Starting phenix.real_space_refine on Fri Dec 15 06:53:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/12_2023/7yvs_34137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/12_2023/7yvs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/12_2023/7yvs_34137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/12_2023/7yvs_34137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/12_2023/7yvs_34137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/12_2023/7yvs_34137.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 47 5.16 5 C 19144 2.51 5 N 4979 2.21 5 O 6402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30593 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "B" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "D" Number of atoms: 3898 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 497, 3898 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} Chain breaks: 1 Chain: "E" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "F" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "G" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 3776 Chain: "H" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3200 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 73 residue: pdb=" N AGLY A 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 488 " occ=0.50 residue: pdb=" N ATHR A 489 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 489 " occ=0.50 residue: pdb=" N ALYS A 490 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 490 " occ=0.50 residue: pdb=" N AASN A 491 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 491 " occ=0.50 residue: pdb=" N ASER A 492 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 492 " occ=0.50 residue: pdb=" N ASER A 493 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 493 " occ=0.50 residue: pdb=" N AGLY A 494 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 494 " occ=0.50 residue: pdb=" N AGLN A 495 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 495 " occ=0.50 residue: pdb=" N AILE A 496 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 496 " occ=0.50 residue: pdb=" N AVAL A 497 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 497 " occ=0.50 residue: pdb=" N THR A 498 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR A 498 " occ=0.50 residue: pdb=" N AGLY B 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 488 " occ=0.50 ... (remaining 61 not shown) Time building chain proxies: 21.81, per 1000 atoms: 0.71 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 - 3.50 Amino acid : False - 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: 11.98 Conformation dependent library (CDL) restraints added in 8.3 seconds 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7300 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 82 sheets defined 20.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 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: 12.28 Time building geometry restraints manager: 12.88 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: 99.60 - 106.52: 633 106.52 - 113.45: 17164 113.45 - 120.38: 11257 120.38 - 127.30: 12916 127.30 - 134.23: 187 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 2.520 nonbonded pdb=" NH2 ARG B 394 " pdb=" O LEU B 444 " model vdw 2.193 2.520 nonbonded pdb=" NH2 ARG A 394 " pdb=" O LEU A 444 " model vdw 2.201 2.520 nonbonded pdb=" OE1 GLU G 231 " pdb=" OG SER G 259 " model vdw 2.216 2.440 nonbonded pdb=" NH2 ARG D 394 " pdb=" O LEU D 444 " model vdw 2.217 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'B' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'C' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'D' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'E' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'F' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'G' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 18.300 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 89.600 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.580 ------------------------------------------------------------------------------- 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= 0.276 Angle : 0.600 11.217 42157 Z= 0.350 Chirality : 0.047 0.180 4747 Planarity : 0.004 0.086 5480 Dihedral : 13.865 89.622 11660 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.98 % Allowed : 0.72 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3872 helix: 0.44 (0.22), residues: 596 sheet: 0.50 (0.16), residues: 1166 loop : -1.03 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 214 HIS 0.014 0.002 HIS H 157 PHE 0.014 0.002 PHE F 707 TYR 0.022 0.001 TYR C 230 ARG 0.007 0.001 ARG F 290 *********************** 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 fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 3.686 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 211 average time/residue: 1.4728 time to fit residues: 368.6565 Evaluate side-chains 138 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 3.646 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 4.7814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 B 376 ASN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31108 Z= 0.256 Angle : 0.559 11.103 42157 Z= 0.303 Chirality : 0.047 0.178 4747 Planarity : 0.004 0.062 5480 Dihedral : 4.564 23.110 4182 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.39 % Allowed : 5.84 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3872 helix: 0.70 (0.22), residues: 605 sheet: 0.69 (0.16), residues: 1176 loop : -0.96 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 214 HIS 0.004 0.001 HIS H 157 PHE 0.015 0.002 PHE F 707 TYR 0.019 0.001 TYR E 230 ARG 0.005 0.001 ARG H 21 *********************** 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 170 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 3.638 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 159 average time/residue: 1.3408 time to fit residues: 258.8270 Evaluate side-chains 143 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 3.497 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.5303 time to fit residues: 9.7241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 236 optimal weight: 0.1980 chunk 95 optimal weight: 8.9990 chunk 347 optimal weight: 3.9990 chunk 375 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 344 optimal weight: 0.1980 chunk 118 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN F 463 ASN G 634 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31108 Z= 0.246 Angle : 0.538 10.893 42157 Z= 0.290 Chirality : 0.046 0.166 4747 Planarity : 0.004 0.058 5480 Dihedral : 4.521 21.702 4182 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.24 % Allowed : 8.16 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 3872 helix: 0.81 (0.21), residues: 605 sheet: 0.67 (0.15), residues: 1200 loop : -0.99 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 214 HIS 0.002 0.001 AHIS A 314 PHE 0.014 0.002 PHE F 707 TYR 0.017 0.001 TYR A 439 ARG 0.005 0.001 ARG D 529 *********************** 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 171 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 3.566 Fit side-chains outliers start: 30 outliers final: 20 residues processed: 162 average time/residue: 1.3596 time to fit residues: 266.5844 Evaluate side-chains 143 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 3.482 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.6159 time to fit residues: 8.0398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 165 optimal weight: 0.4980 chunk 233 optimal weight: 0.9990 chunk 348 optimal weight: 3.9990 chunk 369 optimal weight: 0.0980 chunk 182 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 ASN H 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31108 Z= 0.133 Angle : 0.462 8.254 42157 Z= 0.250 Chirality : 0.044 0.161 4747 Planarity : 0.003 0.057 5480 Dihedral : 4.133 20.666 4182 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.39 % Allowed : 9.26 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3872 helix: 1.12 (0.22), residues: 605 sheet: 0.81 (0.15), residues: 1200 loop : -0.87 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 375 HIS 0.001 0.000 AHIS D 314 PHE 0.013 0.001 PHE A 707 TYR 0.012 0.001 TYR A 439 ARG 0.004 0.000 ARG H 21 *********************** 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 191 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 3.956 Fit side-chains outliers start: 35 outliers final: 17 residues processed: 183 average time/residue: 1.2317 time to fit residues: 277.7979 Evaluate side-chains 158 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 3.427 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 4.6693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 274 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 331 optimal weight: 0.0040 chunk 93 optimal weight: 10.0000 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN B 463 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 ASN H 54 GLN H 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31108 Z= 0.256 Angle : 0.530 10.804 42157 Z= 0.285 Chirality : 0.046 0.160 4747 Planarity : 0.004 0.055 5480 Dihedral : 4.420 18.932 4182 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.94 % Allowed : 9.92 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3872 helix: 0.96 (0.21), residues: 605 sheet: 0.82 (0.16), residues: 1183 loop : -0.95 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 375 HIS 0.002 0.000 AHIS A 314 PHE 0.014 0.002 PHE F 707 TYR 0.017 0.001 TYR B 439 ARG 0.004 0.000 ARG E 529 *********************** 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 197 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 3.366 Fit side-chains outliers start: 53 outliers final: 32 residues processed: 178 average time/residue: 1.3048 time to fit residues: 283.1425 Evaluate side-chains 164 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 3.584 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 0.6810 time to fit residues: 12.3757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN D 634 ASN ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 GLN G 634 ASN H 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 31108 Z= 0.379 Angle : 0.604 13.322 42157 Z= 0.324 Chirality : 0.048 0.166 4747 Planarity : 0.004 0.053 5480 Dihedral : 4.821 18.897 4182 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.88 % Allowed : 11.00 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 3872 helix: 0.72 (0.21), residues: 605 sheet: 0.69 (0.15), residues: 1182 loop : -1.08 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 214 HIS 0.002 0.001 HIS H 199 PHE 0.016 0.002 PHE F 707 TYR 0.020 0.002 TYR B 439 ARG 0.006 0.001 ARG D 529 *********************** 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 199 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 148 time to evaluate : 3.559 Fit side-chains outliers start: 51 outliers final: 36 residues processed: 180 average time/residue: 1.2519 time to fit residues: 275.3149 Evaluate side-chains 172 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 3.647 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 26 residues processed: 11 average time/residue: 0.3737 time to fit residues: 11.7391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 311 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 230 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 463 ASN G 634 ASN H 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31108 Z= 0.150 Angle : 0.480 8.685 42157 Z= 0.260 Chirality : 0.044 0.164 4747 Planarity : 0.004 0.052 5480 Dihedral : 4.251 18.232 4182 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.62 % Allowed : 11.95 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3872 helix: 1.08 (0.22), residues: 605 sheet: 0.93 (0.16), residues: 1159 loop : -0.97 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 375 HIS 0.001 0.000 AHIS A 314 PHE 0.010 0.001 PHE F 487 TYR 0.014 0.001 TYR A 439 ARG 0.003 0.000 ARG H 21 *********************** 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 190 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 3.744 Fit side-chains outliers start: 42 outliers final: 28 residues processed: 179 average time/residue: 1.1382 time to fit residues: 251.0774 Evaluate side-chains 162 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.3026 time to fit residues: 6.2548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN E 523 ASN H 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31108 Z= 0.230 Angle : 0.525 10.248 42157 Z= 0.282 Chirality : 0.045 0.158 4747 Planarity : 0.004 0.051 5480 Dihedral : 4.380 18.212 4182 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.65 % Allowed : 12.24 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3872 helix: 1.01 (0.21), residues: 605 sheet: 0.94 (0.16), residues: 1163 loop : -1.00 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 375 HIS 0.002 0.000 HIS H 199 PHE 0.012 0.001 PHE D 707 TYR 0.016 0.001 TYR A 439 ARG 0.003 0.000 ARG D 529 *********************** 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 184 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 3.617 Fit side-chains outliers start: 43 outliers final: 34 residues processed: 177 average time/residue: 1.1354 time to fit residues: 249.6376 Evaluate side-chains 170 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 3.990 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 5 average time/residue: 0.8430 time to fit residues: 10.5678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 20.0000 chunk 352 optimal weight: 7.9990 chunk 321 optimal weight: 0.8980 chunk 343 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 341 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 463 ASN G 634 ASN H 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31108 Z= 0.276 Angle : 0.550 11.172 42157 Z= 0.296 Chirality : 0.046 0.160 4747 Planarity : 0.004 0.051 5480 Dihedral : 4.535 18.117 4182 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.59 % Allowed : 12.76 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 3872 helix: 0.91 (0.21), residues: 605 sheet: 0.81 (0.15), residues: 1188 loop : -1.02 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 375 HIS 0.002 0.001 HIS H 199 PHE 0.013 0.002 PHE F 707 TYR 0.018 0.001 TYR A 439 ARG 0.004 0.001 ARG D 529 *********************** 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 180 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 3.617 Fit side-chains outliers start: 40 outliers final: 35 residues processed: 172 average time/residue: 1.2940 time to fit residues: 273.0390 Evaluate side-chains 173 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 3.767 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.4523 time to fit residues: 8.6620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 0.9990 chunk 362 optimal weight: 3.9990 chunk 221 optimal weight: 0.0970 chunk 172 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 463 ASN G 634 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1540 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: