Starting phenix.real_space_refine on Wed Feb 21 12:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/02_2024/7yvs_34137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/02_2024/7yvs_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_34137/02_2024/7yvs_34137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/02_2024/7yvs_34137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/02_2024/7yvs_34137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvs_34137/02_2024/7yvs_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 22.87, per 1000 atoms: 0.75 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: 11.35 Conformation dependent library (CDL) restraints added in 8.2 seconds 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7300 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 82 sheets defined 20.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 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: 13.11 Time building geometry restraints manager: 12.17 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: 2.920 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: 0.020 Extract box with map and model: 18.410 Check model and map are aligned: 0.480 Set scattering table: 0.320 Process input model: 90.790 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.320 ------------------------------------------------------------------------------- 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 : 3.522 Fit side-chains REVERT: A 319 GLN cc_start: 0.8074 (pt0) cc_final: 0.7596 (pt0) REVERT: D 657 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7503 (mmmt) REVERT: F 639 ASN cc_start: 0.6583 (p0) cc_final: 0.6345 (p0) REVERT: H 22 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5117 (ttpp) REVERT: H 25 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: H 28 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7662 (tm-30) outliers start: 22 outliers final: 9 residues processed: 211 average time/residue: 1.4071 time to fit residues: 351.9452 Evaluate side-chains 142 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 283 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 28 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 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: 0.8542 moved from start: 0.0836 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= 0.254 Angle : 0.556 11.137 42157 Z= 0.301 Chirality : 0.046 0.177 4747 Planarity : 0.004 0.061 5480 Dihedral : 5.238 57.830 4212 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.33 % Allowed : 6.02 % Favored : 92.65 % 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: -0.27 (0.14), residues: 3872 helix: 0.68 (0.22), residues: 605 sheet: 0.68 (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 0.003 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 175 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 4.427 Fit side-chains REVERT: A 319 GLN cc_start: 0.7743 (pt0) cc_final: 0.7447 (pt0) REVERT: A 627 ASN cc_start: 0.7658 (t0) cc_final: 0.7403 (t0) REVERT: C 657 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7475 (mmmt) REVERT: D 376 ASN cc_start: 0.7767 (m-40) cc_final: 0.7467 (m-40) REVERT: D 561 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.5884 (p0) REVERT: D 657 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7534 (mmmt) REVERT: F 660 MET cc_start: 0.7078 (tpp) cc_final: 0.6724 (tpp) REVERT: G 324 SER cc_start: 0.6353 (t) cc_final: 0.6117 (m) REVERT: H 22 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5148 (ttpp) REVERT: H 25 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: H 28 GLU cc_start: 0.8095 (pp20) cc_final: 0.7701 (tm-30) outliers start: 33 outliers final: 18 residues processed: 167 average time/residue: 1.3081 time to fit residues: 264.6626 Evaluate side-chains 150 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 347 optimal weight: 2.9990 chunk 375 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 344 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 278 optimal weight: 0.0770 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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 368 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN D 567 ASN ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 GLN F 463 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1108 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= 0.383 Angle : 0.614 13.496 42157 Z= 0.330 Chirality : 0.049 0.167 4747 Planarity : 0.005 0.058 5480 Dihedral : 5.241 57.778 4205 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.65 % Allowed : 8.22 % Favored : 90.13 % 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: -0.44 (0.13), residues: 3872 helix: 0.59 (0.21), residues: 605 sheet: 0.56 (0.15), residues: 1201 loop : -1.10 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 214 HIS 0.003 0.001 HIS H 199 PHE 0.016 0.002 PHE F 707 TYR 0.020 0.002 TYR B 439 ARG 0.007 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 186 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 3.885 Fit side-chains REVERT: A 319 GLN cc_start: 0.7906 (pt0) cc_final: 0.7636 (pt0) REVERT: A 627 ASN cc_start: 0.7762 (t0) cc_final: 0.7432 (t0) REVERT: B 660 MET cc_start: 0.7603 (tpp) cc_final: 0.7257 (tpp) REVERT: C 701 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: D 313 GLU cc_start: 0.7644 (tt0) cc_final: 0.7370 (tm-30) REVERT: D 321 LYS cc_start: 0.6382 (mtmt) cc_final: 0.5646 (mtpp) REVERT: D 376 ASN cc_start: 0.7756 (m-40) cc_final: 0.7508 (m-40) REVERT: D 561 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.5983 (p0) REVERT: D 657 LYS cc_start: 0.7717 (mtpp) cc_final: 0.7428 (mmmt) REVERT: D 660 MET cc_start: 0.7705 (tpt) cc_final: 0.7335 (tpt) REVERT: F 660 MET cc_start: 0.7148 (tpp) cc_final: 0.6708 (tpp) REVERT: G 324 SER cc_start: 0.6266 (t) cc_final: 0.5989 (m) REVERT: G 660 MET cc_start: 0.6115 (tmm) cc_final: 0.5878 (tpt) REVERT: H 22 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5264 (ttpp) REVERT: H 25 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: H 28 GLU cc_start: 0.8242 (pp20) cc_final: 0.7804 (tm-30) outliers start: 44 outliers final: 27 residues processed: 172 average time/residue: 1.2947 time to fit residues: 269.7219 Evaluate side-chains 161 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 568 ASP Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 233 ASN Chi-restraints excluded: chain H residue 395 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 348 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 368 GLN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31108 Z= 0.193 Angle : 0.503 9.967 42157 Z= 0.272 Chirality : 0.045 0.163 4747 Planarity : 0.004 0.057 5480 Dihedral : 4.805 57.356 4205 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.65 % Allowed : 9.87 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3872 helix: 0.88 (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 0.012 0.001 TRP G 375 HIS 0.002 0.001 HIS H 199 PHE 0.012 0.001 PHE D 707 TYR 0.015 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 185 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 4.007 Fit side-chains revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7800 (pt0) cc_final: 0.7526 (pt0) REVERT: A 627 ASN cc_start: 0.7614 (t0) cc_final: 0.7259 (t0) REVERT: B 368 GLN cc_start: 0.4796 (OUTLIER) cc_final: 0.4568 (tp-100) REVERT: B 660 MET cc_start: 0.7877 (tpp) cc_final: 0.7524 (tpp) REVERT: C 376 ASN cc_start: 0.7602 (m-40) cc_final: 0.7264 (m110) REVERT: D 313 GLU cc_start: 0.7512 (tt0) cc_final: 0.7306 (tm-30) REVERT: D 321 LYS cc_start: 0.6314 (mtmt) cc_final: 0.5621 (mtpp) REVERT: D 657 LYS cc_start: 0.7657 (mtpp) cc_final: 0.7451 (mmmt) REVERT: D 660 MET cc_start: 0.7748 (tpt) cc_final: 0.7031 (tpp) REVERT: F 660 MET cc_start: 0.7124 (tpp) cc_final: 0.6690 (tpp) REVERT: G 324 SER cc_start: 0.6241 (t) cc_final: 0.5997 (m) REVERT: H 25 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: H 28 GLU cc_start: 0.8168 (pp20) cc_final: 0.7770 (tm-30) outliers start: 43 outliers final: 22 residues processed: 173 average time/residue: 1.3450 time to fit residues: 282.0143 Evaluate side-chains 157 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 331 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 B 463 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 31108 Z= 0.426 Angle : 0.623 13.424 42157 Z= 0.334 Chirality : 0.049 0.167 4747 Planarity : 0.005 0.055 5480 Dihedral : 5.215 57.711 4201 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.82 % Allowed : 11.17 % Favored : 87.01 % 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: -0.44 (0.13), residues: 3872 helix: 0.67 (0.21), residues: 599 sheet: 0.60 (0.15), residues: 1186 loop : -1.14 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 214 HIS 0.003 0.001 HIS H 199 PHE 0.017 0.002 PHE F 707 TYR 0.022 0.002 TYR B 439 ARG 0.006 0.001 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 186 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 3.649 Fit side-chains REVERT: A 319 GLN cc_start: 0.7949 (pt0) cc_final: 0.7669 (pt0) REVERT: A 370 SER cc_start: 0.7210 (m) cc_final: 0.6839 (p) REVERT: A 627 ASN cc_start: 0.7836 (t0) cc_final: 0.7455 (t0) REVERT: B 368 GLN cc_start: 0.5173 (OUTLIER) cc_final: 0.4896 (tp-100) REVERT: B 660 MET cc_start: 0.7741 (tpp) cc_final: 0.7243 (tpp) REVERT: C 701 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: D 561 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6090 (p0) REVERT: D 657 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7310 (mmmt) REVERT: D 660 MET cc_start: 0.7750 (tpt) cc_final: 0.7014 (tpp) REVERT: E 426 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8189 (tp30) REVERT: F 660 MET cc_start: 0.7196 (tpp) cc_final: 0.6725 (tpp) REVERT: F 664 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7838 (mttp) REVERT: G 324 SER cc_start: 0.6282 (t) cc_final: 0.5981 (m) REVERT: H 25 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: H 28 GLU cc_start: 0.8254 (pp20) cc_final: 0.7870 (tm-30) outliers start: 49 outliers final: 33 residues processed: 173 average time/residue: 1.3036 time to fit residues: 273.1627 Evaluate side-chains 171 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 385 GLU Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 568 ASP Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 233 ASN Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 395 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 0.9990 chunk 332 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 369 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- 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 H 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1374 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= 0.151 Angle : 0.483 11.863 42157 Z= 0.261 Chirality : 0.044 0.160 4747 Planarity : 0.004 0.054 5480 Dihedral : 4.673 56.922 4201 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.62 % Allowed : 11.81 % Favored : 86.57 % 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: -0.14 (0.14), residues: 3872 helix: 1.03 (0.22), residues: 605 sheet: 0.81 (0.16), residues: 1172 loop : -0.99 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 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 193 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 3.663 Fit side-chains REVERT: A 319 GLN cc_start: 0.7785 (pt0) cc_final: 0.7447 (pt0) REVERT: A 627 ASN cc_start: 0.7643 (t0) cc_final: 0.7303 (t0) REVERT: A 698 LEU cc_start: 0.8090 (pp) cc_final: 0.7318 (mp) REVERT: B 368 GLN cc_start: 0.4878 (OUTLIER) cc_final: 0.4639 (tp-100) REVERT: B 660 MET cc_start: 0.7849 (tpp) cc_final: 0.7296 (tpp) REVERT: C 376 ASN cc_start: 0.7626 (m-40) cc_final: 0.7258 (m110) REVERT: D 657 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7368 (mmmt) REVERT: D 660 MET cc_start: 0.7645 (tpt) cc_final: 0.6986 (tpp) REVERT: D 687 LYS cc_start: 0.7887 (mppt) cc_final: 0.7670 (mppt) REVERT: F 660 MET cc_start: 0.7095 (tpp) cc_final: 0.6702 (tpp) REVERT: F 664 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7798 (mttp) REVERT: G 324 SER cc_start: 0.6288 (t) cc_final: 0.6055 (m) REVERT: G 740 GLU cc_start: 0.7864 (tt0) cc_final: 0.7615 (tp30) REVERT: H 25 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: H 28 GLU cc_start: 0.8322 (pp20) cc_final: 0.7967 (tm-30) REVERT: H 54 GLN cc_start: 0.8192 (mt0) cc_final: 0.7815 (mt0) outliers start: 41 outliers final: 24 residues processed: 186 average time/residue: 1.2662 time to fit residues: 286.1964 Evaluate side-chains 172 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 568 ASP Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 209 optimal weight: 0.2980 chunk 311 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 368 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 B 463 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN F 463 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN G 634 ASN H 63 GLN H 127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31108 Z= 0.186 Angle : 0.495 9.401 42157 Z= 0.267 Chirality : 0.044 0.157 4747 Planarity : 0.004 0.052 5480 Dihedral : 4.632 56.537 4199 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.71 % Allowed : 12.30 % Favored : 86.00 % 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: -0.11 (0.14), residues: 3872 helix: 1.05 (0.22), residues: 605 sheet: 0.82 (0.16), residues: 1189 loop : -0.98 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 375 HIS 0.002 0.000 HIS H 199 PHE 0.011 0.001 PHE D 707 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 194 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 3.616 Fit side-chains REVERT: A 319 GLN cc_start: 0.7797 (pt0) cc_final: 0.7448 (pt0) REVERT: A 627 ASN cc_start: 0.7684 (t0) cc_final: 0.7322 (t0) REVERT: A 660 MET cc_start: 0.6322 (tpt) cc_final: 0.6092 (tpt) REVERT: B 368 GLN cc_start: 0.4883 (OUTLIER) cc_final: 0.4670 (tp-100) REVERT: B 660 MET cc_start: 0.7779 (tpp) cc_final: 0.7221 (tpp) REVERT: C 376 ASN cc_start: 0.7635 (m-40) cc_final: 0.7252 (m110) REVERT: D 561 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6014 (p0) REVERT: D 660 MET cc_start: 0.7639 (tpt) cc_final: 0.6986 (tpp) REVERT: F 660 MET cc_start: 0.7176 (tpp) cc_final: 0.6765 (tpp) REVERT: F 664 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7791 (mttp) REVERT: G 324 SER cc_start: 0.6246 (t) cc_final: 0.6007 (m) REVERT: G 740 GLU cc_start: 0.7912 (tt0) cc_final: 0.7619 (tp30) REVERT: H 28 GLU cc_start: 0.8333 (pp20) cc_final: 0.8048 (tm-30) outliers start: 44 outliers final: 28 residues processed: 182 average time/residue: 1.3913 time to fit residues: 306.7600 Evaluate side-chains 174 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 395 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 234 optimal weight: 0.8980 chunk 250 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** D 376 ASN E 523 ASN F 463 ASN H 54 GLN H 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1510 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= 0.137 Angle : 0.467 8.405 42157 Z= 0.252 Chirality : 0.044 0.156 4747 Planarity : 0.004 0.051 5480 Dihedral : 4.346 39.280 4196 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.68 % Allowed : 12.76 % Favored : 85.56 % 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: 0.01 (0.14), residues: 3872 helix: 1.18 (0.22), residues: 605 sheet: 0.90 (0.16), residues: 1189 loop : -0.91 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 375 HIS 0.001 0.000 AHIS A 314 PHE 0.011 0.001 PHE C 711 TYR 0.012 0.001 TYR A 439 ARG 0.002 0.000 ARG E 668 *********************** 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 195 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 3.730 Fit side-chains REVERT: A 318 ASP cc_start: 0.6386 (m-30) cc_final: 0.5853 (p0) REVERT: A 319 GLN cc_start: 0.7769 (pt0) cc_final: 0.7406 (pt0) REVERT: A 370 SER cc_start: 0.6969 (m) cc_final: 0.6741 (p) REVERT: A 627 ASN cc_start: 0.7675 (t0) cc_final: 0.7316 (t0) REVERT: B 368 GLN cc_start: 0.4876 (OUTLIER) cc_final: 0.4650 (tp-100) REVERT: B 660 MET cc_start: 0.7846 (tpp) cc_final: 0.7241 (tpp) REVERT: C 376 ASN cc_start: 0.7616 (m-40) cc_final: 0.7248 (m110) REVERT: D 660 MET cc_start: 0.7653 (tpt) cc_final: 0.7040 (tpp) REVERT: F 660 MET cc_start: 0.7173 (tpp) cc_final: 0.6826 (tpp) REVERT: F 664 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7766 (mttp) REVERT: G 324 SER cc_start: 0.6243 (t) cc_final: 0.6028 (m) REVERT: G 740 GLU cc_start: 0.7839 (tt0) cc_final: 0.7564 (tp30) REVERT: H 21 ARG cc_start: 0.5570 (pmm-80) cc_final: 0.4545 (mtt90) outliers start: 43 outliers final: 29 residues processed: 187 average time/residue: 1.2189 time to fit residues: 281.5102 Evaluate side-chains 171 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 268 ASN Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 395 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 9.9990 chunk 352 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 343 optimal weight: 0.0870 chunk 206 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 269 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 341 optimal weight: 0.6980 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31108 Z= 0.184 Angle : 0.494 10.067 42157 Z= 0.265 Chirality : 0.044 0.156 4747 Planarity : 0.004 0.050 5480 Dihedral : 4.423 39.475 4196 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.50 % Allowed : 13.28 % Favored : 85.21 % 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: 0.01 (0.14), residues: 3872 helix: 1.12 (0.22), residues: 605 sheet: 0.95 (0.16), residues: 1189 loop : -0.93 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 375 HIS 0.001 0.000 HIS H 199 PHE 0.011 0.001 PHE C 711 TYR 0.014 0.001 TYR A 439 ARG 0.002 0.000 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 183 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 3.929 Fit side-chains REVERT: A 318 ASP cc_start: 0.6404 (m-30) cc_final: 0.5878 (p0) REVERT: A 319 GLN cc_start: 0.7790 (pt0) cc_final: 0.7492 (pt0) REVERT: A 370 SER cc_start: 0.6989 (m) cc_final: 0.6764 (p) REVERT: A 627 ASN cc_start: 0.7747 (t0) cc_final: 0.7355 (t0) REVERT: B 368 GLN cc_start: 0.4925 (OUTLIER) cc_final: 0.4716 (tp-100) REVERT: B 660 MET cc_start: 0.7801 (tpp) cc_final: 0.7188 (tpp) REVERT: C 376 ASN cc_start: 0.7636 (m-40) cc_final: 0.7258 (m110) REVERT: C 660 MET cc_start: 0.6599 (tpp) cc_final: 0.6397 (tpp) REVERT: D 561 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6052 (p0) REVERT: D 660 MET cc_start: 0.7614 (tpt) cc_final: 0.7003 (tpp) REVERT: F 660 MET cc_start: 0.7190 (tpp) cc_final: 0.6801 (tpp) REVERT: F 664 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7759 (mttp) REVERT: G 324 SER cc_start: 0.6296 (t) cc_final: 0.6074 (m) REVERT: G 740 GLU cc_start: 0.7842 (tt0) cc_final: 0.7567 (tp30) REVERT: H 21 ARG cc_start: 0.5674 (pmm-80) cc_final: 0.4501 (mtt90) REVERT: H 26 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6374 (tpm170) outliers start: 37 outliers final: 30 residues processed: 179 average time/residue: 1.1892 time to fit residues: 261.6190 Evaluate side-chains 174 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 268 ASN Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 395 ASP 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: 7.9990 chunk 221 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 252 optimal weight: 0.0030 chunk 380 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 234 optimal weight: 4.9990 chunk 185 optimal weight: 0.4980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31108 Z= 0.128 Angle : 0.465 9.313 42157 Z= 0.250 Chirality : 0.043 0.155 4747 Planarity : 0.003 0.050 5480 Dihedral : 4.260 39.325 4196 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.30 % Allowed : 13.54 % Favored : 85.16 % 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: 0.08 (0.14), residues: 3872 helix: 1.17 (0.22), residues: 611 sheet: 1.05 (0.16), residues: 1177 loop : -0.91 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 375 HIS 0.001 0.000 HIS H 199 PHE 0.010 0.001 PHE C 711 TYR 0.011 0.001 TYR H 62 ARG 0.002 0.000 ARG H 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 3.878 Fit side-chains REVERT: A 318 ASP cc_start: 0.6394 (m-30) cc_final: 0.5886 (p0) REVERT: A 319 GLN cc_start: 0.7754 (pt0) cc_final: 0.7360 (pt0) REVERT: A 627 ASN cc_start: 0.7693 (t0) cc_final: 0.7328 (t0) REVERT: B 368 GLN cc_start: 0.4911 (OUTLIER) cc_final: 0.4694 (tp-100) REVERT: B 660 MET cc_start: 0.7836 (tpp) cc_final: 0.7166 (tpp) REVERT: C 376 ASN cc_start: 0.7617 (m-40) cc_final: 0.7267 (m110) REVERT: C 660 MET cc_start: 0.6456 (tpp) cc_final: 0.6234 (tpp) REVERT: D 660 MET cc_start: 0.7603 (tpt) cc_final: 0.7017 (tpp) REVERT: F 660 MET cc_start: 0.7192 (tpp) cc_final: 0.6872 (tpp) REVERT: F 664 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7765 (mttp) REVERT: G 324 SER cc_start: 0.6280 (t) cc_final: 0.6073 (m) REVERT: G 740 GLU cc_start: 0.7795 (tt0) cc_final: 0.7547 (tp30) REVERT: H 21 ARG cc_start: 0.5625 (pmm-80) cc_final: 0.4558 (mtt90) outliers start: 30 outliers final: 23 residues processed: 182 average time/residue: 1.3120 time to fit residues: 293.3314 Evaluate side-chains 170 residues out of total 3392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 664 LYS Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 268 ASN Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 395 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 279 optimal weight: 0.4980 chunk 44 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 303 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 463 ASN E 523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.131862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086879 restraints weight = 144421.524| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.51 r_work: 0.2943 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31108 Z= 0.188 Angle : 0.491 9.038 42157 Z= 0.264 Chirality : 0.044 0.155 4747 Planarity : 0.004 0.049 5480 Dihedral : 4.383 39.731 4196 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.27 % Allowed : 13.69 % Favored : 85.04 % 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: 0.06 (0.14), residues: 3872 helix: 1.15 (0.22), residues: 605 sheet: 1.00 (0.16), residues: 1189 loop : -0.90 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 375 HIS 0.002 0.000 AHIS A 314 PHE 0.011 0.001 PHE C 711 TYR 0.014 0.001 TYR A 439 ARG 0.002 0.000 ARG D 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7682.50 seconds wall clock time: 141 minutes 29.51 seconds (8489.51 seconds total)