 " pdb=" CB ASP C 717 " pdb=" CG ASP C 717 " pdb=" OD1 ASP C 717 " ideal model delta sinusoidal sigma weight residual -30.00 -88.54 58.54 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 19061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4173 0.069 - 0.138: 583 0.138 - 0.207: 10 0.207 - 0.276: 1 0.276 - 0.345: 1 Chirality restraints: 4768 Sorted by residual: chirality pdb=" CA SER C 719 " pdb=" N SER C 719 " pdb=" C SER C 719 " pdb=" CB SER C 719 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ASN C 720 " pdb=" N ASN C 720 " pdb=" C ASN C 720 " pdb=" CB ASN C 720 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE G 285 " pdb=" N ILE G 285 " pdb=" C ILE G 285 " pdb=" CB ILE G 285 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4765 not shown) Planarity restraints: 5509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 716 " 0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C LYS E 716 " -0.087 2.00e-02 2.50e+03 pdb=" O LYS E 716 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP E 717 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 664 " 0.060 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO B 665 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 658 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A 659 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 659 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 659 " -0.042 5.00e-02 4.00e+02 ... (remaining 5506 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 800 2.68 - 3.24: 28887 3.24 - 3.79: 45579 3.79 - 4.35: 64653 4.35 - 4.90: 107582 Nonbonded interactions: 247501 Sorted by model distance: nonbonded pdb=" OG SER H 34 " pdb=" OE2 GLU H 75 " model vdw 2.131 3.040 nonbonded pdb=" OG SER D 516 " pdb=" OD1 ASN D 610 " model vdw 2.182 3.040 nonbonded pdb=" OD2 ASP H 138 " pdb=" OG SER H 176 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR C 521 " pdb=" O GLU C 524 " model vdw 2.193 3.040 nonbonded pdb=" NH2 ARG B 394 " pdb=" O LEU B 444 " model vdw 2.197 3.120 ... (remaining 247496 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'B' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'C' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'D' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'E' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'F' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'G' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.780 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: 0.050 Extract box with map and model: 0.730 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.830 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 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 0.483 31261 Z= 0.192 Angle : 0.581 27.183 42364 Z= 0.338 Chirality : 0.045 0.345 4768 Planarity : 0.004 0.089 5509 Dihedral : 14.171 89.824 11726 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.75 % Allowed : 0.84 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.26 (0.14), residues: 3891 helix: 0.87 (0.22), residues: 588 sheet: 0.72 (0.16), residues: 1176 loop : -1.02 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 529 TYR 0.025 0.001 TYR D 709 PHE 0.025 0.001 PHE D 707 TRP 0.015 0.001 TRP F 632 HIS 0.002 0.000 AHIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (31261) covalent geometry : angle 0.58055 / 0.34 (42364) hydrogen bonds : bond 0.21292 / 13.60 ( 710) hydrogen bonds : angle 7.24481 / 5.04 ( 1766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: C 716 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7337 (ttmt) REVERT: H 4 GLU cc_start: 0.5654 (tp30) cc_final: 0.5376 (tp30) REVERT: H 223 TRP cc_start: 0.8196 (t60) cc_final: 0.7881 (t60) REVERT: H 292 THR cc_start: 0.8467 (m) cc_final: 0.8008 (p) outliers start: 15 outliers final: 7 residues processed: 141 average time/residue: 0.2011 time to fit residues: 47.4279 Evaluate side-chains 107 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 225 ASN C 636 ASN E 368 GLN H 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.105223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069283 restraints weight = 231388.982| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.15 r_work: 0.2939 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (8 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31261 Z= 0.142 Angle : 0.508 8.594 42364 Z= 0.273 Chirality : 0.045 0.162 4768 Planarity : 0.004 0.061 5509 Dihedral : 4.603 59.428 4221 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.69 % Allowed : 4.09 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.26 (0.14), residues: 3891 helix: 0.91 (0.22), residues: 600 sheet: 0.68 (0.16), residues: 1180 loop : -1.02 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.014 0.001 TYR E 674 PHE 0.016 0.001 PHE G 707 TRP 0.010 0.001 TRP B 375 HIS 0.004 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (31261) covalent geometry : angle 0.50762 / 0.27 (42364) hydrogen bonds : bond 0.03429 / 2.17 ( 710) hydrogen bonds : angle 5.32045 / 3.68 ( 1766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: C 654 THR cc_start: 0.6022 (p) cc_final: 0.5700 (p) REVERT: C 716 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7031 (ttpt) REVERT: D 668 ARG cc_start: 0.5937 (mmt180) cc_final: 0.5253 (ttm-80) REVERT: H 4 GLU cc_start: 0.5704 (tp30) cc_final: 0.5409 (tp30) REVERT: H 54 GLN cc_start: 0.7587 (mt0) cc_final: 0.7337 (mt0) REVERT: H 292 THR cc_start: 0.8467 (m) cc_final: 0.8028 (p) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 0.1912 time to fit residues: 40.8356 Evaluate side-chains 113 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 377 optimal weight: 4.9990 chunk 261 optimal weight: 0.0570 chunk 249 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 158 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 602 ASN C 634 ASN C 636 ASN D 610 ASN E 368 GLN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.113011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075748 restraints weight = 234680.416| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.88 r_work: 0.2933 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31261 Z= 0.104 Angle : 0.466 8.803 42364 Z= 0.250 Chirality : 0.044 0.155 4768 Planarity : 0.003 0.054 5509 Dihedral : 4.350 55.062 4221 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.81 % Allowed : 5.53 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.18 (0.14), residues: 3891 helix: 1.00 (0.22), residues: 601 sheet: 0.74 (0.16), residues: 1180 loop : -0.98 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 668 TYR 0.017 0.001 TYR D 709 PHE 0.013 0.001 PHE F 707 TRP 0.024 0.001 TRP H 223 HIS 0.002 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (31261) covalent geometry : angle 0.46625 / 0.25 (42364) hydrogen bonds : bond 0.02859 / 1.81 ( 710) hydrogen bonds : angle 4.93276 / 3.41 ( 1766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: C 691 LYS cc_start: 0.6862 (tttt) cc_final: 0.6595 (ttmt) REVERT: C 716 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7081 (ttmt) REVERT: D 668 ARG cc_start: 0.5981 (mmt180) cc_final: 0.5611 (ttm-80) REVERT: E 736 LEU cc_start: 0.8032 (mm) cc_final: 0.7564 (mm) REVERT: H 4 GLU cc_start: 0.5561 (tp30) cc_final: 0.5316 (tp30) REVERT: H 54 GLN cc_start: 0.7478 (mt0) cc_final: 0.7209 (mt0) REVERT: H 223 TRP cc_start: 0.7384 (t-100) cc_final: 0.7083 (t60) REVERT: H 292 THR cc_start: 0.8465 (m) cc_final: 0.8026 (p) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 0.1750 time to fit residues: 36.8445 Evaluate side-chains 113 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 280 optimal weight: 6.9990 chunk 301 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 380 optimal weight: 9.9990 chunk 279 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 GLN C 602 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN G 636 ASN H 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.114605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076278 restraints weight = 162126.158| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.44 r_work: 0.2937 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31261 Z= 0.154 Angle : 0.497 9.163 42364 Z= 0.266 Chirality : 0.045 0.149 4768 Planarity : 0.003 0.052 5509 Dihedral : 4.434 47.234 4221 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.81 % Allowed : 6.88 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3891 helix: 0.93 (0.22), residues: 601 sheet: 0.62 (0.16), residues: 1198 loop : -1.03 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.016 0.001 TYR D 709 PHE 0.014 0.001 PHE F 707 TRP 0.015 0.001 TRP H 223 HIS 0.003 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (31261) covalent geometry : angle 0.49733 / 0.27 (42364) hydrogen bonds : bond 0.02934 / 1.86 ( 710) hydrogen bonds : angle 4.75882 / 3.29 ( 1766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 691 LYS cc_start: 0.6819 (tttt) cc_final: 0.6566 (ttmt) REVERT: C 716 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7132 (ttmt) REVERT: D 668 ARG cc_start: 0.6078 (mmt180) cc_final: 0.5677 (ttm-80) REVERT: E 736 LEU cc_start: 0.8055 (mm) cc_final: 0.7692 (mm) REVERT: F 381 ILE cc_start: 0.8241 (tp) cc_final: 0.7971 (tt) REVERT: G 523 ASN cc_start: 0.8504 (p0) cc_final: 0.7908 (t0) REVERT: H 4 GLU cc_start: 0.5638 (tp30) cc_final: 0.5359 (tp30) REVERT: H 54 GLN cc_start: 0.7471 (mt0) cc_final: 0.7218 (mt0) REVERT: H 223 TRP cc_start: 0.7548 (t-100) cc_final: 0.7224 (t60) REVERT: H 292 THR cc_start: 0.8431 (m) cc_final: 0.7991 (p) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 0.1700 time to fit residues: 35.4240 Evaluate side-chains 116 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 636 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 84 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 339 optimal weight: 0.1980 chunk 234 optimal weight: 9.9990 chunk 354 optimal weight: 0.2980 chunk 165 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.120331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084479 restraints weight = 229706.918| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.47 r_work: 0.2912 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31261 Z= 0.160 Angle : 0.497 9.396 42364 Z= 0.266 Chirality : 0.045 0.147 4768 Planarity : 0.003 0.050 5509 Dihedral : 4.436 47.901 4221 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.92 % Allowed : 7.83 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.34 (0.14), residues: 3891 helix: 0.89 (0.21), residues: 608 sheet: 0.59 (0.16), residues: 1198 loop : -1.07 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.014 0.001 TYR D 709 PHE 0.014 0.001 PHE F 707 TRP 0.012 0.001 TRP B 375 HIS 0.003 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (31261) covalent geometry : angle 0.49722 / 0.27 (42364) hydrogen bonds : bond 0.02840 / 1.80 ( 710) hydrogen bonds : angle 4.70110 / 3.25 ( 1766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 707 PHE cc_start: 0.6432 (p90) cc_final: 0.6024 (p90) REVERT: C 691 LYS cc_start: 0.6853 (tttt) cc_final: 0.6586 (ttmt) REVERT: C 716 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7229 (ttmt) REVERT: D 668 ARG cc_start: 0.6112 (mmt180) cc_final: 0.5683 (ttm-80) REVERT: E 736 LEU cc_start: 0.8099 (mm) cc_final: 0.7827 (mm) REVERT: F 381 ILE cc_start: 0.8327 (tp) cc_final: 0.8057 (tt) REVERT: G 523 ASN cc_start: 0.8464 (p0) cc_final: 0.7893 (t0) REVERT: H 4 GLU cc_start: 0.5587 (tp30) cc_final: 0.5346 (tp30) REVERT: H 54 GLN cc_start: 0.7543 (mt0) cc_final: 0.7314 (mt0) REVERT: H 292 THR cc_start: 0.8444 (m) cc_final: 0.8037 (p) outliers start: 21 outliers final: 11 residues processed: 131 average time/residue: 0.1728 time to fit residues: 37.8210 Evaluate side-chains 122 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 382 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 252 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.120288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084536 restraints weight = 189093.171| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.01 r_work: 0.2918 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31261 Z= 0.193 Angle : 0.527 10.085 42364 Z= 0.281 Chirality : 0.046 0.149 4768 Planarity : 0.004 0.051 5509 Dihedral : 4.583 52.280 4221 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.92 % Allowed : 8.76 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.43 (0.13), residues: 3891 helix: 0.85 (0.21), residues: 608 sheet: 0.55 (0.16), residues: 1169 loop : -1.14 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 394 TYR 0.014 0.001 TYR D 709 PHE 0.015 0.001 PHE F 707 TRP 0.026 0.001 TRP H 223 HIS 0.003 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (31261) covalent geometry : angle 0.52688 / 0.28 (42364) hydrogen bonds : bond 0.03008 / 1.91 ( 710) hydrogen bonds : angle 4.70918 / 3.27 ( 1766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 707 PHE cc_start: 0.6582 (p90) cc_final: 0.6144 (p90) REVERT: C 691 LYS cc_start: 0.6831 (tttt) cc_final: 0.6568 (ttmt) REVERT: C 716 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7288 (ttpt) REVERT: D 668 ARG cc_start: 0.6112 (mmt180) cc_final: 0.5446 (ttm-80) REVERT: F 381 ILE cc_start: 0.8286 (tp) cc_final: 0.8017 (tt) REVERT: G 523 ASN cc_start: 0.8515 (p0) cc_final: 0.7928 (t0) REVERT: H 54 GLN cc_start: 0.7534 (mt0) cc_final: 0.7306 (mt0) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.1785 time to fit residues: 35.3115 Evaluate side-chains 115 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 312 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 290 optimal weight: 8.9990 chunk 311 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.085723 restraints weight = 209106.553| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.94 r_work: 0.2961 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31261 Z= 0.103 Angle : 0.463 10.143 42364 Z= 0.247 Chirality : 0.044 0.146 4768 Planarity : 0.003 0.050 5509 Dihedral : 4.200 45.539 4221 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.89 % Allowed : 9.22 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3891 helix: 1.05 (0.22), residues: 608 sheet: 0.63 (0.16), residues: 1186 loop : -1.02 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 529 TYR 0.012 0.001 TYR D 709 PHE 0.013 0.001 PHE F 707 TRP 0.031 0.001 TRP H 223 HIS 0.002 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (31261) covalent geometry : angle 0.46269 / 0.25 (42364) hydrogen bonds : bond 0.02397 / 1.53 ( 710) hydrogen bonds : angle 4.56741 / 3.16 ( 1766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: B 707 PHE cc_start: 0.6330 (p90) cc_final: 0.5862 (p90) REVERT: C 691 LYS cc_start: 0.6843 (tttt) cc_final: 0.6539 (ttmt) REVERT: D 668 ARG cc_start: 0.6118 (mmt180) cc_final: 0.5721 (ttm-80) REVERT: E 736 LEU cc_start: 0.8326 (mm) cc_final: 0.8106 (mm) REVERT: F 381 ILE cc_start: 0.8334 (tp) cc_final: 0.8057 (tt) REVERT: F 668 ARG cc_start: 0.6452 (ttp-110) cc_final: 0.6226 (ttp-170) REVERT: G 523 ASN cc_start: 0.8412 (p0) cc_final: 0.7863 (t0) REVERT: H 36 LYS cc_start: 0.7094 (mmtp) cc_final: 0.6890 (mmtt) REVERT: H 54 GLN cc_start: 0.7536 (mt0) cc_final: 0.7320 (mt0) REVERT: H 292 THR cc_start: 0.8398 (m) cc_final: 0.7976 (p) outliers start: 18 outliers final: 16 residues processed: 124 average time/residue: 0.1896 time to fit residues: 38.9322 Evaluate side-chains 120 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 350 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 353 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 378 optimal weight: 8.9990 chunk 184 optimal weight: 0.1980 chunk 305 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 602 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085401 restraints weight = 201161.215| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.25 r_work: 0.2929 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31261 Z= 0.145 Angle : 0.488 9.952 42364 Z= 0.260 Chirality : 0.044 0.145 4768 Planarity : 0.003 0.050 5509 Dihedral : 4.290 45.751 4221 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.07 % Allowed : 9.33 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.30 (0.14), residues: 3891 helix: 1.02 (0.22), residues: 608 sheet: 0.59 (0.16), residues: 1187 loop : -1.06 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.012 0.001 TYR D 709 PHE 0.014 0.001 PHE F 707 TRP 0.027 0.001 TRP H 223 HIS 0.002 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (31261) covalent geometry : angle 0.48790 / 0.26 (42364) hydrogen bonds : bond 0.02627 / 1.67 ( 710) hydrogen bonds : angle 4.55878 / 3.15 ( 1766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 TRP cc_start: 0.7870 (m-90) cc_final: 0.7354 (m-90) REVERT: B 707 PHE cc_start: 0.6398 (p90) cc_final: 0.5905 (p90) REVERT: C 643 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7511 (mt) REVERT: C 691 LYS cc_start: 0.6816 (tttt) cc_final: 0.6542 (ttmt) REVERT: D 668 ARG cc_start: 0.6129 (mmt180) cc_final: 0.5725 (ttm-80) REVERT: E 736 LEU cc_start: 0.8379 (mm) cc_final: 0.8146 (mm) REVERT: F 381 ILE cc_start: 0.8363 (tp) cc_final: 0.8090 (tt) REVERT: G 523 ASN cc_start: 0.8526 (p0) cc_final: 0.7913 (t0) REVERT: H 54 GLN cc_start: 0.7498 (mt0) cc_final: 0.7272 (mt0) REVERT: H 292 THR cc_start: 0.8413 (m) cc_final: 0.7979 (p) outliers start: 24 outliers final: 20 residues processed: 124 average time/residue: 0.1869 time to fit residues: 39.1854 Evaluate side-chains 127 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 660 MET Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 329 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 523 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.119929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083951 restraints weight = 243846.005| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.17 r_work: 0.2924 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31261 Z= 0.153 Angle : 0.497 10.342 42364 Z= 0.264 Chirality : 0.045 0.144 4768 Planarity : 0.003 0.049 5509 Dihedral : 4.339 46.682 4221 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.07 % Allowed : 9.74 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.33 (0.14), residues: 3891 helix: 1.00 (0.22), residues: 608 sheet: 0.56 (0.16), residues: 1187 loop : -1.08 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.013 0.001 TYR D 709 PHE 0.013 0.001 PHE F 707 TRP 0.027 0.001 TRP H 223 HIS 0.002 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (31261) covalent geometry : angle 0.49655 / 0.26 (42364) hydrogen bonds : bond 0.02681 / 1.71 ( 710) hydrogen bonds : angle 4.58505 / 3.17 ( 1766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 TRP cc_start: 0.7827 (m-90) cc_final: 0.7289 (m-90) REVERT: B 707 PHE cc_start: 0.6429 (p90) cc_final: 0.5940 (p90) REVERT: C 691 LYS cc_start: 0.6813 (tttt) cc_final: 0.6509 (ttmt) REVERT: D 668 ARG cc_start: 0.6276 (mmt180) cc_final: 0.5867 (ttm-80) REVERT: E 736 LEU cc_start: 0.8402 (mm) cc_final: 0.8146 (mm) REVERT: F 381 ILE cc_start: 0.8365 (tp) cc_final: 0.8110 (tt) REVERT: G 523 ASN cc_start: 0.8581 (p0) cc_final: 0.7929 (t0) REVERT: H 54 GLN cc_start: 0.7555 (mt0) cc_final: 0.7338 (mt0) outliers start: 24 outliers final: 22 residues processed: 127 average time/residue: 0.1916 time to fit residues: 41.0846 Evaluate side-chains 126 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 660 MET Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 373 optimal weight: 0.5980 chunk 349 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 296 optimal weight: 0.6980 chunk 209 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.123283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.087370 restraints weight = 242123.455| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.62 r_work: 0.2957 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31261 Z= 0.083 Angle : 0.446 10.101 42364 Z= 0.237 Chirality : 0.043 0.161 4768 Planarity : 0.003 0.050 5509 Dihedral : 3.904 36.581 4221 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.81 % Allowed : 9.97 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.05 (0.14), residues: 3891 helix: 1.22 (0.22), residues: 602 sheet: 0.84 (0.16), residues: 1169 loop : -0.93 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 458 TYR 0.012 0.001 TYR B 396 PHE 0.012 0.001 PHE F 707 TRP 0.029 0.001 TRP H 223 HIS 0.001 0.000 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.08 (31261) covalent geometry : angle 0.44558 / 0.24 (42364) hydrogen bonds : bond 0.02106 / 1.35 ( 710) hydrogen bonds : angle 4.45766 / 3.07 ( 1766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 375 TRP cc_start: 0.7830 (m-90) cc_final: 0.7327 (m-90) REVERT: B 707 PHE cc_start: 0.6219 (p90) cc_final: 0.5713 (p90) REVERT: C 691 LYS cc_start: 0.6783 (tttt) cc_final: 0.6495 (ttmt) REVERT: D 411 ASN cc_start: 0.8362 (m-40) cc_final: 0.8161 (m110) REVERT: D 668 ARG cc_start: 0.6064 (mmt180) cc_final: 0.5561 (ttm-80) REVERT: E 736 LEU cc_start: 0.8330 (mm) cc_final: 0.8116 (mm) REVERT: F 668 ARG cc_start: 0.6557 (ttp-110) cc_final: 0.6318 (ttp-170) REVERT: G 523 ASN cc_start: 0.8548 (p0) cc_final: 0.7818 (t0) REVERT: H 54 GLN cc_start: 0.7414 (mt0) cc_final: 0.7123 (mt0) REVERT: H 292 THR cc_start: 0.8403 (m) cc_final: 0.8005 (p) outliers start: 15 outliers final: 14 residues processed: 127 average time/residue: 0.2091 time to fit residues: 44.1950 Evaluate side-chains 126 residues out of total 3407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 660 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 64 optimal weight: 0.0060 chunk 296 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 295 optimal weight: 0.0770 chunk 96 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 381 optimal weight: 20.0000 chunk 342 optimal weight: 30.0000 overall best weight: 1.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.121226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085701 restraints weight = 180336.632| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.68 r_work: 0.2965 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31261 Z= 0.131 Angle : 0.477 10.053 42364 Z= 0.254 Chirality : 0.044 0.151 4768 Planarity : 0.003 0.049 5509 Dihedral : 4.037 31.239 4219 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.84 % Allowed : 10.08 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % 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: -0.13 (0.14), residues: 3891 helix: 1.15 (0.22), residues: 609 sheet: 0.74 (0.16), residues: 1180 loop : -0.96 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 458 TYR 0.012 0.001 TYR F 709 PHE 0.014 0.001 PHE B 281 TRP 0.025 0.001 TRP H 223 HIS 0.002 0.001 AHIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (31261) covalent geometry : angle 0.47665 / 0.25 (42364) hydrogen bonds : bond 0.02477 / 1.58 ( 710) hydrogen bonds : angle 4.45959 / 3.07 ( 1766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8966.75 seconds wall clock time: 154 minutes 3.04 seconds (9243.04 seconds total)