Starting phenix.real_space_refine on Thu Jun 26 14:59:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvs_34137/06_2025/7yvs_34137.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvs_34137/06_2025/7yvs_34137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvs_34137/06_2025/7yvs_34137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvs_34137/06_2025/7yvs_34137.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvs_34137/06_2025/7yvs_34137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvs_34137/06_2025/7yvs_34137.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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 19144 2.51 5 N 4979 2.21 5 O 6402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30593 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: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3200 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} 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: 73 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 61 not shown) Time building chain proxies: 26.11, per 1000 atoms: 0.85 Number of scatterers: 30593 At special positions: 0 Unit cell: (177.76, 177.76, 172.48, 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 6402 8.00 N 4979 7.00 C 19144 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: 6.95 Conformation dependent library (CDL) restraints added in 5.9 seconds 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7300 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 82 sheets defined 20.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.679A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.985A 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: 4.650A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.755A 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 595 removed outlier: 3.618A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.139A 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 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.974A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.742A 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: 4.595A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.652A 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 595 removed outlier: 3.622A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) 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: 3.536A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.994A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.971A 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 503 through 513 removed outlier: 4.693A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 3.711A 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 572 through 576 removed outlier: 3.815A pdb=" N VAL C 576 " --> pdb=" O GLU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 594 removed outlier: 3.768A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.106A 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 253 removed outlier: 3.507A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.765A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.926A 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 503 through 513 removed outlier: 4.619A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.637A 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 572 through 576 removed outlier: 3.836A pdb=" N VAL D 576 " --> pdb=" O GLU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.622A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.220A 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: 3.780A 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 291 removed outlier: 4.033A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.057A 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: 4.654A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.653A 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 572 through 576 removed outlier: 3.838A pdb=" N VAL E 576 " --> pdb=" O GLU E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 595 removed outlier: 3.626A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.127A 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: 3.566A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.124A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.819A 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 513 removed outlier: 4.627A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 595 removed outlier: 3.808A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (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 253 removed outlier: 3.865A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.805A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.776A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.660A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.615A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.004A 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 20 through 30 removed outlier: 3.967A pdb=" N LYS H 30 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 45 Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.593A pdb=" N ILE H 49 " --> pdb=" O ASP H 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 67 Processing helix chain 'H' and resid 69 through 83 removed outlier: 4.284A 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 126 Processing helix chain 'H' and resid 216 through 229 removed outlier: 3.601A pdb=" N GLY H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 235 removed outlier: 3.530A pdb=" N LYS H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 250 Processing helix chain 'H' and resid 250 through 260 Processing helix chain 'H' and resid 261 through 266 Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.599A pdb=" N ASP H 272 " --> pdb=" O ASN H 268 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU H 285 " --> pdb=" O ALA H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 315 through 327 removed outlier: 3.821A pdb=" N ILE H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.752A pdb=" N ALA H 350 " --> pdb=" O SER H 347 " (cutoff:3.500A) 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: 5.703A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.831A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 331 removed outlier: 3.505A pdb=" N SER G 374 " --> pdb=" O GLY G 320 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G 367 " --> pdb=" O ASN F 329 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F 370 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER E 316 " --> pdb=" O GLY E 378 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 370 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 316 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 376 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG C 325 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 320 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 322 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.918A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.918A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.244A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 618 through 620 removed outlier: 4.332A pdb=" N LEU A 736 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER A 672 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 738 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 670 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU A 740 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG A 668 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 618 through 620 removed outlier: 4.332A pdb=" N LEU A 736 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER A 672 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 738 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 670 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU A 740 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG A 668 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.540A pdb=" N ILE A 723 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 722 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 698 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 694 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB5, first strand: chain 'B' and resid 300 through 311 removed outlier: 6.853A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.849A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.827A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.827A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC1, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.327A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC3, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.562A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.562A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.652A pdb=" N LEU B 698 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC7, first strand: chain 'C' and resid 300 through 311 removed outlier: 6.771A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.864A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE C 460 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.927A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.927A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'C' and resid 526 through 531 removed outlier: 9.279A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AD5, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.493A pdb=" N LEU C 733 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS C 676 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASN C 735 " --> pdb=" O TYR C 674 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR C 674 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG C 668 " --> pdb=" O LEU C 741 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 675 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 705 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.493A pdb=" N LEU C 733 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS C 676 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASN C 735 " --> pdb=" O TYR C 674 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR C 674 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG C 668 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 655 through 658 removed outlier: 3.598A pdb=" N ILE C 723 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 722 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AD9, first strand: chain 'D' and resid 300 through 311 removed outlier: 6.730A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 438 through 439 removed outlier: 3.945A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.882A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.882A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AE5, first strand: chain 'D' and resid 526 through 531 removed outlier: 9.331A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AE7, first strand: chain 'D' and resid 618 through 620 removed outlier: 5.298A pdb=" N LEU D 733 " --> pdb=" O LYS D 676 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS D 676 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN D 735 " --> pdb=" O TYR D 674 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR D 674 " --> pdb=" O ASN D 735 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 668 " --> pdb=" O LEU D 741 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 618 through 620 removed outlier: 5.298A pdb=" N LEU D 733 " --> pdb=" O LYS D 676 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS D 676 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN D 735 " --> pdb=" O TYR D 674 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR D 674 " --> pdb=" O ASN D 735 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 668 " --> pdb=" O LEU D 741 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 655 through 658 removed outlier: 3.964A pdb=" N ILE D 656 " --> pdb=" O ILE D 723 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 723 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU D 722 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS D 689 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 698 " --> pdb=" O ILE D 684 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AF2, first strand: chain 'E' and resid 300 through 311 removed outlier: 6.734A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 438 through 439 removed outlier: 3.805A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.887A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.887A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AF7, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.194A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AF9, first strand: chain 'E' and resid 618 through 620 removed outlier: 5.180A pdb=" N LEU E 733 " --> pdb=" O LYS E 676 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 676 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN E 735 " --> pdb=" O TYR E 674 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR E 674 " --> pdb=" O ASN E 735 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG E 668 " --> pdb=" O LEU E 741 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 675 " --> pdb=" O THR E 705 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR E 705 " --> pdb=" O SER E 675 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 618 through 620 removed outlier: 5.180A pdb=" N LEU E 733 " --> pdb=" O LYS E 676 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 676 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN E 735 " --> pdb=" O TYR E 674 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR E 674 " --> pdb=" O ASN E 735 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG E 668 " --> pdb=" O LEU E 741 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 655 through 658 removed outlier: 3.598A pdb=" N ILE E 656 " --> pdb=" O ILE E 723 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 723 " --> pdb=" O ILE E 656 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU E 722 " --> pdb=" O LYS E 689 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AG4, first strand: chain 'F' and resid 300 through 311 removed outlier: 6.826A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.901A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.816A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.816A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS F 405 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN F 486 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN F 482 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN F 411 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N THR F 480 " --> pdb=" O ASN F 411 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL F 413 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU F 478 " --> pdb=" O VAL F 413 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AG9, first strand: chain 'F' and resid 524 through 531 removed outlier: 3.696A pdb=" N GLU F 524 " --> pdb=" O THR F 521 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AH2, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.308A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 668 " --> pdb=" O LEU F 741 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER F 675 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 705 " --> pdb=" O SER F 675 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.308A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 668 " --> pdb=" O LEU F 741 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 655 through 658 removed outlier: 3.684A pdb=" N ILE F 656 " --> pdb=" O ILE F 723 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE F 723 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU F 722 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE F 688 " --> pdb=" O LYS F 694 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 694 " --> pdb=" O ILE F 688 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AH6, first strand: chain 'G' and resid 300 through 311 removed outlier: 6.758A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.856A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.846A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL G 406 " --> pdb=" O ASER G 484 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASER G 484 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N AGLN G 482 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR G 410 " --> pdb=" O ATHR G 480 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ATHR G 480 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 412 " --> pdb=" O ALEU G 478 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU G 478 " --> pdb=" O LEU G 412 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AI1, first strand: chain 'G' and resid 525 through 531 Processing sheet with id=AI2, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AI3, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.391A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER G 675 " --> pdb=" O THR G 705 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR G 705 " --> pdb=" O SER G 675 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.391A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 655 through 658 removed outlier: 4.099A pdb=" N GLU G 722 " --> pdb=" O LYS G 689 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS G 689 " --> pdb=" O GLU G 722 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 684 through 685 Processing sheet with id=AI7, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.568A pdb=" N MET H 89 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL H 207 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL H 194 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR H 200 " --> pdb=" O ARG H 192 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG H 192 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS H 202 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE H 190 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU H 204 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER H 184 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR H 183 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 136 through 139 removed outlier: 3.708A pdb=" N THR H 177 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 291 through 297 removed outlier: 4.104A pdb=" N ILE H 354 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 393 " --> pdb=" O ASP H 408 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR H 410 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE H 391 " --> pdb=" O THR H 410 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE H 412 " --> pdb=" O PHE H 389 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE H 389 " --> pdb=" O ILE H 412 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER H 387 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.856A pdb=" N ILE H 337 " --> pdb=" O LEU H 383 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 367 " --> pdb=" O LEU H 382 " (cutoff:3.500A) 1184 hydrogen bonds defined for protein. 3015 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: 14.04 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9987 1.34 - 1.46: 4499 1.46 - 1.57: 16535 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 31108 Sorted by residual: bond pdb=" CA SER F 280 " pdb=" CB SER F 280 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.34e-02 5.57e+03 8.91e+00 bond pdb=" N ASN H 173 " pdb=" CA ASN H 173 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.87e+00 bond pdb=" N ILE D 496 " pdb=" CA ILE D 496 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.08e-02 8.57e+03 8.84e+00 bond pdb=" CA SER E 280 " pdb=" CB SER E 280 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.51e-02 4.39e+03 8.43e+00 bond pdb=" N SER H 176 " pdb=" CA SER H 176 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.64e+00 ... (remaining 31103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 41639 2.24 - 4.49: 478 4.49 - 6.73: 34 6.73 - 8.97: 5 8.97 - 11.22: 1 Bond angle restraints: 42157 Sorted by residual: angle pdb=" CA PHE B 281 " pdb=" CB PHE B 281 " pdb=" CG PHE B 281 " ideal model delta sigma weight residual 113.80 120.35 -6.55 1.00e+00 1.00e+00 4.29e+01 angle pdb=" CA PHE G 281 " pdb=" CB PHE G 281 " pdb=" CG PHE G 281 " ideal model delta sigma weight residual 113.80 120.30 -6.50 1.00e+00 1.00e+00 4.23e+01 angle pdb=" CA PHE F 281 " pdb=" CB PHE F 281 " pdb=" CG PHE F 281 " ideal model delta sigma weight residual 113.80 120.14 -6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" CA PHE C 281 " pdb=" CB PHE C 281 " pdb=" CG PHE C 281 " ideal model delta sigma weight residual 113.80 120.08 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" CA PHE E 281 " pdb=" CB PHE E 281 " pdb=" CG PHE E 281 " ideal model delta sigma weight residual 113.80 119.91 -6.11 1.00e+00 1.00e+00 3.73e+01 ... (remaining 42152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17287 17.92 - 35.85: 1343 35.85 - 53.77: 238 53.77 - 71.70: 70 71.70 - 89.62: 22 Dihedral angle restraints: 18960 sinusoidal: 7556 harmonic: 11404 Sorted by residual: dihedral pdb=" CA PHE D 707 " pdb=" C PHE D 707 " pdb=" N SER D 708 " pdb=" CA SER D 708 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO A 659 " pdb=" C PRO A 659 " pdb=" N MET A 660 " pdb=" CA MET A 660 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASN A 567 " pdb=" C ASN A 567 " pdb=" N ASP A 568 " pdb=" CA ASP A 568 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 18957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3070 0.036 - 0.072: 1069 0.072 - 0.108: 390 0.108 - 0.144: 213 0.144 - 0.180: 5 Chirality restraints: 4747 Sorted by residual: chirality pdb=" CA ASN H 173 " pdb=" N ASN H 173 " pdb=" C ASN H 173 " pdb=" CB ASN H 173 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA GLU H 20 " pdb=" N GLU H 20 " pdb=" C GLU H 20 " pdb=" CB GLU H 20 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA ILE H 27 " pdb=" N ILE H 27 " pdb=" C ILE H 27 " pdb=" CB ILE H 27 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 4744 not shown) Planarity restraints: 5480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 699 " -0.056 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO D 700 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 700 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 700 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 664 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO G 665 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 665 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 665 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 664 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 665 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " -0.029 5.00e-02 4.00e+02 ... (remaining 5477 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1474 2.72 - 3.26: 28977 3.26 - 3.81: 47862 3.81 - 4.35: 62698 4.35 - 4.90: 107496 Nonbonded interactions: 248507 Sorted by model distance: nonbonded pdb=" NH2 ARG F 394 " pdb=" O LEU F 444 " model vdw 2.173 3.120 nonbonded pdb=" NH2 ARG B 394 " pdb=" O LEU B 444 " model vdw 2.193 3.120 nonbonded pdb=" NH2 ARG A 394 " pdb=" O LEU A 444 " model vdw 2.201 3.120 nonbonded pdb=" OE1 GLU G 231 " pdb=" OG SER G 259 " model vdw 2.216 3.040 nonbonded pdb=" NH2 ARG D 394 " pdb=" O LEU D 444 " model vdw 2.217 3.120 ... (remaining 248502 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 742 or resid 901 through 903)) selection = (chain 'B' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'C' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'D' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'E' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'F' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'G' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.270 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: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 81.480 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.170 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 0.044 31108 Z= 0.200 Angle : 0.600 11.217 42157 Z= 0.350 Chirality : 0.047 0.180 4747 Planarity : 0.004 0.086 5480 Dihedral : 13.865 89.622 11660 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.98 % Allowed : 0.72 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3872 helix: 0.44 (0.22), residues: 596 sheet: 0.50 (0.16), residues: 1166 loop : -1.03 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 214 HIS 0.014 0.002 HIS H 157 PHE 0.014 0.002 PHE F 707 TYR 0.022 0.001 TYR C 230 ARG 0.007 0.001 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.22349 ( 1118) hydrogen bonds : angle 8.55870 ( 3015) covalent geometry : bond 0.00427 (31108) covalent geometry : angle 0.60039 (42157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 3.198 Fit side-chains REVERT: A 319 GLN cc_start: 0.8074 (pt0) cc_final: 0.7596 (pt0) REVERT: D 657 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7503 (mmmt) REVERT: F 639 ASN cc_start: 0.6583 (p0) cc_final: 0.6345 (p0) REVERT: H 22 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5117 (ttpp) REVERT: H 25 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: H 28 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7662 (tm-30) outliers start: 22 outliers final: 9 residues processed: 211 average time/residue: 1.4674 time to fit residues: 365.7681 Evaluate side-chains 142 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 283 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 28 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN A 634 ASN B 314 HIS A C 376 ASN C 392 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN D 376 ASN D 567 ASN E 702 GLN H 57 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.082819 restraints weight = 165362.990| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.52 r_work: 0.2883 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 31108 Z= 0.271 Angle : 0.665 13.563 42157 Z= 0.359 Chirality : 0.051 0.180 4747 Planarity : 0.005 0.064 5480 Dihedral : 5.607 58.446 4212 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.30 % Allowed : 6.11 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3872 helix: 0.43 (0.21), residues: 599 sheet: 0.54 (0.15), residues: 1182 loop : -1.09 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 214 HIS 0.004 0.002 HIS H 157 PHE 0.017 0.002 PHE F 707 TYR 0.023 0.002 TYR E 230 ARG 0.007 0.001 ARG E 529 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1118) hydrogen bonds : angle 5.46144 ( 3015) covalent geometry : bond 0.00674 (31108) covalent geometry : angle 0.66517 (42157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 3.399 Fit side-chains REVERT: A 251 GLU cc_start: 0.7616 (mp0) cc_final: 0.7321 (mp0) REVERT: A 319 GLN cc_start: 0.7925 (pt0) cc_final: 0.7618 (pt0) REVERT: A 627 ASN cc_start: 0.7923 (t0) cc_final: 0.7569 (t0) REVERT: C 314 HIS cc_start: 0.6665 (m-70) cc_final: 0.6233 (t70) REVERT: C 657 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7423 (mmmt) REVERT: D 376 ASN cc_start: 0.7808 (m-40) cc_final: 0.7573 (m-40) REVERT: D 657 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7524 (mmmt) REVERT: D 660 MET cc_start: 0.7664 (tpt) cc_final: 0.7285 (tpt) REVERT: F 323 VAL cc_start: 0.7202 (t) cc_final: 0.6936 (m) REVERT: F 660 MET cc_start: 0.7047 (tpp) cc_final: 0.6557 (tpp) REVERT: G 324 SER cc_start: 0.6306 (t) cc_final: 0.6014 (m) REVERT: G 403 MET cc_start: 0.9102 (ttt) cc_final: 0.8766 (ttt) REVERT: H 22 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5069 (ttpp) REVERT: H 25 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: H 28 GLU cc_start: 0.8275 (pp20) cc_final: 0.7954 (tm-30) outliers start: 32 outliers final: 16 residues processed: 164 average time/residue: 1.2915 time to fit residues: 256.1901 Evaluate side-chains 146 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 596 SER 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 569 ILE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 324 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 320 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 344 optimal weight: 5.9990 chunk 350 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN B 376 ASN ** C 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 = 0.3792 r_free = 0.3792 target = 0.130098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083974 restraints weight = 156219.456| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.32 r_work: 0.2919 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31108 Z= 0.126 Angle : 0.528 9.870 42157 Z= 0.286 Chirality : 0.046 0.167 4747 Planarity : 0.004 0.059 5480 Dihedral : 4.930 57.659 4203 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.24 % Allowed : 7.87 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 3872 helix: 0.74 (0.21), residues: 599 sheet: 0.63 (0.15), residues: 1199 loop : -1.00 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 231 HIS 0.003 0.001 AHIS F 314 PHE 0.012 0.001 PHE F 707 TYR 0.016 0.001 TYR A 439 ARG 0.005 0.000 ARG H 21 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 1118) hydrogen bonds : angle 4.92558 ( 3015) covalent geometry : bond 0.00298 (31108) covalent geometry : angle 0.52840 (42157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 3.254 Fit side-chains REVERT: A 251 GLU cc_start: 0.7570 (mp0) cc_final: 0.7370 (mp0) REVERT: A 319 GLN cc_start: 0.7800 (pt0) cc_final: 0.7493 (pt0) REVERT: A 627 ASN cc_start: 0.7679 (t0) cc_final: 0.7226 (t0) REVERT: B 368 GLN cc_start: 0.4781 (OUTLIER) cc_final: 0.4432 (tp-100) REVERT: B 740 GLU cc_start: 0.7564 (pm20) cc_final: 0.7093 (pm20) REVERT: C 314 HIS cc_start: 0.6564 (m-70) cc_final: 0.6180 (t70) REVERT: D 313 GLU cc_start: 0.8060 (tt0) cc_final: 0.7598 (tm-30) REVERT: D 321 LYS cc_start: 0.6035 (mtmt) cc_final: 0.5366 (mtpp) REVERT: D 657 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7477 (mmmt) REVERT: D 660 MET cc_start: 0.7738 (tpt) cc_final: 0.7112 (tpp) REVERT: E 694 LYS cc_start: 0.7553 (tptp) cc_final: 0.7348 (tptp) REVERT: F 641 ASP cc_start: 0.6752 (m-30) cc_final: 0.6479 (t0) REVERT: F 660 MET cc_start: 0.6931 (tpp) cc_final: 0.6519 (tpp) REVERT: G 324 SER cc_start: 0.6175 (t) cc_final: 0.5885 (m) REVERT: H 22 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5211 (ttpp) REVERT: H 25 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: H 28 GLU cc_start: 0.8308 (pp20) cc_final: 0.7905 (tm-30) outliers start: 30 outliers final: 14 residues processed: 174 average time/residue: 1.3872 time to fit residues: 289.7450 Evaluate side-chains 152 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 3.328 ------------------------------------------------------------------------------- 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 368 GLN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 596 SER 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 H residue 22 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 238 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 286 optimal weight: 0.0170 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN B 463 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN F 463 ASN F 491 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.083780 restraints weight = 143016.230| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.20 r_work: 0.2918 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31108 Z= 0.136 Angle : 0.523 9.738 42157 Z= 0.284 Chirality : 0.046 0.163 4747 Planarity : 0.004 0.057 5480 Dihedral : 4.825 57.712 4203 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.33 % Allowed : 9.20 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3872 helix: 0.85 (0.21), residues: 600 sheet: 0.70 (0.15), residues: 1197 loop : -0.99 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 231 HIS 0.002 0.001 AHIS F 314 PHE 0.013 0.001 PHE F 707 TYR 0.016 0.001 TYR A 439 ARG 0.004 0.000 ARG H 21 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 1118) hydrogen bonds : angle 4.72378 ( 3015) covalent geometry : bond 0.00328 (31108) covalent geometry : angle 0.52251 (42157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 3.435 Fit side-chains REVERT: A 251 GLU cc_start: 0.7672 (mp0) cc_final: 0.7438 (mp0) REVERT: A 319 GLN cc_start: 0.7916 (pt0) cc_final: 0.7621 (pt0) REVERT: A 370 SER cc_start: 0.7017 (m) cc_final: 0.6678 (p) REVERT: A 499 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 627 ASN cc_start: 0.7733 (t0) cc_final: 0.7252 (t0) REVERT: B 660 MET cc_start: 0.7524 (tpp) cc_final: 0.7174 (tpt) REVERT: B 740 GLU cc_start: 0.7614 (pm20) cc_final: 0.7104 (pm20) REVERT: C 314 HIS cc_start: 0.6775 (m-70) cc_final: 0.6312 (t70) REVERT: C 376 ASN cc_start: 0.7730 (m-40) cc_final: 0.7356 (m110) REVERT: C 701 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: D 313 GLU cc_start: 0.8171 (tt0) cc_final: 0.7901 (tt0) REVERT: D 321 LYS cc_start: 0.6137 (mtmt) cc_final: 0.5429 (mtpp) REVERT: D 561 ASP cc_start: 0.7077 (p0) cc_final: 0.6468 (p0) REVERT: D 657 LYS cc_start: 0.7775 (mtpp) cc_final: 0.7493 (mmmt) REVERT: D 660 MET cc_start: 0.7662 (tpt) cc_final: 0.6885 (tpp) REVERT: E 694 LYS cc_start: 0.7508 (tptp) cc_final: 0.7260 (tptp) REVERT: F 522 GLU cc_start: 0.7292 (mp0) cc_final: 0.7079 (mp0) REVERT: F 641 ASP cc_start: 0.6773 (m-30) cc_final: 0.6548 (t0) REVERT: F 660 MET cc_start: 0.7018 (tpp) cc_final: 0.6624 (tpp) REVERT: F 664 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (mttp) REVERT: G 324 SER cc_start: 0.6224 (t) cc_final: 0.5923 (m) REVERT: H 25 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: H 28 GLU cc_start: 0.8477 (pp20) cc_final: 0.8180 (tm-30) outliers start: 33 outliers final: 20 residues processed: 176 average time/residue: 1.3501 time to fit residues: 286.5146 Evaluate side-chains 167 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 13 optimal weight: 0.0870 chunk 186 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 296 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.084263 restraints weight = 153373.647| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.46 r_work: 0.2913 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31108 Z= 0.135 Angle : 0.518 9.603 42157 Z= 0.280 Chirality : 0.045 0.161 4747 Planarity : 0.004 0.055 5480 Dihedral : 4.740 57.532 4199 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.62 % Allowed : 10.10 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3872 helix: 0.90 (0.21), residues: 600 sheet: 0.80 (0.16), residues: 1170 loop : -1.01 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 375 HIS 0.002 0.001 AHIS F 314 PHE 0.013 0.001 PHE F 707 TYR 0.016 0.001 TYR A 439 ARG 0.003 0.000 ARG H 21 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 1118) hydrogen bonds : angle 4.59183 ( 3015) covalent geometry : bond 0.00325 (31108) covalent geometry : angle 0.51821 (42157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 3.435 Fit side-chains REVERT: A 251 GLU cc_start: 0.7594 (mp0) cc_final: 0.7373 (mp0) REVERT: A 319 GLN cc_start: 0.7809 (pt0) cc_final: 0.7503 (pt0) REVERT: A 627 ASN cc_start: 0.7655 (t0) cc_final: 0.7167 (t0) REVERT: A 698 LEU cc_start: 0.8076 (pp) cc_final: 0.7319 (mp) REVERT: B 252 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8317 (mp10) REVERT: B 368 GLN cc_start: 0.4544 (OUTLIER) cc_final: 0.4335 (tp-100) REVERT: B 660 MET cc_start: 0.7718 (tpp) cc_final: 0.7245 (tpp) REVERT: C 376 ASN cc_start: 0.7571 (m-40) cc_final: 0.7205 (m110) REVERT: C 660 MET cc_start: 0.6370 (tpp) cc_final: 0.6167 (tpp) REVERT: C 701 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: D 321 LYS cc_start: 0.6103 (mtmt) cc_final: 0.5384 (mtpp) REVERT: D 657 LYS cc_start: 0.7708 (mtpp) cc_final: 0.7409 (mmmt) REVERT: D 660 MET cc_start: 0.7525 (tpt) cc_final: 0.6992 (tpp) REVERT: D 687 LYS cc_start: 0.7945 (mppt) cc_final: 0.7718 (mppt) REVERT: E 694 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7222 (tptp) REVERT: F 522 GLU cc_start: 0.7206 (mp0) cc_final: 0.6999 (mp0) REVERT: F 641 ASP cc_start: 0.6905 (m-30) cc_final: 0.6642 (t0) REVERT: F 660 MET cc_start: 0.7019 (tpp) cc_final: 0.6584 (tpp) REVERT: G 324 SER cc_start: 0.6135 (t) cc_final: 0.5863 (m) REVERT: G 740 GLU cc_start: 0.8220 (tt0) cc_final: 0.7794 (tp30) REVERT: H 25 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7787 (mm-30) REVERT: H 28 GLU cc_start: 0.8540 (pp20) cc_final: 0.8280 (tm-30) REVERT: H 51 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8061 (tptp) outliers start: 43 outliers final: 22 residues processed: 179 average time/residue: 1.3180 time to fit residues: 283.1967 Evaluate side-chains 172 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 355 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 375 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 325 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 372 optimal weight: 4.9990 chunk 284 optimal weight: 20.0000 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN B 368 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN E 411 ASN F 463 ASN H 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083113 restraints weight = 160652.944| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.48 r_work: 0.2890 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31108 Z= 0.190 Angle : 0.564 10.718 42157 Z= 0.305 Chirality : 0.047 0.161 4747 Planarity : 0.004 0.053 5480 Dihedral : 4.943 57.297 4199 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.74 % Allowed : 10.73 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 3872 helix: 0.79 (0.21), residues: 600 sheet: 0.70 (0.15), residues: 1196 loop : -1.06 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 375 HIS 0.002 0.001 HIS H 199 PHE 0.015 0.002 PHE D 707 TYR 0.019 0.001 TYR A 439 ARG 0.004 0.001 ARG D 529 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 1118) hydrogen bonds : angle 4.67385 ( 3015) covalent geometry : bond 0.00470 (31108) covalent geometry : angle 0.56410 (42157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 3.204 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7560 (mp0) cc_final: 0.7295 (mp0) REVERT: A 319 GLN cc_start: 0.7893 (pt0) cc_final: 0.7585 (pt0) REVERT: A 627 ASN cc_start: 0.7719 (t0) cc_final: 0.7179 (t0) REVERT: B 252 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8342 (mp10) REVERT: B 368 GLN cc_start: 0.4704 (OUTLIER) cc_final: 0.4440 (tp-100) REVERT: B 660 MET cc_start: 0.7623 (tpp) cc_final: 0.7113 (tpp) REVERT: C 314 HIS cc_start: 0.6602 (m-70) cc_final: 0.6192 (t70) REVERT: C 376 ASN cc_start: 0.7658 (m-40) cc_final: 0.7295 (m110) REVERT: C 660 MET cc_start: 0.6527 (tpp) cc_final: 0.6265 (tpp) REVERT: C 701 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: D 321 LYS cc_start: 0.6150 (mtmt) cc_final: 0.5398 (mtpp) REVERT: D 660 MET cc_start: 0.7561 (tpt) cc_final: 0.6826 (tpp) REVERT: D 687 LYS cc_start: 0.7962 (mppt) cc_final: 0.7730 (mppt) REVERT: D 721 ILE cc_start: 0.6779 (mm) cc_final: 0.6459 (tt) REVERT: E 694 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7230 (tptp) REVERT: F 641 ASP cc_start: 0.6908 (m-30) cc_final: 0.6646 (t0) REVERT: F 660 MET cc_start: 0.7040 (tpp) cc_final: 0.6646 (tpp) REVERT: F 664 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7832 (mttp) REVERT: G 324 SER cc_start: 0.6184 (t) cc_final: 0.5876 (m) REVERT: H 28 GLU cc_start: 0.8547 (pp20) cc_final: 0.8343 (tm-30) REVERT: H 51 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8084 (tptp) outliers start: 47 outliers final: 29 residues processed: 181 average time/residue: 1.4272 time to fit residues: 310.4256 Evaluate side-chains 175 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 385 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 355 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7958 > 50: distance: 15 - 143: 17.996 distance: 18 - 140: 8.850 distance: 33 - 81: 9.400 distance: 36 - 78: 10.030 distance: 65 - 71: 6.959 distance: 71 - 72: 14.786 distance: 72 - 73: 14.209 distance: 72 - 75: 17.122 distance: 73 - 74: 21.912 distance: 73 - 78: 16.825 distance: 75 - 76: 7.443 distance: 75 - 77: 6.402 distance: 78 - 79: 11.324 distance: 79 - 82: 4.439 distance: 80 - 90: 4.908 distance: 82 - 83: 6.635 distance: 83 - 84: 6.516 distance: 83 - 85: 10.842 distance: 84 - 86: 7.125 distance: 85 - 87: 5.983 distance: 86 - 88: 8.118 distance: 87 - 88: 7.327 distance: 90 - 91: 4.552 distance: 90 - 96: 3.332 distance: 91 - 92: 16.521 distance: 91 - 94: 13.276 distance: 92 - 93: 20.697 distance: 92 - 97: 10.073 distance: 94 - 95: 8.370 distance: 95 - 96: 15.006 distance: 97 - 98: 13.291 distance: 98 - 99: 13.864 distance: 98 - 101: 11.710 distance: 99 - 100: 7.017 distance: 99 - 106: 6.808 distance: 101 - 102: 4.782 distance: 102 - 103: 22.606 distance: 103 - 104: 13.130 distance: 104 - 105: 25.127 distance: 106 - 107: 9.588 distance: 107 - 108: 12.082 distance: 107 - 110: 5.320 distance: 108 - 109: 25.303 distance: 108 - 115: 8.132 distance: 110 - 111: 4.450 distance: 111 - 112: 11.488 distance: 112 - 113: 8.967 distance: 113 - 114: 12.038 distance: 115 - 116: 15.053 distance: 116 - 117: 6.650 distance: 117 - 118: 9.741 distance: 117 - 119: 11.063 distance: 119 - 120: 12.839 distance: 120 - 121: 14.511 distance: 120 - 123: 15.156 distance: 121 - 122: 24.224 distance: 121 - 127: 10.760 distance: 123 - 124: 9.911 distance: 124 - 125: 19.970 distance: 124 - 126: 13.170 distance: 127 - 128: 16.015 distance: 128 - 129: 18.235 distance: 128 - 131: 5.832 distance: 129 - 130: 15.865 distance: 129 - 133: 13.851 distance: 131 - 132: 20.049 distance: 133 - 134: 13.296 distance: 133 - 139: 31.485 distance: 134 - 135: 11.662 distance: 134 - 137: 18.328 distance: 135 - 136: 8.484 distance: 137 - 138: 14.266 distance: 138 - 139: 16.216 distance: 140 - 141: 13.309 distance: 141 - 142: 17.262 distance: 141 - 144: 7.015 distance: 142 - 143: 12.199 distance: 142 - 148: 8.423 distance: 144 - 145: 4.913 distance: 145 - 146: 12.243 distance: 145 - 147: 12.175