Starting phenix.real_space_refine on Mon Aug 25 20:41:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvs_34137/08_2025/7yvs_34137.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvs_34137/08_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_34137/08_2025/7yvs_34137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvs_34137/08_2025/7yvs_34137.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvs_34137/08_2025/7yvs_34137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvs_34137/08_2025/7yvs_34137.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 8.19, per 1000 atoms: 0.27 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: 2.07 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.24 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: 6.61 Time building geometry restraints manager: 2.76 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 903)) selection = (chain 'B' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'C' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'D' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'E' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'F' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'G' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.130 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 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:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.160 ------------------------------------------------------------------------------- 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 : 6.17 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG F 290 TYR 0.022 0.001 TYR C 230 PHE 0.014 0.002 PHE F 707 TRP 0.032 0.001 TRP D 214 HIS 0.014 0.002 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00427 (31108) covalent geometry : angle 0.60039 (42157) hydrogen bonds : bond 0.22349 ( 1118) hydrogen bonds : angle 8.55870 ( 3015) *********************** 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 : 0.799 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: 0.5116 (ttpp) REVERT: H 25 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: H 28 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7670 (tm-30) outliers start: 22 outliers final: 9 residues processed: 211 average time/residue: 0.6001 time to fit residues: 148.9878 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 : 0.914 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 376 ASN H 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.130267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084193 restraints weight = 156499.468| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.41 r_work: 0.2916 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31108 Z= 0.184 Angle : 0.592 11.458 42157 Z= 0.321 Chirality : 0.048 0.180 4747 Planarity : 0.004 0.063 5480 Dihedral : 5.351 58.115 4212 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.22 % Allowed : 5.64 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.14), residues: 3872 helix: 0.61 (0.21), residues: 599 sheet: 0.64 (0.16), residues: 1190 loop : -0.98 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 21 TYR 0.019 0.001 TYR E 230 PHE 0.015 0.002 PHE F 707 TRP 0.016 0.001 TRP D 214 HIS 0.004 0.001 AHIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00449 (31108) covalent geometry : angle 0.59182 (42157) hydrogen bonds : bond 0.04075 ( 1118) hydrogen bonds : angle 5.35923 ( 3015) *********************** 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: 29 poor density : 144 time to evaluate : 1.040 Fit side-chains REVERT: A 251 GLU cc_start: 0.7593 (mp0) cc_final: 0.7375 (mp0) REVERT: A 319 GLN cc_start: 0.7818 (pt0) cc_final: 0.7478 (pt0) REVERT: A 627 ASN cc_start: 0.7802 (t0) cc_final: 0.7410 (t0) REVERT: C 314 HIS cc_start: 0.6593 (m-70) cc_final: 0.6161 (t70) REVERT: C 657 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7400 (mmmt) REVERT: D 376 ASN cc_start: 0.7783 (m-40) cc_final: 0.7540 (m-40) REVERT: D 634 ASN cc_start: 0.6858 (m110) cc_final: 0.6657 (m110) REVERT: D 657 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7573 (mmmt) REVERT: E 318 ASP cc_start: 0.6900 (m-30) cc_final: 0.6558 (t70) REVERT: F 323 VAL cc_start: 0.7156 (t) cc_final: 0.6910 (m) REVERT: F 660 MET cc_start: 0.6976 (tpp) cc_final: 0.6609 (tpp) REVERT: G 324 SER cc_start: 0.6288 (t) cc_final: 0.6007 (m) REVERT: H 22 LYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5139 (ttpp) REVERT: H 25 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: H 28 GLU cc_start: 0.8280 (pp20) cc_final: 0.7996 (tm-30) outliers start: 29 outliers final: 17 residues processed: 166 average time/residue: 0.5419 time to fit residues: 107.7030 Evaluate side-chains 153 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 342 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN B 463 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 ASN E 702 GLN F 491 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 634 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082190 restraints weight = 166270.648| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.39 r_work: 0.2885 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31108 Z= 0.193 Angle : 0.582 11.605 42157 Z= 0.315 Chirality : 0.048 0.167 4747 Planarity : 0.004 0.059 5480 Dihedral : 5.097 57.928 4203 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.27 % Allowed : 7.70 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.13), residues: 3872 helix: 0.65 (0.21), residues: 599 sheet: 0.60 (0.15), residues: 1199 loop : -1.04 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 529 TYR 0.019 0.001 TYR A 439 PHE 0.015 0.002 PHE F 707 TRP 0.020 0.001 TRP D 214 HIS 0.003 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00475 (31108) covalent geometry : angle 0.58240 (42157) hydrogen bonds : bond 0.03748 ( 1118) hydrogen bonds : angle 4.97949 ( 3015) *********************** 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 181 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.999 Fit side-chains REVERT: A 251 GLU cc_start: 0.7551 (mp0) cc_final: 0.7281 (mp0) REVERT: A 319 GLN cc_start: 0.7912 (pt0) cc_final: 0.7608 (pt0) REVERT: A 627 ASN cc_start: 0.7772 (t0) cc_final: 0.7297 (t0) REVERT: B 368 GLN cc_start: 0.4831 (OUTLIER) cc_final: 0.4506 (tp-100) REVERT: B 660 MET cc_start: 0.7563 (tpp) cc_final: 0.7184 (tpp) REVERT: B 740 GLU cc_start: 0.7595 (pm20) cc_final: 0.7117 (pm20) REVERT: C 314 HIS cc_start: 0.6619 (m-70) cc_final: 0.6228 (t70) REVERT: D 313 GLU cc_start: 0.8102 (tt0) cc_final: 0.7631 (tm-30) REVERT: D 321 LYS cc_start: 0.6156 (mtmt) cc_final: 0.5433 (mtpp) REVERT: D 634 ASN cc_start: 0.6887 (m-40) cc_final: 0.6661 (m110) REVERT: D 657 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7490 (mmmt) REVERT: D 660 MET cc_start: 0.7628 (tpt) cc_final: 0.7200 (tpt) REVERT: D 712 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7297 (mt-10) REVERT: D 721 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5783 (tp) REVERT: E 694 LYS cc_start: 0.7508 (tptp) cc_final: 0.7289 (tptp) REVERT: F 323 VAL cc_start: 0.7166 (t) cc_final: 0.6912 (m) REVERT: F 641 ASP cc_start: 0.6766 (m-30) cc_final: 0.6437 (t70) REVERT: F 660 MET cc_start: 0.7000 (tpp) cc_final: 0.6650 (tpp) REVERT: G 324 SER cc_start: 0.6194 (t) cc_final: 0.5893 (m) REVERT: H 22 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5211 (ttpp) REVERT: H 25 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: H 28 GLU cc_start: 0.8339 (pp20) cc_final: 0.8006 (tm-30) outliers start: 31 outliers final: 18 residues processed: 170 average time/residue: 0.5296 time to fit residues: 108.6080 Evaluate side-chains 161 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 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 596 SER Chi-restraints excluded: chain D residue 721 ILE 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 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 332 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 523 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 ASN F 463 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 = 0.3780 r_free = 0.3780 target = 0.128980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083142 restraints weight = 146078.346| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.21 r_work: 0.2903 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31108 Z= 0.174 Angle : 0.557 10.749 42157 Z= 0.301 Chirality : 0.047 0.164 4747 Planarity : 0.004 0.057 5480 Dihedral : 5.009 57.702 4203 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.56 % Allowed : 9.06 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.13), residues: 3872 helix: 0.73 (0.21), residues: 599 sheet: 0.63 (0.15), residues: 1195 loop : -1.05 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 529 TYR 0.018 0.001 TYR A 439 PHE 0.014 0.002 PHE F 707 TRP 0.011 0.001 TRP D 214 HIS 0.002 0.001 AHIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00429 (31108) covalent geometry : angle 0.55730 (42157) hydrogen bonds : bond 0.03405 ( 1118) hydrogen bonds : angle 4.81809 ( 3015) *********************** 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 187 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7712 (mp0) cc_final: 0.7456 (mp0) REVERT: A 319 GLN cc_start: 0.8038 (pt0) cc_final: 0.7761 (pt0) REVERT: A 627 ASN cc_start: 0.7762 (t0) cc_final: 0.7269 (t0) REVERT: B 368 GLN cc_start: 0.4849 (OUTLIER) cc_final: 0.4602 (tp-100) REVERT: B 660 MET cc_start: 0.7839 (tpp) cc_final: 0.7350 (tpp) REVERT: B 740 GLU cc_start: 0.7643 (pm20) cc_final: 0.7156 (pm20) REVERT: C 314 HIS cc_start: 0.6859 (m-70) cc_final: 0.6417 (t70) REVERT: C 376 ASN cc_start: 0.7816 (m-40) cc_final: 0.7438 (m110) REVERT: C 701 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: D 313 GLU cc_start: 0.8236 (tt0) cc_final: 0.8008 (tt0) REVERT: D 321 LYS cc_start: 0.6321 (mtmt) cc_final: 0.5552 (mtpp) REVERT: D 634 ASN cc_start: 0.6952 (m-40) cc_final: 0.6683 (m110) REVERT: D 660 MET cc_start: 0.7756 (tpt) cc_final: 0.6969 (tpp) REVERT: E 694 LYS cc_start: 0.7528 (tptp) cc_final: 0.7269 (tptp) REVERT: F 641 ASP cc_start: 0.6800 (m-30) cc_final: 0.6569 (t0) REVERT: F 660 MET cc_start: 0.7051 (tpp) cc_final: 0.6718 (tpp) REVERT: G 324 SER cc_start: 0.6308 (t) cc_final: 0.6001 (m) REVERT: H 25 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: H 28 GLU cc_start: 0.8554 (pp20) cc_final: 0.8256 (tm-30) REVERT: H 51 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8132 (tptp) outliers start: 41 outliers final: 22 residues processed: 176 average time/residue: 0.5508 time to fit residues: 116.4092 Evaluate side-chains 164 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 368 GLN Chi-restraints excluded: chain B residue 379 LEU 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 E residue 403 MET 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 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 61 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 282 optimal weight: 0.9980 chunk 309 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN H 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083033 restraints weight = 168768.036| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.73 r_work: 0.2876 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 31108 Z= 0.192 Angle : 0.568 10.923 42157 Z= 0.307 Chirality : 0.047 0.172 4747 Planarity : 0.004 0.055 5480 Dihedral : 5.019 57.400 4199 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.53 % Allowed : 10.45 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.13), residues: 3872 helix: 0.73 (0.21), residues: 599 sheet: 0.64 (0.15), residues: 1181 loop : -1.09 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 529 TYR 0.019 0.001 TYR A 439 PHE 0.015 0.002 PHE D 707 TRP 0.012 0.001 TRP G 375 HIS 0.002 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00476 (31108) covalent geometry : angle 0.56818 (42157) hydrogen bonds : bond 0.03447 ( 1118) hydrogen bonds : angle 4.78080 ( 3015) *********************** 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 180 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7601 (mp0) cc_final: 0.7352 (mp0) REVERT: A 319 GLN cc_start: 0.7962 (pt0) cc_final: 0.7674 (pt0) REVERT: A 627 ASN cc_start: 0.7718 (t0) cc_final: 0.7201 (t0) REVERT: B 368 GLN cc_start: 0.4891 (OUTLIER) cc_final: 0.4618 (tp-100) REVERT: B 660 MET cc_start: 0.7681 (tpp) cc_final: 0.7136 (tpp) REVERT: B 740 GLU cc_start: 0.7378 (pm20) cc_final: 0.7057 (tm-30) REVERT: C 314 HIS cc_start: 0.6642 (m-70) cc_final: 0.6262 (t70) REVERT: C 376 ASN cc_start: 0.7729 (m-40) cc_final: 0.7363 (m110) REVERT: C 660 MET cc_start: 0.6409 (tpp) cc_final: 0.6096 (tpp) REVERT: C 701 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: D 321 LYS cc_start: 0.6240 (mtmt) cc_final: 0.5463 (mtpp) REVERT: D 634 ASN cc_start: 0.6999 (m-40) cc_final: 0.6657 (m110) REVERT: D 660 MET cc_start: 0.7638 (tpt) cc_final: 0.6852 (tpp) REVERT: E 426 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8791 (tp30) REVERT: E 694 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7237 (tptp) REVERT: F 323 VAL cc_start: 0.7194 (t) cc_final: 0.6959 (m) REVERT: F 641 ASP cc_start: 0.6903 (m-30) cc_final: 0.6638 (t0) REVERT: F 660 MET cc_start: 0.7020 (tpp) cc_final: 0.6630 (tpp) REVERT: F 664 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7827 (mttp) REVERT: G 324 SER cc_start: 0.6230 (t) cc_final: 0.5919 (m) REVERT: H 25 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7808 (mm-30) REVERT: H 28 GLU cc_start: 0.8481 (pp20) cc_final: 0.8180 (tm-30) REVERT: H 51 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8105 (tptp) outliers start: 40 outliers final: 25 residues processed: 171 average time/residue: 0.5415 time to fit residues: 111.4386 Evaluate side-chains 165 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 379 LEU 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 452 MET 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 426 GLU Chi-restraints excluded: chain E residue 694 LYS 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 569 ILE 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 259 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 463 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.082502 restraints weight = 148019.322| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.30 r_work: 0.2890 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31108 Z= 0.192 Angle : 0.565 11.014 42157 Z= 0.306 Chirality : 0.047 0.164 4747 Planarity : 0.004 0.053 5480 Dihedral : 5.024 57.142 4199 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.71 % Allowed : 10.85 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.13), residues: 3872 helix: 0.74 (0.21), residues: 599 sheet: 0.65 (0.15), residues: 1181 loop : -1.10 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 529 TYR 0.019 0.001 TYR A 439 PHE 0.015 0.002 PHE D 707 TRP 0.014 0.001 TRP G 375 HIS 0.002 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00474 (31108) covalent geometry : angle 0.56541 (42157) hydrogen bonds : bond 0.03410 ( 1118) hydrogen bonds : angle 4.75167 ( 3015) *********************** 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 188 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7727 (mp0) cc_final: 0.7456 (mp0) REVERT: A 319 GLN cc_start: 0.8102 (pt0) cc_final: 0.7824 (pt0) REVERT: A 627 ASN cc_start: 0.7753 (t0) cc_final: 0.7249 (t0) REVERT: B 368 GLN cc_start: 0.4984 (OUTLIER) cc_final: 0.4703 (tp-100) REVERT: B 660 MET cc_start: 0.7791 (tpp) cc_final: 0.7218 (tpp) REVERT: C 314 HIS cc_start: 0.6856 (m-70) cc_final: 0.6413 (t70) REVERT: C 660 MET cc_start: 0.6629 (tpp) cc_final: 0.6297 (tpp) REVERT: C 701 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: D 634 ASN cc_start: 0.7027 (m-40) cc_final: 0.6659 (m110) REVERT: D 660 MET cc_start: 0.7694 (tpt) cc_final: 0.6922 (tpp) REVERT: E 426 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8952 (tp30) REVERT: E 694 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7302 (tptp) REVERT: F 323 VAL cc_start: 0.7343 (t) cc_final: 0.7104 (m) REVERT: F 641 ASP cc_start: 0.6934 (m-30) cc_final: 0.6663 (t0) REVERT: F 660 MET cc_start: 0.7095 (tpp) cc_final: 0.6681 (tpp) REVERT: F 664 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7841 (mttp) REVERT: G 324 SER cc_start: 0.6350 (t) cc_final: 0.6034 (m) REVERT: G 740 GLU cc_start: 0.8441 (tt0) cc_final: 0.7997 (tp30) REVERT: H 25 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: H 28 GLU cc_start: 0.8648 (pp20) cc_final: 0.8339 (tm-30) REVERT: H 51 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8169 (tptp) outliers start: 46 outliers final: 26 residues processed: 175 average time/residue: 0.5437 time to fit residues: 114.1415 Evaluate side-chains 166 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain B residue 324 SER 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 319 GLN Chi-restraints excluded: chain C residue 542 THR 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 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 721 ILE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 694 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 86 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 chunk 308 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 375 optimal weight: 7.9990 chunk 317 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082709 restraints weight = 148839.874| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.30 r_work: 0.2897 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31108 Z= 0.175 Angle : 0.553 10.637 42157 Z= 0.300 Chirality : 0.047 0.162 4747 Planarity : 0.004 0.052 5480 Dihedral : 4.978 56.830 4199 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.74 % Allowed : 11.20 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.13), residues: 3872 helix: 0.79 (0.21), residues: 599 sheet: 0.67 (0.15), residues: 1181 loop : -1.10 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 529 TYR 0.018 0.001 TYR A 439 PHE 0.014 0.002 PHE D 707 TRP 0.017 0.001 TRP G 375 HIS 0.002 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00431 (31108) covalent geometry : angle 0.55316 (42157) hydrogen bonds : bond 0.03275 ( 1118) hydrogen bonds : angle 4.70889 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 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 187 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7715 (mp0) cc_final: 0.7465 (mp0) REVERT: A 319 GLN cc_start: 0.8035 (pt0) cc_final: 0.7753 (pt0) REVERT: A 627 ASN cc_start: 0.7791 (t0) cc_final: 0.7266 (t0) REVERT: B 252 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: B 368 GLN cc_start: 0.4876 (OUTLIER) cc_final: 0.4672 (tp-100) REVERT: B 660 MET cc_start: 0.7748 (tpp) cc_final: 0.7139 (tpp) REVERT: C 314 HIS cc_start: 0.6815 (m-70) cc_final: 0.6359 (t70) REVERT: C 660 MET cc_start: 0.6594 (tpp) cc_final: 0.6322 (tpp) REVERT: C 701 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: D 304 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9096 (ttt) REVERT: D 495 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: D 634 ASN cc_start: 0.6914 (m-40) cc_final: 0.6541 (m110) REVERT: D 660 MET cc_start: 0.7636 (tpt) cc_final: 0.6902 (tpp) REVERT: E 426 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8926 (tp30) REVERT: E 694 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7303 (tptp) REVERT: F 323 VAL cc_start: 0.7261 (t) cc_final: 0.7027 (m) REVERT: F 641 ASP cc_start: 0.6892 (m-30) cc_final: 0.6623 (t0) REVERT: F 660 MET cc_start: 0.7059 (tpp) cc_final: 0.6649 (tpp) REVERT: F 664 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7824 (mttp) REVERT: G 324 SER cc_start: 0.6281 (t) cc_final: 0.5964 (m) REVERT: G 740 GLU cc_start: 0.8401 (tt0) cc_final: 0.7937 (tp30) REVERT: H 51 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8129 (tptp) outliers start: 47 outliers final: 29 residues processed: 174 average time/residue: 0.5302 time to fit residues: 110.3588 Evaluate side-chains 172 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE 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 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 542 THR 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 670 VAL Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 495 GLN 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 D residue 721 ILE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 694 LYS 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 568 ASP Chi-restraints excluded: chain H residue 89 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 353 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 463 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084032 restraints weight = 151251.737| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.36 r_work: 0.2909 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31108 Z= 0.133 Angle : 0.520 9.588 42157 Z= 0.282 Chirality : 0.045 0.159 4747 Planarity : 0.004 0.051 5480 Dihedral : 4.743 39.295 4196 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.77 % Allowed : 11.57 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.13), residues: 3872 helix: 0.89 (0.21), residues: 600 sheet: 0.73 (0.15), residues: 1184 loop : -1.06 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 21 TYR 0.016 0.001 TYR A 439 PHE 0.012 0.001 PHE D 707 TRP 0.020 0.001 TRP G 375 HIS 0.002 0.001 AHIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00321 (31108) covalent geometry : angle 0.51962 (42157) hydrogen bonds : bond 0.02949 ( 1118) hydrogen bonds : angle 4.61077 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 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 198 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7897 (pt0) cc_final: 0.7602 (pt0) REVERT: A 627 ASN cc_start: 0.7737 (t0) cc_final: 0.7235 (t0) REVERT: B 252 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8317 (mp10) REVERT: B 368 GLN cc_start: 0.4909 (OUTLIER) cc_final: 0.4704 (tp-100) REVERT: B 660 MET cc_start: 0.7756 (tpp) cc_final: 0.7172 (tpp) REVERT: C 314 HIS cc_start: 0.6583 (m-70) cc_final: 0.6217 (t70) REVERT: C 376 ASN cc_start: 0.7648 (m-40) cc_final: 0.7270 (m110) REVERT: C 660 MET cc_start: 0.6482 (tpp) cc_final: 0.6231 (tpp) REVERT: C 701 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: D 495 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: D 634 ASN cc_start: 0.6920 (m-40) cc_final: 0.6556 (m110) REVERT: D 657 LYS cc_start: 0.7684 (mtpp) cc_final: 0.7284 (mmmt) REVERT: D 660 MET cc_start: 0.7543 (tpt) cc_final: 0.6749 (tpp) REVERT: D 687 LYS cc_start: 0.7977 (mppt) cc_final: 0.7753 (mppt) REVERT: E 694 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7281 (tptp) REVERT: F 323 VAL cc_start: 0.7162 (t) cc_final: 0.6955 (m) REVERT: F 641 ASP cc_start: 0.6930 (m-30) cc_final: 0.6661 (t0) REVERT: F 660 MET cc_start: 0.7051 (tpp) cc_final: 0.6599 (tpp) REVERT: F 664 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7836 (mttp) REVERT: G 324 SER cc_start: 0.6222 (t) cc_final: 0.5917 (m) REVERT: G 740 GLU cc_start: 0.8146 (tt0) cc_final: 0.7812 (tp30) REVERT: H 51 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8070 (tptp) outliers start: 48 outliers final: 29 residues processed: 185 average time/residue: 0.5405 time to fit residues: 119.7785 Evaluate side-chains 174 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 368 GLN Chi-restraints excluded: chain B residue 724 THR 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 480 THR Chi-restraints excluded: chain C residue 542 THR 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 670 VAL 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 495 GLN 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 D residue 721 ILE 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 F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE 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 248 ARG Chi-restraints excluded: chain H residue 355 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 238 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 204 optimal weight: 0.4980 chunk 171 optimal weight: 0.0370 chunk 380 optimal weight: 7.9990 chunk 336 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- 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** E 523 ASN H 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.130777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084880 restraints weight = 147425.141| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.05 r_work: 0.2944 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31108 Z= 0.105 Angle : 0.492 8.322 42157 Z= 0.267 Chirality : 0.044 0.157 4747 Planarity : 0.004 0.050 5480 Dihedral : 4.517 37.936 4196 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.48 % Allowed : 12.12 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3872 helix: 1.05 (0.21), residues: 600 sheet: 0.82 (0.15), residues: 1184 loop : -0.99 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 607 TYR 0.013 0.001 TYR A 439 PHE 0.014 0.001 PHE C 711 TRP 0.021 0.001 TRP G 375 HIS 0.002 0.000 AHIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00242 (31108) covalent geometry : angle 0.49157 (42157) hydrogen bonds : bond 0.02597 ( 1118) hydrogen bonds : angle 4.47745 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 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 198 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7949 (pt0) cc_final: 0.7577 (pt0) REVERT: A 370 SER cc_start: 0.6905 (m) cc_final: 0.6670 (p) REVERT: A 627 ASN cc_start: 0.7737 (t0) cc_final: 0.7251 (t0) REVERT: A 689 LYS cc_start: 0.7563 (tmtt) cc_final: 0.7343 (tptp) REVERT: B 660 MET cc_start: 0.7761 (tpp) cc_final: 0.7150 (tpp) REVERT: C 314 HIS cc_start: 0.6768 (m-70) cc_final: 0.6333 (t70) REVERT: C 376 ASN cc_start: 0.7741 (m-40) cc_final: 0.7346 (m110) REVERT: C 660 MET cc_start: 0.6396 (tpp) cc_final: 0.6112 (tpt) REVERT: C 701 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: D 634 ASN cc_start: 0.6919 (m-40) cc_final: 0.6516 (m110) REVERT: D 657 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7254 (mmmt) REVERT: D 660 MET cc_start: 0.7502 (tpt) cc_final: 0.6857 (tpp) REVERT: D 687 LYS cc_start: 0.7976 (mppt) cc_final: 0.7746 (mppt) REVERT: E 411 ASN cc_start: 0.8744 (m-40) cc_final: 0.8533 (m110) REVERT: E 694 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7294 (tptp) REVERT: F 641 ASP cc_start: 0.6922 (m-30) cc_final: 0.6661 (t0) REVERT: F 660 MET cc_start: 0.7033 (tpp) cc_final: 0.6627 (tpp) REVERT: F 664 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7842 (mttp) REVERT: G 324 SER cc_start: 0.6325 (t) cc_final: 0.6053 (m) REVERT: G 740 GLU cc_start: 0.8279 (tt0) cc_final: 0.7905 (tp30) REVERT: H 21 ARG cc_start: 0.5555 (pmm-80) cc_final: 0.4416 (mtt90) REVERT: H 51 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8172 (tptp) outliers start: 38 outliers final: 26 residues processed: 190 average time/residue: 0.4992 time to fit residues: 113.9105 Evaluate side-chains 184 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 724 THR 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 670 VAL Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 498 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 F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 248 ARG Chi-restraints excluded: chain H residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 84 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 255 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 chunk 251 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 491 ASN H 54 GLN H 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085400 restraints weight = 142948.173| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.17 r_work: 0.2949 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31108 Z= 0.102 Angle : 0.489 8.267 42157 Z= 0.265 Chirality : 0.044 0.155 4747 Planarity : 0.004 0.050 5480 Dihedral : 4.436 38.012 4196 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.36 % Allowed : 12.44 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.14), residues: 3872 helix: 1.10 (0.21), residues: 602 sheet: 0.97 (0.16), residues: 1162 loop : -0.98 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 394 TYR 0.013 0.001 TYR A 439 PHE 0.014 0.001 PHE C 711 TRP 0.020 0.001 TRP G 375 HIS 0.001 0.000 AHIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00238 (31108) covalent geometry : angle 0.48867 (42157) hydrogen bonds : bond 0.02548 ( 1118) hydrogen bonds : angle 4.40621 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 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 195 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 318 ASP cc_start: 0.6795 (m-30) cc_final: 0.6019 (p0) REVERT: A 319 GLN cc_start: 0.7951 (pt0) cc_final: 0.7599 (pt0) REVERT: A 627 ASN cc_start: 0.7712 (t0) cc_final: 0.7247 (t0) REVERT: A 689 LYS cc_start: 0.7567 (tmtt) cc_final: 0.7349 (tptp) REVERT: B 657 LYS cc_start: 0.7015 (tptt) cc_final: 0.6586 (pptt) REVERT: B 660 MET cc_start: 0.7760 (tpp) cc_final: 0.7439 (tpp) REVERT: C 314 HIS cc_start: 0.6751 (m-70) cc_final: 0.6304 (t70) REVERT: C 376 ASN cc_start: 0.7718 (m-40) cc_final: 0.7332 (m110) REVERT: C 660 MET cc_start: 0.6331 (tpp) cc_final: 0.6038 (tpt) REVERT: C 701 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: D 634 ASN cc_start: 0.6752 (m-40) cc_final: 0.6357 (m110) REVERT: D 657 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7250 (mmmt) REVERT: D 660 MET cc_start: 0.7433 (tpt) cc_final: 0.6831 (tpp) REVERT: D 687 LYS cc_start: 0.7979 (mppt) cc_final: 0.7763 (mppt) REVERT: E 694 LYS cc_start: 0.7522 (tptp) cc_final: 0.7270 (tptp) REVERT: F 641 ASP cc_start: 0.6902 (m-30) cc_final: 0.6654 (t0) REVERT: F 660 MET cc_start: 0.7025 (tpp) cc_final: 0.6647 (tpp) REVERT: G 324 SER cc_start: 0.6285 (t) cc_final: 0.6023 (m) REVERT: G 740 GLU cc_start: 0.8258 (tt0) cc_final: 0.7856 (tp30) REVERT: H 21 ARG cc_start: 0.5707 (pmm-80) cc_final: 0.4538 (mtt90) REVERT: H 51 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8176 (tptp) outliers start: 34 outliers final: 26 residues processed: 187 average time/residue: 0.5704 time to fit residues: 128.5670 Evaluate side-chains 175 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 724 THR 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 670 VAL Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 498 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 F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 568 ASP Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 248 ARG Chi-restraints excluded: chain H residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 130 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 305 optimal weight: 20.0000 chunk 300 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 342 optimal weight: 7.9990 chunk 287 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083375 restraints weight = 138892.007| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.22 r_work: 0.2905 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31108 Z= 0.192 Angle : 0.568 10.304 42157 Z= 0.305 Chirality : 0.048 0.544 4747 Planarity : 0.004 0.050 5480 Dihedral : 4.756 39.460 4196 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.53 % Allowed : 12.62 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.13), residues: 3872 helix: 0.89 (0.21), residues: 602 sheet: 0.83 (0.16), residues: 1173 loop : -1.06 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 529 TYR 0.018 0.001 TYR B 439 PHE 0.016 0.002 PHE C 711 TRP 0.019 0.001 TRP G 375 HIS 0.002 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00475 (31108) covalent geometry : angle 0.56773 (42157) hydrogen bonds : bond 0.03259 ( 1118) hydrogen bonds : angle 4.54146 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10994.05 seconds wall clock time: 187 minutes 37.00 seconds (11257.00 seconds total)