Starting phenix.real_space_refine on Tue Dec 31 01:46:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvi_27008/12_2024/8cvi_27008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvi_27008/12_2024/8cvi_27008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cvi_27008/12_2024/8cvi_27008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvi_27008/12_2024/8cvi_27008.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvi_27008/12_2024/8cvi_27008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvi_27008/12_2024/8cvi_27008.cif" } resolution = 3.4 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= 0.003 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 39585 2.51 5 N 12069 2.21 5 O 14310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66030 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1985 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1985 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1985 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "N" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "X" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "O" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "Y" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "P" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "Z" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "Q" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "a" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "H" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "R" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "b" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "I" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "S" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "c" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "J" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "T" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "d" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "K" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "U" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "e" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "L" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "V" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "f" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "M" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "W" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "g" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" N AILE I 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE I 38 " occ=0.50 residue: pdb=" N AILE S 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE S 38 " occ=0.50 residue: pdb=" N AILE c 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE c 38 " occ=0.50 residue: pdb=" N AILE J 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE J 38 " occ=0.50 residue: pdb=" N AILE T 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE T 38 " occ=0.50 residue: pdb=" N AILE d 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE d 38 " occ=0.50 residue: pdb=" N AILE K 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE K 38 " occ=0.50 residue: pdb=" N AILE U 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE U 38 " occ=0.50 residue: pdb=" N AILE e 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE e 38 " occ=0.50 residue: pdb=" N AILE L 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE L 38 " occ=0.50 residue: pdb=" N AILE V 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE V 38 " occ=0.50 residue: pdb=" N AILE f 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE f 38 " occ=0.50 ... (remaining 3 not shown) Time building chain proxies: 38.77, per 1000 atoms: 0.59 Number of scatterers: 66030 At special positions: 0 Unit cell: (145.8, 140.4, 319.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 14310 8.00 N 12069 7.00 C 39585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.43 Conformation dependent library (CDL) restraints added in 9.3 seconds 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16686 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 53 sheets defined 73.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.571A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 100 removed outlier: 3.655A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 129 removed outlier: 3.667A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 459 through 508 removed outlier: 3.748A pdb=" N ALA A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'B' and resid 8 through 35 removed outlier: 3.703A pdb=" N LEU B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 100 removed outlier: 3.687A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 129 removed outlier: 4.258A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 459 through 508 removed outlier: 3.889A pdb=" N VAL B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.961A pdb=" N SER B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.836A pdb=" N LEU B 543 " --> pdb=" O PRO B 539 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 35 removed outlier: 3.610A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 100 removed outlier: 3.642A pdb=" N ASN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 130 removed outlier: 4.244A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 459 through 508 removed outlier: 3.626A pdb=" N ALA C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 482 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 536 removed outlier: 3.718A pdb=" N GLU C 514 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.768A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 546 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 3.860A pdb=" N ALA D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 100 Processing helix chain 'D' and resid 105 through 129 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 459 through 507 removed outlier: 3.942A pdb=" N VAL D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 536 Processing helix chain 'D' and resid 539 through 547 removed outlier: 3.832A pdb=" N LEU D 543 " --> pdb=" O PRO D 539 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 546 " --> pdb=" O VAL D 542 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 35 removed outlier: 3.853A pdb=" N SER N 23 " --> pdb=" O ASN N 19 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA N 24 " --> pdb=" O LYS N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 101 removed outlier: 4.131A pdb=" N THR N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 130 removed outlier: 3.618A pdb=" N THR N 130 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 507 removed outlier: 4.365A pdb=" N VAL N 481 " --> pdb=" O SER N 477 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN N 482 " --> pdb=" O LEU N 478 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN N 483 " --> pdb=" O GLY N 479 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 536 removed outlier: 3.832A pdb=" N SER N 516 " --> pdb=" O ALA N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 537 through 540 Processing helix chain 'N' and resid 541 through 547 removed outlier: 4.093A pdb=" N LEU N 545 " --> pdb=" O GLN N 541 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU N 546 " --> pdb=" O VAL N 542 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 35 removed outlier: 3.709A pdb=" N SER X 23 " --> pdb=" O ASN X 19 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 100 removed outlier: 3.905A pdb=" N ASP X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA X 46 " --> pdb=" O LYS X 42 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY X 47 " --> pdb=" O ASP X 43 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 130 removed outlier: 4.036A pdb=" N THR X 130 " --> pdb=" O VAL X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 169 Processing helix chain 'X' and resid 459 through 507 removed outlier: 3.800A pdb=" N VAL X 481 " --> pdb=" O SER X 477 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN X 482 " --> pdb=" O LEU X 478 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN X 483 " --> pdb=" O GLY X 479 " (cutoff:3.500A) Processing helix chain 'X' and resid 510 through 536 removed outlier: 3.509A pdb=" N GLU X 514 " --> pdb=" O ASP X 510 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER X 516 " --> pdb=" O ALA X 512 " (cutoff:3.500A) Processing helix chain 'X' and resid 537 through 540 Processing helix chain 'X' and resid 541 through 547 removed outlier: 3.600A pdb=" N LEU X 545 " --> pdb=" O GLN X 541 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU X 546 " --> pdb=" O VAL X 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 34 removed outlier: 3.650A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 100 removed outlier: 3.971A pdb=" N ASP E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ALA E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 Processing helix chain 'E' and resid 459 through 507 removed outlier: 4.241A pdb=" N VAL E 481 " --> pdb=" O SER E 477 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 484 " --> pdb=" O ALA E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 536 Processing helix chain 'E' and resid 537 through 540 Processing helix chain 'E' and resid 541 through 547 removed outlier: 4.123A pdb=" N LEU E 545 " --> pdb=" O GLN E 541 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU E 546 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 541 through 547' Processing helix chain 'O' and resid 8 through 34 removed outlier: 3.842A pdb=" N ASN O 21 " --> pdb=" O ASN O 17 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER O 23 " --> pdb=" O ASN O 19 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 100 removed outlier: 3.591A pdb=" N ALA O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 129 Processing helix chain 'O' and resid 459 through 507 removed outlier: 4.199A pdb=" N VAL O 481 " --> pdb=" O SER O 477 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN O 482 " --> pdb=" O LEU O 478 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG O 505 " --> pdb=" O GLU O 501 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE O 506 " --> pdb=" O ALA O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 510 through 536 Processing helix chain 'O' and resid 537 through 542 removed outlier: 3.766A pdb=" N GLN O 541 " --> pdb=" O GLN O 537 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL O 542 " --> pdb=" O VAL O 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 537 through 542' Processing helix chain 'O' and resid 542 through 547 removed outlier: 4.202A pdb=" N LEU O 546 " --> pdb=" O VAL O 542 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN O 547 " --> pdb=" O LEU O 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 542 through 547' Processing helix chain 'Y' and resid 8 through 34 removed outlier: 4.430A pdb=" N SER Y 23 " --> pdb=" O ASN Y 19 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 101 removed outlier: 3.529A pdb=" N ALA Y 49 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER Y 73 " --> pdb=" O ASN Y 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA Y 75 " --> pdb=" O GLY Y 71 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU Y 84 " --> pdb=" O GLY Y 80 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR Y 101 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 129 Processing helix chain 'Y' and resid 459 through 507 removed outlier: 3.620A pdb=" N VAL Y 481 " --> pdb=" O SER Y 477 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN Y 482 " --> pdb=" O LEU Y 478 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE Y 506 " --> pdb=" O ALA Y 502 " (cutoff:3.500A) Processing helix chain 'Y' and resid 510 through 537 removed outlier: 3.771A pdb=" N GLN Y 537 " --> pdb=" O ALA Y 533 " (cutoff:3.500A) Processing helix chain 'Y' and resid 538 through 541 Processing helix chain 'Y' and resid 542 through 547 removed outlier: 3.646A pdb=" N LEU Y 546 " --> pdb=" O VAL Y 542 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN Y 547 " --> pdb=" O LEU Y 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 542 through 547' Processing helix chain 'F' and resid 8 through 35 removed outlier: 3.993A pdb=" N LEU F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 100 removed outlier: 3.612A pdb=" N ARG F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 459 through 507 removed outlier: 3.656A pdb=" N VAL F 481 " --> pdb=" O SER F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 536 Processing helix chain 'F' and resid 537 through 539 No H-bonds generated for 'chain 'F' and resid 537 through 539' Processing helix chain 'F' and resid 540 through 547 removed outlier: 3.726A pdb=" N SER F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 35 removed outlier: 3.846A pdb=" N SER P 23 " --> pdb=" O ASN P 19 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA P 24 " --> pdb=" O LYS P 20 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER P 33 " --> pdb=" O ILE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 100 removed outlier: 3.661A pdb=" N VAL P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA P 75 " --> pdb=" O GLY P 71 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 129 Processing helix chain 'P' and resid 459 through 507 removed outlier: 3.771A pdb=" N VAL P 481 " --> pdb=" O SER P 477 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN P 482 " --> pdb=" O LEU P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 510 through 537 removed outlier: 3.941A pdb=" N GLN P 537 " --> pdb=" O ALA P 533 " (cutoff:3.500A) Processing helix chain 'P' and resid 540 through 547 removed outlier: 3.872A pdb=" N SER P 544 " --> pdb=" O GLN P 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 35 removed outlier: 3.566A pdb=" N ILE Z 13 " --> pdb=" O SER Z 9 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER Z 23 " --> pdb=" O ASN Z 19 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER Z 33 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 100 removed outlier: 3.607A pdb=" N ARG Z 66 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU Z 84 " --> pdb=" O GLY Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 129 Processing helix chain 'Z' and resid 459 through 507 removed outlier: 3.887A pdb=" N VAL Z 481 " --> pdb=" O SER Z 477 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN Z 482 " --> pdb=" O LEU Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 510 through 537 removed outlier: 3.689A pdb=" N SER Z 516 " --> pdb=" O ALA Z 512 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN Z 537 " --> pdb=" O ALA Z 533 " (cutoff:3.500A) Processing helix chain 'Z' and resid 540 through 547 removed outlier: 3.776A pdb=" N SER Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 35 removed outlier: 4.033A pdb=" N SER G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 100 removed outlier: 3.857A pdb=" N ALA G 81 " --> pdb=" O THR G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 130 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 459 through 507 removed outlier: 3.570A pdb=" N ALA G 463 " --> pdb=" O ASP G 459 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G 481 " --> pdb=" O SER G 477 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN G 482 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 483 " --> pdb=" O GLY G 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 506 " --> pdb=" O ALA G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 537 removed outlier: 3.739A pdb=" N GLN G 537 " --> pdb=" O ALA G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 547 removed outlier: 3.990A pdb=" N SER G 544 " --> pdb=" O GLN G 540 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 35 removed outlier: 4.026A pdb=" N SER Q 23 " --> pdb=" O ASN Q 19 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA Q 24 " --> pdb=" O LYS Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 100 removed outlier: 3.782A pdb=" N ALA Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Q 81 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 130 removed outlier: 3.638A pdb=" N THR Q 130 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 169 Processing helix chain 'Q' and resid 459 through 507 removed outlier: 3.578A pdb=" N SER Q 477 " --> pdb=" O LYS Q 473 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU Q 478 " --> pdb=" O PHE Q 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 510 through 537 removed outlier: 3.954A pdb=" N SER Q 516 " --> pdb=" O ALA Q 512 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN Q 537 " --> pdb=" O ALA Q 533 " (cutoff:3.500A) Processing helix chain 'Q' and resid 540 through 547 removed outlier: 3.979A pdb=" N SER Q 544 " --> pdb=" O GLN Q 540 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 35 removed outlier: 3.556A pdb=" N ASN a 21 " --> pdb=" O ASN a 17 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER a 23 " --> pdb=" O ASN a 19 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA a 24 " --> pdb=" O LYS a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 101 removed outlier: 3.547A pdb=" N ALA a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN a 63 " --> pdb=" O LYS a 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR a 101 " --> pdb=" O VAL a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 130 removed outlier: 3.509A pdb=" N THR a 130 " --> pdb=" O VAL a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 169 Processing helix chain 'a' and resid 459 through 507 removed outlier: 3.503A pdb=" N ALA a 463 " --> pdb=" O ASP a 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL a 481 " --> pdb=" O SER a 477 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE a 506 " --> pdb=" O ALA a 502 " (cutoff:3.500A) Processing helix chain 'a' and resid 510 through 537 removed outlier: 3.621A pdb=" N GLN a 537 " --> pdb=" O ALA a 533 " (cutoff:3.500A) Processing helix chain 'a' and resid 540 through 547 removed outlier: 4.028A pdb=" N SER a 544 " --> pdb=" O GLN a 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 35 removed outlier: 3.888A pdb=" N SER H 23 " --> pdb=" O ASN H 19 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 100 removed outlier: 3.873A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 130 Processing helix chain 'H' and resid 459 through 507 removed outlier: 3.989A pdb=" N VAL H 481 " --> pdb=" O SER H 477 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN H 482 " --> pdb=" O LEU H 478 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER H 487 " --> pdb=" O ASN H 483 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG H 505 " --> pdb=" O GLU H 501 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE H 506 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 537 removed outlier: 3.665A pdb=" N SER H 516 " --> pdb=" O ALA H 512 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN H 537 " --> pdb=" O ALA H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 547 removed outlier: 3.609A pdb=" N SER H 544 " --> pdb=" O GLN H 540 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN H 547 " --> pdb=" O LEU H 543 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 35 removed outlier: 3.512A pdb=" N ASN R 21 " --> pdb=" O ASN R 17 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER R 23 " --> pdb=" O ASN R 19 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA R 24 " --> pdb=" O LYS R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 100 removed outlier: 3.573A pdb=" N ARG R 53 " --> pdb=" O ALA R 49 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU R 84 " --> pdb=" O GLY R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 130 removed outlier: 3.662A pdb=" N THR R 130 " --> pdb=" O VAL R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 459 through 507 removed outlier: 4.063A pdb=" N VAL R 481 " --> pdb=" O SER R 477 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN R 482 " --> pdb=" O LEU R 478 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG R 505 " --> pdb=" O GLU R 501 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE R 506 " --> pdb=" O ALA R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 510 through 537 removed outlier: 3.822A pdb=" N SER R 516 " --> pdb=" O ALA R 512 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN R 537 " --> pdb=" O ALA R 533 " (cutoff:3.500A) Processing helix chain 'R' and resid 540 through 547 removed outlier: 3.565A pdb=" N SER R 544 " --> pdb=" O GLN R 540 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN R 547 " --> pdb=" O LEU R 543 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 35 removed outlier: 3.686A pdb=" N SER b 23 " --> pdb=" O ASN b 19 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA b 24 " --> pdb=" O LYS b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 101 removed outlier: 3.697A pdb=" N GLU b 84 " --> pdb=" O GLY b 80 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR b 101 " --> pdb=" O VAL b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 130 removed outlier: 3.622A pdb=" N THR b 130 " --> pdb=" O VAL b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 507 removed outlier: 3.539A pdb=" N ALA b 463 " --> pdb=" O ASP b 459 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL b 481 " --> pdb=" O SER b 477 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN b 482 " --> pdb=" O LEU b 478 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER b 487 " --> pdb=" O ASN b 483 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG b 505 " --> pdb=" O GLU b 501 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE b 506 " --> pdb=" O ALA b 502 " (cutoff:3.500A) Processing helix chain 'b' and resid 510 through 536 removed outlier: 3.597A pdb=" N SER b 516 " --> pdb=" O ALA b 512 " (cutoff:3.500A) Processing helix chain 'b' and resid 537 through 539 No H-bonds generated for 'chain 'b' and resid 537 through 539' Processing helix chain 'b' and resid 540 through 547 removed outlier: 3.947A pdb=" N SER b 544 " --> pdb=" O GLN b 540 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN b 547 " --> pdb=" O LEU b 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 34 removed outlier: 3.821A pdb=" N SER I 23 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA I 24 " --> pdb=" O LYS I 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 100 removed outlier: 4.379A pdb=" N GLU I 84 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 94 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 129 Processing helix chain 'I' and resid 459 through 508 removed outlier: 3.622A pdb=" N PHE I 474 " --> pdb=" O GLN I 470 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG I 505 " --> pdb=" O GLU I 501 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE I 506 " --> pdb=" O ALA I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 537 removed outlier: 3.726A pdb=" N SER I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN I 537 " --> pdb=" O ALA I 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 547 removed outlier: 3.550A pdb=" N GLN I 547 " --> pdb=" O LEU I 543 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 34 removed outlier: 3.510A pdb=" N ASN S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER S 23 " --> pdb=" O ASN S 19 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 100 removed outlier: 3.515A pdb=" N GLN S 48 " --> pdb=" O ASP S 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY S 71 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU S 84 " --> pdb=" O GLY S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 129 Processing helix chain 'S' and resid 459 through 508 removed outlier: 3.846A pdb=" N ALA S 463 " --> pdb=" O ASP S 459 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG S 505 " --> pdb=" O GLU S 501 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE S 506 " --> pdb=" O ALA S 502 " (cutoff:3.500A) Processing helix chain 'S' and resid 510 through 537 removed outlier: 3.707A pdb=" N VAL S 515 " --> pdb=" O TYR S 511 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER S 516 " --> pdb=" O ALA S 512 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN S 537 " --> pdb=" O ALA S 533 " (cutoff:3.500A) Processing helix chain 'S' and resid 540 through 547 removed outlier: 3.628A pdb=" N GLN S 547 " --> pdb=" O LEU S 543 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 34 removed outlier: 3.896A pdb=" N ASN c 16 " --> pdb=" O LEU c 12 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER c 23 " --> pdb=" O ASN c 19 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA c 24 " --> pdb=" O LYS c 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 100 removed outlier: 3.675A pdb=" N SER c 73 " --> pdb=" O ASN c 69 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE c 85 " --> pdb=" O ALA c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 129 Processing helix chain 'c' and resid 459 through 508 removed outlier: 3.631A pdb=" N ALA c 463 " --> pdb=" O ASP c 459 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG c 505 " --> pdb=" O GLU c 501 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE c 506 " --> pdb=" O ALA c 502 " (cutoff:3.500A) Processing helix chain 'c' and resid 510 through 535 Processing helix chain 'c' and resid 540 through 547 removed outlier: 3.705A pdb=" N SER c 544 " --> pdb=" O GLN c 540 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN c 547 " --> pdb=" O LEU c 543 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 34 removed outlier: 3.547A pdb=" N LEU J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 100 removed outlier: 4.335A pdb=" N GLN J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE J 72 " --> pdb=" O ALA J 68 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU J 84 " --> pdb=" O GLY J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 129 Processing helix chain 'J' and resid 459 through 505 removed outlier: 3.554A pdb=" N THR J 497 " --> pdb=" O ASN J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 536 Processing helix chain 'J' and resid 539 through 546 removed outlier: 4.285A pdb=" N LEU J 543 " --> pdb=" O PRO J 539 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 34 removed outlier: 3.650A pdb=" N SER T 23 " --> pdb=" O ASN T 19 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA T 24 " --> pdb=" O LYS T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 100 removed outlier: 4.253A pdb=" N SER T 73 " --> pdb=" O ASN T 69 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL T 74 " --> pdb=" O ASP T 70 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA T 75 " --> pdb=" O GLY T 71 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU T 84 " --> pdb=" O GLY T 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 129 Processing helix chain 'T' and resid 459 through 483 removed outlier: 3.876A pdb=" N ALA T 463 " --> pdb=" O ASP T 459 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU T 464 " --> pdb=" O PRO T 460 " (cutoff:3.500A) Processing helix chain 'T' and resid 484 through 505 Processing helix chain 'T' and resid 510 through 536 Processing helix chain 'T' and resid 537 through 539 No H-bonds generated for 'chain 'T' and resid 537 through 539' Processing helix chain 'T' and resid 540 through 547 removed outlier: 3.567A pdb=" N SER T 544 " --> pdb=" O GLN T 540 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN T 547 " --> pdb=" O LEU T 543 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 34 removed outlier: 3.791A pdb=" N SER d 23 " --> pdb=" O ASN d 19 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA d 24 " --> pdb=" O LYS d 20 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER d 34 " --> pdb=" O GLU d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 100 removed outlier: 3.570A pdb=" N ILE d 72 " --> pdb=" O ALA d 68 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER d 73 " --> pdb=" O ASN d 69 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL d 74 " --> pdb=" O ASP d 70 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN d 98 " --> pdb=" O GLU d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 129 Processing helix chain 'd' and resid 459 through 507 removed outlier: 4.154A pdb=" N ALA d 467 " --> pdb=" O ALA d 463 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE d 506 " --> pdb=" O ALA d 502 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN d 507 " --> pdb=" O GLN d 503 " (cutoff:3.500A) Processing helix chain 'd' and resid 512 through 537 removed outlier: 3.923A pdb=" N GLN d 537 " --> pdb=" O ALA d 533 " (cutoff:3.500A) Processing helix chain 'd' and resid 539 through 547 removed outlier: 4.123A pdb=" N LEU d 543 " --> pdb=" O PRO d 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER d 544 " --> pdb=" O GLN d 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 34 removed outlier: 3.590A pdb=" N LEU K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER K 23 " --> pdb=" O ASN K 19 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 100 removed outlier: 3.719A pdb=" N GLN K 48 " --> pdb=" O ASP K 44 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER K 73 " --> pdb=" O ASN K 69 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 129 removed outlier: 3.583A pdb=" N GLU K 115 " --> pdb=" O SER K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 169 Processing helix chain 'K' and resid 459 through 507 removed outlier: 3.760A pdb=" N ASP K 466 " --> pdb=" O ALA K 462 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA K 467 " --> pdb=" O ALA K 463 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 536 Processing helix chain 'K' and resid 537 through 539 No H-bonds generated for 'chain 'K' and resid 537 through 539' Processing helix chain 'K' and resid 540 through 547 removed outlier: 3.805A pdb=" N SER K 544 " --> pdb=" O GLN K 540 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 34 removed outlier: 3.924A pdb=" N SER U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA U 24 " --> pdb=" O LYS U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 100 removed outlier: 3.730A pdb=" N GLN U 48 " --> pdb=" O ASP U 44 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 129 Processing helix chain 'U' and resid 459 through 505 Processing helix chain 'U' and resid 512 through 537 removed outlier: 3.924A pdb=" N GLN U 537 " --> pdb=" O ALA U 533 " (cutoff:3.500A) Processing helix chain 'U' and resid 540 through 547 removed outlier: 4.115A pdb=" N SER U 544 " --> pdb=" O GLN U 540 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 34 removed outlier: 3.837A pdb=" N SER e 23 " --> pdb=" O ASN e 19 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA e 24 " --> pdb=" O LYS e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 100 removed outlier: 4.492A pdb=" N ALA e 49 " --> pdb=" O ALA e 45 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE e 50 " --> pdb=" O ALA e 46 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER e 73 " --> pdb=" O ASN e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 129 Processing helix chain 'e' and resid 164 through 169 Processing helix chain 'e' and resid 459 through 507 removed outlier: 3.647A pdb=" N ALA e 467 " --> pdb=" O ALA e 463 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE e 506 " --> pdb=" O ALA e 502 " (cutoff:3.500A) Processing helix chain 'e' and resid 513 through 537 removed outlier: 4.103A pdb=" N GLN e 537 " --> pdb=" O ALA e 533 " (cutoff:3.500A) Processing helix chain 'e' and resid 540 through 547 removed outlier: 4.275A pdb=" N SER e 544 " --> pdb=" O GLN e 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 34 removed outlier: 3.954A pdb=" N THR L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 100 removed outlier: 3.916A pdb=" N GLN L 48 " --> pdb=" O ASP L 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR L 77 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 130 Processing helix chain 'L' and resid 459 through 507 removed outlier: 3.602A pdb=" N ALA L 463 " --> pdb=" O ASP L 459 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG L 505 " --> pdb=" O GLU L 501 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE L 506 " --> pdb=" O ALA L 502 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN L 507 " --> pdb=" O GLN L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 536 removed outlier: 3.733A pdb=" N SER L 516 " --> pdb=" O ALA L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 539 No H-bonds generated for 'chain 'L' and resid 537 through 539' Processing helix chain 'L' and resid 540 through 547 removed outlier: 3.942A pdb=" N SER L 544 " --> pdb=" O GLN L 540 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN L 547 " --> pdb=" O LEU L 543 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 34 Processing helix chain 'V' and resid 44 through 101 removed outlier: 4.345A pdb=" N GLN V 48 " --> pdb=" O ASP V 44 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG V 53 " --> pdb=" O ALA V 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR V 101 " --> pdb=" O VAL V 97 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 130 removed outlier: 3.617A pdb=" N THR V 130 " --> pdb=" O VAL V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 459 through 507 removed outlier: 3.554A pdb=" N ALA V 463 " --> pdb=" O ASP V 459 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG V 505 " --> pdb=" O GLU V 501 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE V 506 " --> pdb=" O ALA V 502 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN V 507 " --> pdb=" O GLN V 503 " (cutoff:3.500A) Processing helix chain 'V' and resid 510 through 536 removed outlier: 3.853A pdb=" N SER V 516 " --> pdb=" O ALA V 512 " (cutoff:3.500A) Processing helix chain 'V' and resid 537 through 540 Processing helix chain 'V' and resid 541 through 547 removed outlier: 3.828A pdb=" N LEU V 545 " --> pdb=" O GLN V 541 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 34 removed outlier: 3.643A pdb=" N SER f 23 " --> pdb=" O ASN f 19 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 100 removed outlier: 3.659A pdb=" N ASN f 88 " --> pdb=" O GLU f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 130 Processing helix chain 'f' and resid 164 through 169 Processing helix chain 'f' and resid 459 through 505 removed outlier: 3.776A pdb=" N ALA f 463 " --> pdb=" O ASP f 459 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG f 505 " --> pdb=" O GLU f 501 " (cutoff:3.500A) Processing helix chain 'f' and resid 510 through 537 removed outlier: 3.818A pdb=" N SER f 516 " --> pdb=" O ALA f 512 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN f 537 " --> pdb=" O ALA f 533 " (cutoff:3.500A) Processing helix chain 'f' and resid 540 through 547 removed outlier: 4.037A pdb=" N SER f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 34 removed outlier: 3.757A pdb=" N SER M 23 " --> pdb=" O ASN M 19 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA M 24 " --> pdb=" O LYS M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 100 removed outlier: 3.518A pdb=" N SER M 56 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 129 removed outlier: 3.569A pdb=" N SER M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE M 112 " --> pdb=" O ASP M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 508 removed outlier: 3.909A pdb=" N THR M 497 " --> pdb=" O ASN M 493 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN M 498 " --> pdb=" O ASN M 494 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG M 505 " --> pdb=" O GLU M 501 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE M 506 " --> pdb=" O ALA M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 536 Processing helix chain 'M' and resid 537 through 541 removed outlier: 3.763A pdb=" N GLN M 541 " --> pdb=" O VAL M 538 " (cutoff:3.500A) Processing helix chain 'M' and resid 542 through 547 removed outlier: 4.227A pdb=" N LEU M 546 " --> pdb=" O VAL M 542 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN M 547 " --> pdb=" O LEU M 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 542 through 547' Processing helix chain 'W' and resid 8 through 34 removed outlier: 3.633A pdb=" N SER W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA W 24 " --> pdb=" O LYS W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 101 removed outlier: 3.933A pdb=" N ALA W 49 " --> pdb=" O ALA W 45 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR W 101 " --> pdb=" O VAL W 97 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 129 removed outlier: 4.139A pdb=" N SER W 111 " --> pdb=" O SER W 107 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 459 through 508 removed outlier: 3.556A pdb=" N ALA W 463 " --> pdb=" O ASP W 459 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR W 497 " --> pdb=" O ASN W 493 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN W 498 " --> pdb=" O ASN W 494 " (cutoff:3.500A) Processing helix chain 'W' and resid 510 through 537 removed outlier: 3.661A pdb=" N GLU W 514 " --> pdb=" O ASP W 510 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER W 516 " --> pdb=" O ALA W 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN W 537 " --> pdb=" O ALA W 533 " (cutoff:3.500A) Processing helix chain 'W' and resid 538 through 541 Processing helix chain 'W' and resid 542 through 547 removed outlier: 4.127A pdb=" N LEU W 546 " --> pdb=" O VAL W 542 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN W 547 " --> pdb=" O LEU W 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 542 through 547' Processing helix chain 'g' and resid 8 through 34 removed outlier: 3.676A pdb=" N SER g 23 " --> pdb=" O ASN g 19 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA g 24 " --> pdb=" O LYS g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 42 removed outlier: 4.129A pdb=" N LYS g 42 " --> pdb=" O ASN g 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 101 removed outlier: 3.599A pdb=" N ILE g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR g 101 " --> pdb=" O VAL g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 129 Processing helix chain 'g' and resid 164 through 169 removed outlier: 3.500A pdb=" N GLY g 169 " --> pdb=" O SER g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 459 through 508 removed outlier: 3.529A pdb=" N ALA g 463 " --> pdb=" O ASP g 459 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR g 497 " --> pdb=" O ASN g 493 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN g 498 " --> pdb=" O ASN g 494 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE g 506 " --> pdb=" O ALA g 502 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 536 Processing helix chain 'g' and resid 537 through 539 No H-bonds generated for 'chain 'g' and resid 537 through 539' Processing helix chain 'g' and resid 540 through 547 removed outlier: 4.012A pdb=" N SER g 544 " --> pdb=" O GLN g 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA3, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain 'B' and resid 144 through 147 Processing sheet with id=AA5, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'C' and resid 143 through 147 Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA8, first strand: chain 'D' and resid 143 through 146 Processing sheet with id=AA9, first strand: chain 'N' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'N' and resid 143 through 146 Processing sheet with id=AB2, first strand: chain 'X' and resid 131 through 132 Processing sheet with id=AB3, first strand: chain 'X' and resid 143 through 147 Processing sheet with id=AB4, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AB5, first strand: chain 'E' and resid 144 through 146 Processing sheet with id=AB6, first strand: chain 'O' and resid 131 through 132 Processing sheet with id=AB7, first strand: chain 'O' and resid 143 through 147 Processing sheet with id=AB8, first strand: chain 'Y' and resid 131 through 132 Processing sheet with id=AB9, first strand: chain 'Y' and resid 143 through 146 Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC2, first strand: chain 'F' and resid 144 through 147 Processing sheet with id=AC3, first strand: chain 'P' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'P' and resid 144 through 147 Processing sheet with id=AC5, first strand: chain 'Z' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'Z' and resid 144 through 146 Processing sheet with id=AC7, first strand: chain 'G' and resid 143 through 146 Processing sheet with id=AC8, first strand: chain 'Q' and resid 131 through 132 Processing sheet with id=AC9, first strand: chain 'Q' and resid 143 through 147 Processing sheet with id=AD1, first strand: chain 'a' and resid 143 through 146 Processing sheet with id=AD2, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AD3, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AD4, first strand: chain 'R' and resid 143 through 147 Processing sheet with id=AD5, first strand: chain 'b' and resid 143 through 146 Processing sheet with id=AD6, first strand: chain 'I' and resid 131 through 132 Processing sheet with id=AD7, first strand: chain 'I' and resid 143 through 147 Processing sheet with id=AD8, first strand: chain 'S' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'S' and resid 144 through 147 removed outlier: 3.564A pdb=" N MET S 144 " --> pdb=" O ILE S 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 131 through 132 Processing sheet with id=AE2, first strand: chain 'c' and resid 143 through 147 removed outlier: 3.533A pdb=" N ILE c 146 " --> pdb=" O ILE c 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 144 through 147 Processing sheet with id=AE4, first strand: chain 'T' and resid 131 through 132 Processing sheet with id=AE5, first strand: chain 'T' and resid 143 through 147 Processing sheet with id=AE6, first strand: chain 'd' and resid 131 through 132 Processing sheet with id=AE7, first strand: chain 'd' and resid 144 through 147 Processing sheet with id=AE8, first strand: chain 'K' and resid 143 through 147 Processing sheet with id=AE9, first strand: chain 'U' and resid 131 through 132 Processing sheet with id=AF1, first strand: chain 'U' and resid 143 through 147 Processing sheet with id=AF2, first strand: chain 'e' and resid 143 through 147 removed outlier: 3.681A pdb=" N ILE e 156 " --> pdb=" O ILE e 146 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 142 through 147 Processing sheet with id=AF4, first strand: chain 'V' and resid 142 through 147 Processing sheet with id=AF5, first strand: chain 'f' and resid 142 through 146 Processing sheet with id=AF6, first strand: chain 'M' and resid 143 through 147 Processing sheet with id=AF7, first strand: chain 'W' and resid 143 through 147 Processing sheet with id=AF8, first strand: chain 'g' and resid 143 through 147 5390 hydrogen bonds defined for protein. 16017 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: 20.88 Time building geometry restraints manager: 15.59 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: 24213 1.34 - 1.45: 3631 1.45 - 1.57: 38234 1.57 - 1.69: 0 1.69 - 1.80: 132 Bond restraints: 66210 Sorted by residual: bond pdb=" C VAL F 538 " pdb=" N PRO F 539 " ideal model delta sigma weight residual 1.334 1.364 -0.030 8.40e-03 1.42e+04 1.30e+01 bond pdb=" C VAL J 538 " pdb=" N PRO J 539 " ideal model delta sigma weight residual 1.337 1.352 -0.015 9.80e-03 1.04e+04 2.36e+00 bond pdb=" C VAL a 538 " pdb=" N PRO a 539 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.30e+00 bond pdb=" CA VAL A 148 " pdb=" CB VAL A 148 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.57e+00 bond pdb=" CA ASP J 508 " pdb=" CB ASP J 508 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.61e-02 3.86e+03 1.56e+00 ... (remaining 66205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 88868 2.03 - 4.06: 598 4.06 - 6.09: 83 6.09 - 8.12: 11 8.12 - 10.15: 8 Bond angle restraints: 89568 Sorted by residual: angle pdb=" N ILE d 5 " pdb=" CA ILE d 5 " pdb=" C ILE d 5 " ideal model delta sigma weight residual 113.71 109.47 4.24 9.50e-01 1.11e+00 1.99e+01 angle pdb=" N ILE I 5 " pdb=" CA ILE I 5 " pdb=" C ILE I 5 " ideal model delta sigma weight residual 112.96 109.53 3.43 1.00e+00 1.00e+00 1.17e+01 angle pdb=" C TYR e 511 " pdb=" N ALA e 512 " pdb=" CA ALA e 512 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N ILE U 5 " pdb=" CA ILE U 5 " pdb=" C ILE U 5 " ideal model delta sigma weight residual 113.42 109.43 3.99 1.17e+00 7.31e-01 1.16e+01 angle pdb=" C GLU V 94 " pdb=" N LEU V 95 " pdb=" CA LEU V 95 " ideal model delta sigma weight residual 121.58 114.96 6.62 1.95e+00 2.63e-01 1.15e+01 ... (remaining 89563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 37985 17.99 - 35.99: 2761 35.99 - 53.98: 445 53.98 - 71.97: 103 71.97 - 89.97: 70 Dihedral angle restraints: 41364 sinusoidal: 15825 harmonic: 25539 Sorted by residual: dihedral pdb=" CA SER V 40 " pdb=" C SER V 40 " pdb=" N ALA V 41 " pdb=" CA ALA V 41 " ideal model delta harmonic sigma weight residual 180.00 -146.42 -33.58 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA VAL S 538 " pdb=" C VAL S 538 " pdb=" N PRO S 539 " pdb=" CA PRO S 539 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA ALA V 41 " pdb=" C ALA V 41 " pdb=" N LYS V 42 " pdb=" CA LYS V 42 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 41361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 8729 0.038 - 0.076: 1815 0.076 - 0.113: 369 0.113 - 0.151: 74 0.151 - 0.189: 8 Chirality restraints: 10995 Sorted by residual: chirality pdb=" CG LEU g 170 " pdb=" CB LEU g 170 " pdb=" CD1 LEU g 170 " pdb=" CD2 LEU g 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA ASP U 508 " pdb=" N ASP U 508 " pdb=" C ASP U 508 " pdb=" CB ASP U 508 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ASP T 508 " pdb=" N ASP T 508 " pdb=" C ASP T 508 " pdb=" CB ASP T 508 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 10992 not shown) Planarity restraints: 12150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA d 512 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA d 512 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA d 512 " 0.021 2.00e-02 2.50e+03 pdb=" N THR d 513 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 512 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ALA U 512 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA U 512 " 0.020 2.00e-02 2.50e+03 pdb=" N THR U 513 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 512 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C ALA K 512 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA K 512 " 0.018 2.00e-02 2.50e+03 pdb=" N THR K 513 " 0.016 2.00e-02 2.50e+03 ... (remaining 12147 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1211 2.64 - 3.20: 67952 3.20 - 3.77: 107811 3.77 - 4.33: 136764 4.33 - 4.90: 232456 Nonbonded interactions: 546194 Sorted by model distance: nonbonded pdb=" OG1 THR I 497 " pdb=" OD1 ASN S 16 " model vdw 2.073 3.040 nonbonded pdb=" OG SER Y 127 " pdb=" O ILE Y 163 " model vdw 2.106 3.040 nonbonded pdb=" OG SER T 34 " pdb=" ND2 ASN T 39 " model vdw 2.116 3.120 nonbonded pdb=" OG SER W 127 " pdb=" O ILE W 163 " model vdw 2.116 3.040 nonbonded pdb=" O PHE H 173 " pdb=" OG1 THR H 457 " model vdw 2.128 3.040 ... (remaining 546189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 37 or resid 39 through 546)) selection = (chain 'B' and (resid 3 through 37 or resid 39 through 546)) selection = (chain 'C' and (resid 3 through 37 or resid 39 through 546)) selection = (chain 'D' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'E' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'F' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'G' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'H' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'I' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'J' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'K' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'L' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'M' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'N' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'O' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'P' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'Q' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'R' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'S' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'T' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'U' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'V' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'W' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'X' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'Y' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'Z' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'a' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'b' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'c' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'd' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'e' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'f' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'g' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) } 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=1.00 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: 2.560 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: 0.070 Extract box with map and model: 1.930 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 122.760 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.270 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:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.003 0.039 66210 Z= 0.171 Angle : 0.490 10.145 89568 Z= 0.299 Chirality : 0.034 0.189 10995 Planarity : 0.002 0.064 12150 Dihedral : 13.535 89.969 24678 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.05 % 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: 1.49 (0.09), residues: 8769 helix: 1.98 (0.06), residues: 6288 sheet: 0.01 (0.23), residues: 462 loop : -2.08 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE S 173 TYR 0.010 0.001 TYR F 511 ARG 0.004 0.000 ARG V 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1899 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1899 time to evaluate : 5.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.8056 (mtm-85) REVERT: A 161 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8555 (mmtm) REVERT: A 459 ASP cc_start: 0.7972 (p0) cc_final: 0.7557 (p0) REVERT: A 508 ASP cc_start: 0.8558 (m-30) cc_final: 0.8246 (m-30) REVERT: B 42 LYS cc_start: 0.8526 (pttp) cc_final: 0.8197 (tttp) REVERT: B 486 ASP cc_start: 0.7778 (p0) cc_final: 0.7265 (p0) REVERT: C 459 ASP cc_start: 0.8151 (p0) cc_final: 0.7821 (p0) REVERT: C 514 GLU cc_start: 0.7675 (mp0) cc_final: 0.7245 (mp0) REVERT: C 525 GLN cc_start: 0.7015 (tp40) cc_final: 0.6788 (tp-100) REVERT: D 44 ASP cc_start: 0.6746 (t0) cc_final: 0.6521 (m-30) REVERT: D 122 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8281 (tp30) REVERT: D 493 ASN cc_start: 0.8540 (m110) cc_final: 0.7949 (m110) REVERT: N 123 ILE cc_start: 0.8354 (mt) cc_final: 0.8127 (mt) REVERT: N 157 THR cc_start: 0.8739 (t) cc_final: 0.8523 (m) REVERT: N 518 MET cc_start: 0.7351 (tmm) cc_final: 0.6953 (tmm) REVERT: X 94 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7906 (tm-30) REVERT: X 114 ASP cc_start: 0.8738 (m-30) cc_final: 0.8508 (m-30) REVERT: X 117 LYS cc_start: 0.9157 (tptp) cc_final: 0.8927 (tppt) REVERT: X 464 LEU cc_start: 0.8642 (mt) cc_final: 0.8394 (mt) REVERT: X 494 ASN cc_start: 0.8329 (m110) cc_final: 0.8101 (m110) REVERT: E 459 ASP cc_start: 0.7735 (p0) cc_final: 0.7283 (p0) REVERT: E 466 ASP cc_start: 0.8093 (m-30) cc_final: 0.7849 (m-30) REVERT: E 505 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6994 (mtp180) REVERT: O 459 ASP cc_start: 0.6741 (p0) cc_final: 0.6404 (p0) REVERT: Y 472 ASP cc_start: 0.7941 (m-30) cc_final: 0.7668 (m-30) REVERT: F 21 ASN cc_start: 0.7919 (t0) cc_final: 0.7677 (t0) REVERT: F 171 ASN cc_start: 0.8507 (t0) cc_final: 0.8237 (t0) REVERT: P 30 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7338 (tm-30) REVERT: P 122 GLU cc_start: 0.8879 (tp30) cc_final: 0.8381 (tp30) REVERT: P 140 LYS cc_start: 0.8256 (mtmm) cc_final: 0.8021 (mtmm) REVERT: P 141 ASP cc_start: 0.7636 (p0) cc_final: 0.7181 (t0) REVERT: P 174 ASN cc_start: 0.8198 (t0) cc_final: 0.7906 (t0) REVERT: Z 6 ASN cc_start: 0.8375 (t0) cc_final: 0.8082 (t0) REVERT: Z 22 GLN cc_start: 0.8421 (tp40) cc_final: 0.8165 (tt0) REVERT: Z 72 ILE cc_start: 0.8959 (mt) cc_final: 0.8723 (mt) REVERT: Z 161 LYS cc_start: 0.8655 (mttm) cc_final: 0.8452 (mttt) REVERT: G 510 ASP cc_start: 0.8130 (t0) cc_final: 0.7806 (t0) REVERT: G 534 LYS cc_start: 0.8744 (mttm) cc_final: 0.8489 (mtpt) REVERT: Q 22 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7925 (tm-30) REVERT: Q 140 LYS cc_start: 0.8184 (tttm) cc_final: 0.7936 (ttmm) REVERT: a 98 GLN cc_start: 0.8707 (tt0) cc_final: 0.6590 (mm110) REVERT: a 117 LYS cc_start: 0.8809 (tptp) cc_final: 0.8467 (tppt) REVERT: a 122 GLU cc_start: 0.8601 (tp30) cc_final: 0.7899 (tp30) REVERT: H 84 GLU cc_start: 0.7921 (tp30) cc_final: 0.7679 (tp30) REVERT: H 110 ASP cc_start: 0.8243 (m-30) cc_final: 0.8035 (m-30) REVERT: H 473 LYS cc_start: 0.8505 (ptmm) cc_final: 0.8153 (ptmt) REVERT: R 486 ASP cc_start: 0.7761 (p0) cc_final: 0.7497 (p0) REVERT: R 501 GLU cc_start: 0.8033 (tt0) cc_final: 0.7815 (tt0) REVERT: b 94 GLU cc_start: 0.7019 (tt0) cc_final: 0.6721 (tt0) REVERT: b 117 LYS cc_start: 0.8627 (tptt) cc_final: 0.8075 (tppt) REVERT: b 121 ASP cc_start: 0.8156 (m-30) cc_final: 0.7901 (m-30) REVERT: I 42 LYS cc_start: 0.9106 (ptmt) cc_final: 0.8495 (tptm) REVERT: I 57 ASN cc_start: 0.8420 (t0) cc_final: 0.8181 (t0) REVERT: I 518 MET cc_start: 0.8294 (ttp) cc_final: 0.8094 (ttt) REVERT: S 42 LYS cc_start: 0.8620 (ptmt) cc_final: 0.8346 (ptmt) REVERT: S 151 ASN cc_start: 0.7945 (m-40) cc_final: 0.7505 (m-40) REVERT: c 70 ASP cc_start: 0.7753 (m-30) cc_final: 0.7550 (m-30) REVERT: c 79 GLU cc_start: 0.8352 (tp30) cc_final: 0.7981 (tp30) REVERT: c 145 LYS cc_start: 0.8625 (mttm) cc_final: 0.8413 (mttt) REVERT: J 501 GLU cc_start: 0.7662 (tt0) cc_final: 0.7199 (tt0) REVERT: J 514 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7545 (mp0) REVERT: T 20 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8632 (mtpp) REVERT: T 117 LYS cc_start: 0.8893 (tptm) cc_final: 0.8599 (tptm) REVERT: T 162 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8655 (ttpp) REVERT: T 537 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8061 (mm110) REVERT: d 66 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.8068 (ttm-80) REVERT: d 90 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7775 (mm-40) REVERT: d 115 GLU cc_start: 0.8619 (tp30) cc_final: 0.8409 (tp30) REVERT: d 459 ASP cc_start: 0.6497 (t0) cc_final: 0.6293 (m-30) REVERT: K 154 GLN cc_start: 0.6960 (pt0) cc_final: 0.6590 (tt0) REVERT: U 8 ASN cc_start: 0.8793 (t0) cc_final: 0.8242 (t0) REVERT: U 82 LEU cc_start: 0.8888 (mm) cc_final: 0.8588 (mm) REVERT: U 473 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8279 (mtpt) REVERT: e 21 ASN cc_start: 0.8600 (t0) cc_final: 0.8398 (t0) REVERT: e 79 GLU cc_start: 0.7626 (tp30) cc_final: 0.7350 (tp30) REVERT: e 94 GLU cc_start: 0.8428 (tt0) cc_final: 0.8140 (mm-30) REVERT: e 113 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8130 (tp40) REVERT: e 115 GLU cc_start: 0.8242 (tp30) cc_final: 0.7998 (tp30) REVERT: e 144 MET cc_start: 0.8871 (ttm) cc_final: 0.8359 (ttm) REVERT: L 70 ASP cc_start: 0.7898 (m-30) cc_final: 0.7505 (m-30) REVERT: L 518 MET cc_start: 0.8597 (ttp) cc_final: 0.8359 (ttm) REVERT: V 518 MET cc_start: 0.8801 (ttp) cc_final: 0.8600 (ttp) REVERT: f 42 LYS cc_start: 0.8513 (tttm) cc_final: 0.8261 (tttm) REVERT: f 91 ARG cc_start: 0.8514 (tpt170) cc_final: 0.8085 (tpp-160) REVERT: f 121 ASP cc_start: 0.8360 (m-30) cc_final: 0.7628 (t0) REVERT: f 122 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8248 (tm-30) REVERT: f 125 ARG cc_start: 0.7692 (tmm160) cc_final: 0.6993 (ttt180) REVERT: f 484 ARG cc_start: 0.8246 (mtp180) cc_final: 0.6941 (mtp85) REVERT: f 505 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7822 (ttm-80) REVERT: f 520 LYS cc_start: 0.7360 (mttt) cc_final: 0.6948 (mmtt) REVERT: M 20 LYS cc_start: 0.9173 (ttpt) cc_final: 0.8927 (ttpp) REVERT: W 16 ASN cc_start: 0.7625 (p0) cc_final: 0.7294 (m110) REVERT: W 122 GLU cc_start: 0.8245 (tp30) cc_final: 0.7982 (tp30) REVERT: W 510 ASP cc_start: 0.6975 (t70) cc_final: 0.6473 (t70) REVERT: W 514 GLU cc_start: 0.8144 (mp0) cc_final: 0.7433 (mp0) REVERT: g 115 GLU cc_start: 0.8226 (tt0) cc_final: 0.7965 (tt0) REVERT: g 166 ASP cc_start: 0.8284 (p0) cc_final: 0.7813 (p0) REVERT: g 486 ASP cc_start: 0.7474 (m-30) cc_final: 0.7014 (m-30) REVERT: g 537 GLN cc_start: 0.7530 (mp10) cc_final: 0.7147 (mp10) outliers start: 0 outliers final: 0 residues processed: 1899 average time/residue: 0.6226 time to fit residues: 2007.5427 Evaluate side-chains 1330 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1330 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 724 optimal weight: 6.9990 chunk 650 optimal weight: 3.9990 chunk 360 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 438 optimal weight: 6.9990 chunk 347 optimal weight: 2.9990 chunk 672 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 408 optimal weight: 5.9990 chunk 500 optimal weight: 5.9990 chunk 779 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 86 ASN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN A 529 ASN B 86 ASN B 470 GLN B 482 GLN C 3 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 86 ASN C 174 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 21 ASN D 63 GLN D 67 ASN D 86 ASN D 129 GLN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN N 536 ASN N 537 GLN X 17 ASN X 48 GLN X 67 ASN X 86 ASN X 503 GLN X 522 GLN E 6 ASN E 22 GLN E 136 ASN O 503 GLN O 525 GLN Y 491 ASN Y 503 GLN Y 522 GLN F 21 ASN F 22 GLN F 39 ASN F 129 GLN F 482 GLN F 537 GLN P 6 ASN P 129 GLN P 136 ASN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 536 ASN Z 17 ASN Z 129 GLN Z 154 GLN Z 494 ASN G 98 GLN Q 498 ASN Q 503 GLN Q 540 GLN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN H 537 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN b 21 ASN b 86 ASN b 174 ASN b 537 GLN I 136 ASN S 3 GLN S 90 GLN S 113 GLN S 154 GLN S 507 GLN S 547 GLN c 39 ASN c 86 ASN c 147 GLN c 540 GLN T 16 ASN T 22 GLN T 63 GLN T 86 ASN T 491 ASN ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 522 GLN d 526 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 547 GLN U 3 GLN U 6 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 498 ASN U 525 GLN U 540 GLN e 16 ASN e 63 GLN e 67 ASN e 86 ASN e 113 GLN e 503 GLN e 547 GLN L 76 GLN L 133 ASN L 525 GLN L 526 GLN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 498 ASN V 503 GLN V 507 GLN V 526 GLN f 147 GLN f 470 GLN f 540 GLN f 541 GLN M 76 GLN M 171 ASN M 483 ASN M 529 ASN W 131 GLN W 136 ASN W 526 GLN g 48 GLN g 86 ASN g 507 GLN g 536 ASN Total number of N/Q/H flips: 116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 66210 Z= 0.284 Angle : 0.584 10.405 89568 Z= 0.320 Chirality : 0.040 0.279 10995 Planarity : 0.003 0.066 12150 Dihedral : 3.974 36.904 9216 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer: Outliers : 1.97 % Allowed : 12.64 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 2.69 (0.09), residues: 8769 helix: 2.97 (0.06), residues: 6330 sheet: 0.40 (0.23), residues: 462 loop : -2.14 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE S 173 TYR 0.018 0.002 TYR O 511 ARG 0.008 0.001 ARG W 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1425 time to evaluate : 5.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.5518 (OUTLIER) cc_final: 0.2606 (tp-100) REVERT: A 36 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7965 (pp) REVERT: A 161 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8566 (mmtm) REVERT: A 171 ASN cc_start: 0.7280 (t0) cc_final: 0.7012 (t0) REVERT: A 459 ASP cc_start: 0.8050 (p0) cc_final: 0.7646 (p0) REVERT: B 42 LYS cc_start: 0.8609 (pttp) cc_final: 0.8328 (tttp) REVERT: B 486 ASP cc_start: 0.7977 (p0) cc_final: 0.7387 (p0) REVERT: B 536 ASN cc_start: 0.8287 (m110) cc_final: 0.7696 (p0) REVERT: C 8 ASN cc_start: 0.8410 (t0) cc_final: 0.8192 (t0) REVERT: C 31 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7532 (mtt-85) REVERT: C 459 ASP cc_start: 0.8152 (p0) cc_final: 0.7750 (p0) REVERT: D 44 ASP cc_start: 0.6835 (t0) cc_final: 0.6634 (m-30) REVERT: D 493 ASN cc_start: 0.8605 (m110) cc_final: 0.8029 (m110) REVERT: N 123 ILE cc_start: 0.8442 (mt) cc_final: 0.8198 (mt) REVERT: N 145 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7519 (mmmt) REVERT: N 518 MET cc_start: 0.7611 (tmm) cc_final: 0.7193 (tmm) REVERT: X 6 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8289 (m-40) REVERT: X 20 LYS cc_start: 0.9331 (ttmt) cc_final: 0.9105 (mttt) REVERT: X 94 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8017 (tm-30) REVERT: X 114 ASP cc_start: 0.8777 (m-30) cc_final: 0.8513 (m-30) REVERT: X 176 ASN cc_start: 0.8800 (p0) cc_final: 0.8287 (p0) REVERT: X 494 ASN cc_start: 0.8310 (m110) cc_final: 0.8106 (m110) REVERT: E 459 ASP cc_start: 0.7728 (p0) cc_final: 0.7231 (p0) REVERT: E 466 ASP cc_start: 0.8266 (m-30) cc_final: 0.7955 (m-30) REVERT: E 494 ASN cc_start: 0.8473 (t0) cc_final: 0.8207 (t0) REVERT: E 505 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7166 (mtp180) REVERT: O 79 GLU cc_start: 0.8238 (tt0) cc_final: 0.7612 (mt-10) REVERT: O 459 ASP cc_start: 0.6906 (p0) cc_final: 0.6548 (p0) REVERT: Y 472 ASP cc_start: 0.8096 (m-30) cc_final: 0.7816 (m-30) REVERT: F 21 ASN cc_start: 0.8163 (t0) cc_final: 0.7870 (t0) REVERT: P 30 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7493 (tm-30) REVERT: P 140 LYS cc_start: 0.8265 (mtmm) cc_final: 0.8063 (mtmm) REVERT: P 141 ASP cc_start: 0.7674 (p0) cc_final: 0.7202 (t0) REVERT: P 174 ASN cc_start: 0.8202 (t0) cc_final: 0.7953 (t0) REVERT: Z 22 GLN cc_start: 0.8505 (tp40) cc_final: 0.8163 (tt0) REVERT: Z 72 ILE cc_start: 0.9017 (mt) cc_final: 0.8771 (mt) REVERT: Z 117 LYS cc_start: 0.8833 (tppt) cc_final: 0.8476 (tppt) REVERT: Q 22 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7877 (tm-30) REVERT: Q 30 GLU cc_start: 0.8337 (tt0) cc_final: 0.8042 (tt0) REVERT: Q 140 LYS cc_start: 0.8274 (tttm) cc_final: 0.8021 (ttmm) REVERT: a 30 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7875 (tt0) REVERT: a 31 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8617 (ttm170) REVERT: a 122 GLU cc_start: 0.8654 (tp30) cc_final: 0.7926 (tp30) REVERT: H 129 GLN cc_start: 0.7894 (mm110) cc_final: 0.7680 (mm110) REVERT: H 473 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8306 (ptpt) REVERT: R 70 ASP cc_start: 0.7141 (m-30) cc_final: 0.6883 (m-30) REVERT: R 501 GLU cc_start: 0.8022 (tt0) cc_final: 0.7809 (tt0) REVERT: b 94 GLU cc_start: 0.7100 (tt0) cc_final: 0.6734 (tt0) REVERT: b 117 LYS cc_start: 0.8751 (tptt) cc_final: 0.8170 (tppt) REVERT: b 121 ASP cc_start: 0.8232 (m-30) cc_final: 0.7908 (m-30) REVERT: I 29 ILE cc_start: 0.8318 (mm) cc_final: 0.8051 (mm) REVERT: S 140 LYS cc_start: 0.8264 (tptt) cc_final: 0.7939 (tppt) REVERT: S 514 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8112 (mm-30) REVERT: c 70 ASP cc_start: 0.7879 (m-30) cc_final: 0.7672 (m-30) REVERT: c 79 GLU cc_start: 0.8466 (tp30) cc_final: 0.8045 (tp30) REVERT: J 514 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7571 (mp0) REVERT: d 52 ASN cc_start: 0.7770 (t0) cc_final: 0.7385 (t0) REVERT: d 70 ASP cc_start: 0.7926 (m-30) cc_final: 0.7697 (m-30) REVERT: d 90 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7896 (mm-40) REVERT: d 115 GLU cc_start: 0.8763 (tp30) cc_final: 0.8525 (tp30) REVERT: d 117 LYS cc_start: 0.8659 (tppt) cc_final: 0.8419 (tppt) REVERT: K 154 GLN cc_start: 0.7389 (pt0) cc_final: 0.6647 (tt0) REVERT: U 82 LEU cc_start: 0.8991 (mm) cc_final: 0.8553 (mm) REVERT: e 79 GLU cc_start: 0.7618 (tp30) cc_final: 0.7330 (tp30) REVERT: e 94 GLU cc_start: 0.8583 (tt0) cc_final: 0.8113 (mm-30) REVERT: e 115 GLU cc_start: 0.8363 (tp30) cc_final: 0.8122 (tp30) REVERT: e 144 MET cc_start: 0.8944 (ttm) cc_final: 0.8446 (ttm) REVERT: L 70 ASP cc_start: 0.7915 (m-30) cc_final: 0.7534 (m-30) REVERT: V 84 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7063 (tm-30) REVERT: V 505 ARG cc_start: 0.7841 (mtt90) cc_final: 0.7509 (mtt180) REVERT: V 511 TYR cc_start: 0.8902 (m-80) cc_final: 0.8623 (m-80) REVERT: f 91 ARG cc_start: 0.8537 (tpt170) cc_final: 0.8150 (tpp-160) REVERT: f 117 LYS cc_start: 0.8993 (tppt) cc_final: 0.8336 (tppt) REVERT: f 122 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8510 (tm-30) REVERT: f 125 ARG cc_start: 0.7652 (tmm160) cc_final: 0.6969 (ttt180) REVERT: f 484 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7879 (mtp85) REVERT: f 505 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7828 (ttm-80) REVERT: M 20 LYS cc_start: 0.9164 (ttpt) cc_final: 0.8875 (ttpp) REVERT: M 131 GLN cc_start: 0.8586 (pm20) cc_final: 0.8240 (pt0) REVERT: M 466 ASP cc_start: 0.8227 (t0) cc_final: 0.7842 (t0) REVERT: W 3 GLN cc_start: 0.8466 (mt0) cc_final: 0.8259 (mt0) REVERT: W 122 GLU cc_start: 0.8305 (tp30) cc_final: 0.7977 (tp30) REVERT: g 115 GLU cc_start: 0.8347 (tt0) cc_final: 0.8062 (tt0) REVERT: g 147 GLN cc_start: 0.8164 (pt0) cc_final: 0.7938 (pt0) REVERT: g 504 SER cc_start: 0.9055 (t) cc_final: 0.8686 (p) REVERT: g 537 GLN cc_start: 0.7519 (mp10) cc_final: 0.7125 (mp10) outliers start: 143 outliers final: 79 residues processed: 1501 average time/residue: 0.6269 time to fit residues: 1618.3562 Evaluate side-chains 1330 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1248 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 542 VAL Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 157 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 489 VAL Chi-restraints excluded: chain P residue 516 SER Chi-restraints excluded: chain P residue 536 ASN Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 537 GLN Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 21 ASN Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 481 VAL Chi-restraints excluded: chain b residue 497 THR Chi-restraints excluded: chain b residue 542 VAL Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 481 VAL Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 542 VAL Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 108 ASP Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain g residue 170 LEU Chi-restraints excluded: chain g residue 543 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 433 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 648 optimal weight: 5.9990 chunk 530 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 780 optimal weight: 9.9990 chunk 843 optimal weight: 0.9990 chunk 695 optimal weight: 1.9990 chunk 774 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 626 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 3 GLN C 21 ASN C 63 GLN C 69 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN N 537 GLN X 48 GLN X 171 ASN X 537 GLN E 22 GLN E 537 GLN O 57 ASN O 525 GLN F 22 GLN F 491 ASN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 525 GLN Z 129 GLN G 16 ASN G 63 GLN G 498 ASN G 517 ASN a 491 ASN a 517 ASN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 537 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN b 21 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 ASN S 498 ASN S 547 GLN J 154 GLN ** T 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN U 6 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN e 86 ASN e 88 ASN e 547 GLN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 498 ASN M 76 GLN W 171 ASN g 67 ASN g 86 ASN g 529 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 66210 Z= 0.268 Angle : 0.562 10.053 89568 Z= 0.310 Chirality : 0.039 0.357 10995 Planarity : 0.003 0.062 12150 Dihedral : 3.999 36.591 9216 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 15.03 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.00 (0.09), residues: 8769 helix: 3.22 (0.06), residues: 6330 sheet: 0.51 (0.23), residues: 462 loop : -2.13 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE M 474 TYR 0.023 0.002 TYR O 511 ARG 0.011 0.000 ARG W 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1484 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1314 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.5440 (OUTLIER) cc_final: 0.2206 (tp40) REVERT: A 161 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8742 (mmtm) REVERT: A 459 ASP cc_start: 0.8154 (p0) cc_final: 0.7760 (p0) REVERT: A 492 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 508 ASP cc_start: 0.8405 (m-30) cc_final: 0.8182 (m-30) REVERT: B 84 GLU cc_start: 0.8173 (tp30) cc_final: 0.7886 (tp30) REVERT: B 486 ASP cc_start: 0.7909 (p0) cc_final: 0.7387 (p0) REVERT: B 536 ASN cc_start: 0.8302 (m110) cc_final: 0.7706 (p0) REVERT: C 8 ASN cc_start: 0.8466 (t0) cc_final: 0.8245 (t0) REVERT: C 42 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7625 (tptp) REVERT: C 162 LYS cc_start: 0.8259 (tptm) cc_final: 0.7999 (tptp) REVERT: C 459 ASP cc_start: 0.8060 (p0) cc_final: 0.7662 (p0) REVERT: D 32 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7242 (mm) REVERT: D 122 GLU cc_start: 0.8937 (tp30) cc_final: 0.8521 (tp30) REVERT: N 123 ILE cc_start: 0.8462 (mt) cc_final: 0.8231 (mt) REVERT: N 518 MET cc_start: 0.7586 (tmm) cc_final: 0.7143 (tmm) REVERT: X 6 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8337 (m-40) REVERT: X 20 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9079 (mttt) REVERT: X 94 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7869 (tm-30) REVERT: X 114 ASP cc_start: 0.8824 (m-30) cc_final: 0.8502 (m-30) REVERT: X 176 ASN cc_start: 0.8800 (p0) cc_final: 0.8347 (p0) REVERT: X 494 ASN cc_start: 0.8341 (m110) cc_final: 0.8119 (m110) REVERT: E 15 GLN cc_start: 0.8896 (mt0) cc_final: 0.8477 (mp10) REVERT: E 459 ASP cc_start: 0.7791 (p0) cc_final: 0.7286 (p0) REVERT: E 466 ASP cc_start: 0.8316 (m-30) cc_final: 0.7956 (m-30) REVERT: E 505 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7189 (mtp180) REVERT: O 79 GLU cc_start: 0.8257 (tt0) cc_final: 0.7659 (mt-10) REVERT: O 459 ASP cc_start: 0.6896 (p0) cc_final: 0.6532 (p0) REVERT: Y 472 ASP cc_start: 0.8080 (m-30) cc_final: 0.7788 (m-30) REVERT: F 21 ASN cc_start: 0.8278 (t0) cc_final: 0.8032 (t0) REVERT: P 30 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7451 (tm-30) REVERT: P 122 GLU cc_start: 0.9059 (tp30) cc_final: 0.8749 (tp30) REVERT: P 133 ASN cc_start: 0.8577 (t0) cc_final: 0.8359 (t0) REVERT: P 141 ASP cc_start: 0.7660 (p0) cc_final: 0.7158 (t0) REVERT: P 174 ASN cc_start: 0.8162 (t0) cc_final: 0.7912 (t0) REVERT: P 501 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7660 (mm-30) REVERT: Z 72 ILE cc_start: 0.9015 (mt) cc_final: 0.8776 (mt) REVERT: Z 114 ASP cc_start: 0.7897 (m-30) cc_final: 0.7602 (m-30) REVERT: Z 117 LYS cc_start: 0.8873 (tppt) cc_final: 0.8558 (tppt) REVERT: Z 121 ASP cc_start: 0.8703 (m-30) cc_final: 0.8458 (m-30) REVERT: Q 22 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7874 (tm-30) REVERT: Q 30 GLU cc_start: 0.8345 (tt0) cc_final: 0.8060 (tt0) REVERT: Q 140 LYS cc_start: 0.8241 (tttm) cc_final: 0.7990 (ttmm) REVERT: a 30 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7884 (tt0) REVERT: a 31 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8669 (ttm170) REVERT: a 140 LYS cc_start: 0.7649 (pttt) cc_final: 0.7345 (pttp) REVERT: H 473 LYS cc_start: 0.8619 (ptmm) cc_final: 0.8273 (ptpt) REVERT: R 52 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7486 (m110) REVERT: R 70 ASP cc_start: 0.7071 (m-30) cc_final: 0.6806 (m-30) REVERT: R 486 ASP cc_start: 0.7857 (p0) cc_final: 0.7656 (p0) REVERT: R 501 GLU cc_start: 0.8033 (tt0) cc_final: 0.7793 (tt0) REVERT: b 94 GLU cc_start: 0.7109 (tt0) cc_final: 0.6730 (tt0) REVERT: b 117 LYS cc_start: 0.8785 (tptt) cc_final: 0.8179 (tppt) REVERT: b 121 ASP cc_start: 0.8277 (m-30) cc_final: 0.7930 (m-30) REVERT: S 140 LYS cc_start: 0.8307 (tptt) cc_final: 0.7983 (tppt) REVERT: S 514 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8063 (mm-30) REVERT: c 70 ASP cc_start: 0.7898 (m-30) cc_final: 0.7672 (m-30) REVERT: c 79 GLU cc_start: 0.8377 (tp30) cc_final: 0.7962 (tp30) REVERT: J 514 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7586 (mp0) REVERT: T 537 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8063 (mm-40) REVERT: d 52 ASN cc_start: 0.7866 (t0) cc_final: 0.7561 (t0) REVERT: d 70 ASP cc_start: 0.8005 (m-30) cc_final: 0.7700 (m-30) REVERT: d 90 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7903 (mm-40) REVERT: d 115 GLU cc_start: 0.8748 (tp30) cc_final: 0.8493 (tp30) REVERT: d 117 LYS cc_start: 0.8677 (tppt) cc_final: 0.8084 (tptp) REVERT: K 154 GLN cc_start: 0.7335 (pt0) cc_final: 0.6553 (tt0) REVERT: U 82 LEU cc_start: 0.8939 (mm) cc_final: 0.8528 (mm) REVERT: e 94 GLU cc_start: 0.8577 (tt0) cc_final: 0.8112 (mm-30) REVERT: e 115 GLU cc_start: 0.8371 (tp30) cc_final: 0.8128 (tp30) REVERT: e 144 MET cc_start: 0.8890 (ttm) cc_final: 0.8447 (ttm) REVERT: L 70 ASP cc_start: 0.7910 (m-30) cc_final: 0.7520 (m-30) REVERT: V 84 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7067 (tm-30) REVERT: V 106 ASP cc_start: 0.7901 (p0) cc_final: 0.7639 (p0) REVERT: V 473 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8486 (mtmm) REVERT: f 122 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8204 (tm-30) REVERT: f 125 ARG cc_start: 0.7640 (tmm160) cc_final: 0.6935 (ttt180) REVERT: f 520 LYS cc_start: 0.7616 (mttt) cc_final: 0.7129 (mmtt) REVERT: M 42 LYS cc_start: 0.7697 (ptmm) cc_final: 0.6760 (tptt) REVERT: M 131 GLN cc_start: 0.8539 (pm20) cc_final: 0.8135 (pt0) REVERT: M 466 ASP cc_start: 0.8239 (t0) cc_final: 0.7857 (t0) REVERT: W 122 GLU cc_start: 0.8305 (tp30) cc_final: 0.8020 (tp30) REVERT: W 514 GLU cc_start: 0.8219 (mp0) cc_final: 0.7586 (mp0) REVERT: g 115 GLU cc_start: 0.8267 (tt0) cc_final: 0.7896 (tt0) REVERT: g 504 SER cc_start: 0.9072 (t) cc_final: 0.8726 (p) REVERT: g 537 GLN cc_start: 0.7549 (mp10) cc_final: 0.7138 (mp10) outliers start: 170 outliers final: 116 residues processed: 1408 average time/residue: 0.5898 time to fit residues: 1432.8833 Evaluate side-chains 1351 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1230 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 542 VAL Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 157 THR Chi-restraints excluded: chain X residue 171 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 489 VAL Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 516 SER Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 457 THR Chi-restraints excluded: chain Q residue 476 SER Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 466 ASP Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 52 ASN Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 144 MET Chi-restraints excluded: chain b residue 481 VAL Chi-restraints excluded: chain b residue 497 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 154 GLN Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 481 VAL Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 542 VAL Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 155 THR Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain d residue 534 LYS Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain V residue 498 ASN Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 108 ASP Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 170 LEU Chi-restraints excluded: chain g residue 543 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 771 optimal weight: 0.9980 chunk 586 optimal weight: 4.9990 chunk 405 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 372 optimal weight: 3.9990 chunk 524 optimal weight: 3.9990 chunk 783 optimal weight: 9.9990 chunk 829 optimal weight: 3.9990 chunk 409 optimal weight: 0.4980 chunk 742 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 3 GLN C 21 ASN C 69 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN N 63 GLN N 98 GLN N 537 GLN X 48 GLN X 171 ASN X 537 GLN E 22 GLN E 87 ASN O 540 GLN F 22 GLN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN G 16 ASN Q 498 ASN H 537 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 21 ASN ** b 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 537 GLN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN S 507 GLN J 76 GLN T 39 ASN T 86 ASN d 48 GLN ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 522 GLN d 526 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN e 547 GLN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 498 ASN f 507 GLN f 522 GLN W 171 ASN g 147 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 66210 Z= 0.243 Angle : 0.551 11.791 89568 Z= 0.303 Chirality : 0.038 0.337 10995 Planarity : 0.003 0.062 12150 Dihedral : 3.977 36.574 9216 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.61 % Allowed : 16.07 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.15 (0.09), residues: 8769 helix: 3.34 (0.06), residues: 6330 sheet: 0.56 (0.22), residues: 462 loop : -2.08 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE W 474 TYR 0.023 0.002 TYR V 511 ARG 0.009 0.000 ARG W 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1288 time to evaluate : 5.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.5603 (OUTLIER) cc_final: 0.2722 (tp40) REVERT: A 36 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7959 (pp) REVERT: A 161 LYS cc_start: 0.8980 (mmtm) cc_final: 0.8774 (mmtm) REVERT: A 459 ASP cc_start: 0.8132 (p0) cc_final: 0.7729 (p0) REVERT: A 473 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8292 (mtpp) REVERT: A 492 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7469 (mp) REVERT: B 84 GLU cc_start: 0.8167 (tp30) cc_final: 0.7898 (tp30) REVERT: B 486 ASP cc_start: 0.7826 (p0) cc_final: 0.7344 (p0) REVERT: B 536 ASN cc_start: 0.8361 (m110) cc_final: 0.7700 (p0) REVERT: C 8 ASN cc_start: 0.8457 (t0) cc_final: 0.8234 (t0) REVERT: C 459 ASP cc_start: 0.8096 (p0) cc_final: 0.7712 (p0) REVERT: D 32 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7257 (mm) REVERT: D 117 LYS cc_start: 0.8742 (tptp) cc_final: 0.8331 (tptp) REVERT: D 121 ASP cc_start: 0.7874 (m-30) cc_final: 0.7653 (m-30) REVERT: D 122 GLU cc_start: 0.8949 (tp30) cc_final: 0.8686 (tp30) REVERT: D 493 ASN cc_start: 0.8583 (m110) cc_final: 0.8215 (m-40) REVERT: N 145 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7640 (mmmt) REVERT: N 518 MET cc_start: 0.7585 (tmm) cc_final: 0.7131 (tmm) REVERT: X 6 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8359 (m-40) REVERT: X 94 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8063 (tm-30) REVERT: X 114 ASP cc_start: 0.8862 (m-30) cc_final: 0.8526 (m-30) REVERT: X 176 ASN cc_start: 0.8800 (p0) cc_final: 0.8426 (p0) REVERT: X 494 ASN cc_start: 0.8278 (m110) cc_final: 0.8061 (m110) REVERT: E 15 GLN cc_start: 0.8900 (mt0) cc_final: 0.8450 (mp10) REVERT: E 101 THR cc_start: 0.9258 (t) cc_final: 0.8789 (m) REVERT: E 459 ASP cc_start: 0.7738 (p0) cc_final: 0.7407 (p0) REVERT: E 461 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8162 (mm) REVERT: E 466 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: E 505 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7238 (mtp180) REVERT: O 79 GLU cc_start: 0.8241 (tt0) cc_final: 0.7655 (mt-10) REVERT: O 459 ASP cc_start: 0.6880 (p0) cc_final: 0.6530 (p0) REVERT: Y 472 ASP cc_start: 0.8115 (m-30) cc_final: 0.7793 (m-30) REVERT: F 21 ASN cc_start: 0.8296 (t0) cc_final: 0.8049 (t0) REVERT: P 30 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7438 (tm-30) REVERT: P 141 ASP cc_start: 0.7611 (p0) cc_final: 0.7077 (t0) REVERT: P 174 ASN cc_start: 0.8147 (t0) cc_final: 0.7915 (t0) REVERT: P 501 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7654 (mm-30) REVERT: Z 72 ILE cc_start: 0.9012 (mt) cc_final: 0.8792 (mt) REVERT: Z 114 ASP cc_start: 0.7957 (m-30) cc_final: 0.7610 (m-30) REVERT: Z 117 LYS cc_start: 0.8877 (tppt) cc_final: 0.8468 (tppt) REVERT: Z 121 ASP cc_start: 0.8689 (m-30) cc_final: 0.8356 (m-30) REVERT: Z 173 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.6948 (m-10) REVERT: G 534 LYS cc_start: 0.8881 (mttm) cc_final: 0.8602 (mtpt) REVERT: Q 22 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7859 (tm-30) REVERT: Q 30 GLU cc_start: 0.8331 (tt0) cc_final: 0.8043 (tt0) REVERT: Q 140 LYS cc_start: 0.8249 (tttm) cc_final: 0.8000 (ttmm) REVERT: a 30 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7837 (tt0) REVERT: a 140 LYS cc_start: 0.7684 (pttt) cc_final: 0.7309 (pttp) REVERT: H 473 LYS cc_start: 0.8578 (ptmm) cc_final: 0.8237 (ptpt) REVERT: R 70 ASP cc_start: 0.7097 (m-30) cc_final: 0.6833 (m-30) REVERT: R 486 ASP cc_start: 0.7891 (p0) cc_final: 0.7648 (p0) REVERT: R 501 GLU cc_start: 0.8073 (tt0) cc_final: 0.7828 (tt0) REVERT: b 94 GLU cc_start: 0.7291 (tt0) cc_final: 0.6903 (tt0) REVERT: b 117 LYS cc_start: 0.8801 (tptt) cc_final: 0.8188 (tppt) REVERT: b 121 ASP cc_start: 0.8269 (m-30) cc_final: 0.7927 (m-30) REVERT: S 140 LYS cc_start: 0.8308 (tptt) cc_final: 0.7977 (tppt) REVERT: S 514 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8054 (mm-30) REVERT: c 70 ASP cc_start: 0.7883 (m-30) cc_final: 0.7659 (m-30) REVERT: J 514 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7553 (mp0) REVERT: d 52 ASN cc_start: 0.7865 (t0) cc_final: 0.7536 (t0) REVERT: d 70 ASP cc_start: 0.7991 (m-30) cc_final: 0.7653 (m-30) REVERT: d 84 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8432 (mm-30) REVERT: d 90 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7896 (mm-40) REVERT: d 115 GLU cc_start: 0.8737 (tp30) cc_final: 0.8483 (tp30) REVERT: d 117 LYS cc_start: 0.8651 (tppt) cc_final: 0.8100 (tptp) REVERT: K 154 GLN cc_start: 0.7326 (pt0) cc_final: 0.6540 (tt0) REVERT: U 82 LEU cc_start: 0.8935 (mm) cc_final: 0.8522 (mm) REVERT: e 94 GLU cc_start: 0.8529 (tt0) cc_final: 0.8067 (mm-30) REVERT: e 115 GLU cc_start: 0.8367 (tp30) cc_final: 0.8113 (tp30) REVERT: e 144 MET cc_start: 0.8844 (ttm) cc_final: 0.8440 (ttm) REVERT: L 70 ASP cc_start: 0.7910 (m-30) cc_final: 0.7494 (m-30) REVERT: L 159 ASP cc_start: 0.7327 (p0) cc_final: 0.6923 (p0) REVERT: f 122 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8216 (tm-30) REVERT: f 520 LYS cc_start: 0.7608 (mttt) cc_final: 0.7126 (mmtt) REVERT: M 42 LYS cc_start: 0.7721 (ptmm) cc_final: 0.6731 (tptt) REVERT: M 131 GLN cc_start: 0.8565 (pm20) cc_final: 0.8117 (pt0) REVERT: M 466 ASP cc_start: 0.8231 (t0) cc_final: 0.7851 (t0) REVERT: W 122 GLU cc_start: 0.8300 (tp30) cc_final: 0.8019 (tp30) REVERT: g 115 GLU cc_start: 0.8239 (tt0) cc_final: 0.7872 (tt0) REVERT: g 504 SER cc_start: 0.9062 (t) cc_final: 0.8714 (p) REVERT: g 537 GLN cc_start: 0.7512 (mp10) cc_final: 0.7147 (mp10) outliers start: 191 outliers final: 135 residues processed: 1399 average time/residue: 0.5818 time to fit residues: 1409.4514 Evaluate side-chains 1350 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1207 time to evaluate : 5.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 542 VAL Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 157 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 541 GLN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 489 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 516 SER Chi-restraints excluded: chain P residue 546 LEU Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 154 GLN Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 173 PHE Chi-restraints excluded: chain Z residue 534 LYS Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 476 SER Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 466 ASP Chi-restraints excluded: chain H residue 537 GLN Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 155 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 144 MET Chi-restraints excluded: chain b residue 481 VAL Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 154 GLN Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 57 ASN Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 461 LEU Chi-restraints excluded: chain c residue 481 VAL Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 542 VAL Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 155 THR Chi-restraints excluded: chain d residue 464 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain d residue 545 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 504 SER Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 489 VAL Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 498 ASN Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 108 ASP Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 170 LEU Chi-restraints excluded: chain g residue 543 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 690 optimal weight: 7.9990 chunk 470 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 617 optimal weight: 0.8980 chunk 342 optimal weight: 4.9990 chunk 707 optimal weight: 5.9990 chunk 573 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 423 optimal weight: 0.9990 chunk 744 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 3 GLN C 69 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 525 GLN N 98 GLN X 48 GLN X 482 GLN X 537 GLN X 547 GLN E 21 ASN O 540 GLN F 22 GLN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN G 16 ASN Q 498 ASN H 154 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 GLN R 154 GLN b 174 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN J 63 GLN J 67 ASN J 76 GLN T 39 ASN d 522 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 21 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 498 ASN ** M 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 66210 Z= 0.265 Angle : 0.563 11.518 89568 Z= 0.308 Chirality : 0.039 0.313 10995 Planarity : 0.003 0.062 12150 Dihedral : 4.003 36.657 9216 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.92 % Allowed : 17.02 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.16 (0.09), residues: 8769 helix: 3.35 (0.06), residues: 6330 sheet: 0.53 (0.22), residues: 462 loop : -2.07 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE c 474 TYR 0.021 0.002 TYR O 511 ARG 0.007 0.000 ARG H 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 1274 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.5617 (OUTLIER) cc_final: 0.3051 (tp40) REVERT: A 36 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7931 (pp) REVERT: A 459 ASP cc_start: 0.8177 (p0) cc_final: 0.7777 (p0) REVERT: A 473 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8298 (mtpp) REVERT: A 492 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7527 (mp) REVERT: B 84 GLU cc_start: 0.8159 (tp30) cc_final: 0.7901 (tp30) REVERT: B 459 ASP cc_start: 0.7989 (m-30) cc_final: 0.7716 (t70) REVERT: B 486 ASP cc_start: 0.7881 (p0) cc_final: 0.7420 (p0) REVERT: B 536 ASN cc_start: 0.8405 (m110) cc_final: 0.7864 (p0) REVERT: C 8 ASN cc_start: 0.8472 (t0) cc_final: 0.8248 (t0) REVERT: C 42 LYS cc_start: 0.8040 (tptp) cc_final: 0.7815 (tptp) REVERT: C 459 ASP cc_start: 0.8107 (p0) cc_final: 0.7721 (p0) REVERT: D 21 ASN cc_start: 0.9012 (t0) cc_final: 0.8732 (t0) REVERT: D 117 LYS cc_start: 0.8739 (tptp) cc_final: 0.8223 (tptp) REVERT: D 121 ASP cc_start: 0.7852 (m-30) cc_final: 0.7602 (m-30) REVERT: D 493 ASN cc_start: 0.8604 (m110) cc_final: 0.8211 (m-40) REVERT: N 145 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7602 (mmmt) REVERT: N 518 MET cc_start: 0.7599 (tmm) cc_final: 0.7133 (tmm) REVERT: X 6 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8388 (m-40) REVERT: X 94 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7913 (tm-30) REVERT: X 114 ASP cc_start: 0.8885 (m-30) cc_final: 0.8529 (m-30) REVERT: X 176 ASN cc_start: 0.8758 (p0) cc_final: 0.8408 (p0) REVERT: X 494 ASN cc_start: 0.8275 (m110) cc_final: 0.8067 (m110) REVERT: E 15 GLN cc_start: 0.8914 (mt0) cc_final: 0.8586 (mp10) REVERT: E 459 ASP cc_start: 0.7743 (p0) cc_final: 0.7419 (p0) REVERT: E 461 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (mm) REVERT: E 466 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: E 505 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7361 (mtp180) REVERT: O 79 GLU cc_start: 0.8268 (tt0) cc_final: 0.7693 (mt-10) REVERT: O 459 ASP cc_start: 0.6924 (p0) cc_final: 0.6568 (p0) REVERT: O 492 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8026 (mm) REVERT: Y 472 ASP cc_start: 0.8152 (m-30) cc_final: 0.7825 (m-30) REVERT: F 21 ASN cc_start: 0.8360 (t0) cc_final: 0.8097 (t0) REVERT: P 30 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7430 (tm-30) REVERT: P 122 GLU cc_start: 0.9064 (tp30) cc_final: 0.8766 (tp30) REVERT: P 141 ASP cc_start: 0.7655 (p0) cc_final: 0.7131 (t0) REVERT: P 174 ASN cc_start: 0.8157 (t0) cc_final: 0.7924 (t0) REVERT: Z 72 ILE cc_start: 0.9051 (mt) cc_final: 0.8807 (mt) REVERT: Z 114 ASP cc_start: 0.7984 (m-30) cc_final: 0.7603 (m-30) REVERT: Z 117 LYS cc_start: 0.8874 (tppt) cc_final: 0.8500 (tppt) REVERT: Z 121 ASP cc_start: 0.8725 (m-30) cc_final: 0.8366 (m-30) REVERT: Z 173 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6999 (m-10) REVERT: G 534 LYS cc_start: 0.8898 (mttm) cc_final: 0.8596 (mtpt) REVERT: Q 22 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7916 (tm-30) REVERT: Q 30 GLU cc_start: 0.8339 (tt0) cc_final: 0.8050 (tt0) REVERT: Q 140 LYS cc_start: 0.8247 (tttm) cc_final: 0.7994 (ttmm) REVERT: a 30 GLU cc_start: 0.8634 (tm-30) cc_final: 0.7871 (tt0) REVERT: a 140 LYS cc_start: 0.7727 (pttt) cc_final: 0.7352 (pttp) REVERT: H 473 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8249 (ptpt) REVERT: H 501 GLU cc_start: 0.7917 (tt0) cc_final: 0.7631 (tt0) REVERT: R 70 ASP cc_start: 0.7122 (m-30) cc_final: 0.6837 (m-30) REVERT: R 486 ASP cc_start: 0.7913 (p0) cc_final: 0.7684 (p0) REVERT: R 501 GLU cc_start: 0.8081 (tt0) cc_final: 0.7843 (tt0) REVERT: b 94 GLU cc_start: 0.7204 (tt0) cc_final: 0.6819 (tt0) REVERT: b 117 LYS cc_start: 0.8822 (tptt) cc_final: 0.8188 (tppt) REVERT: b 121 ASP cc_start: 0.8284 (m-30) cc_final: 0.7924 (m-30) REVERT: S 140 LYS cc_start: 0.8314 (tptt) cc_final: 0.7998 (tppt) REVERT: S 514 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8069 (mm-30) REVERT: c 70 ASP cc_start: 0.7897 (m-30) cc_final: 0.7662 (m-30) REVERT: c 79 GLU cc_start: 0.8336 (tp30) cc_final: 0.8039 (tp30) REVERT: d 52 ASN cc_start: 0.7874 (t0) cc_final: 0.7504 (t0) REVERT: d 70 ASP cc_start: 0.7926 (m-30) cc_final: 0.7616 (m-30) REVERT: d 84 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8450 (mm-30) REVERT: d 90 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7895 (mm-40) REVERT: d 115 GLU cc_start: 0.8703 (tp30) cc_final: 0.8433 (tp30) REVERT: d 131 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: K 154 GLN cc_start: 0.7379 (pt0) cc_final: 0.6550 (tt0) REVERT: K 455 GLU cc_start: 0.7405 (tp30) cc_final: 0.6895 (pm20) REVERT: U 82 LEU cc_start: 0.8947 (mm) cc_final: 0.8529 (mm) REVERT: e 94 GLU cc_start: 0.8547 (tt0) cc_final: 0.8093 (mm-30) REVERT: e 115 GLU cc_start: 0.8375 (tp30) cc_final: 0.8109 (tp30) REVERT: e 144 MET cc_start: 0.8791 (ttm) cc_final: 0.8532 (ttm) REVERT: L 70 ASP cc_start: 0.7910 (m-30) cc_final: 0.7484 (m-30) REVERT: f 122 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8226 (tm-30) REVERT: f 520 LYS cc_start: 0.7618 (mttt) cc_final: 0.7134 (mmtt) REVERT: M 42 LYS cc_start: 0.7736 (ptmm) cc_final: 0.6725 (tptt) REVERT: M 131 GLN cc_start: 0.8540 (pm20) cc_final: 0.8077 (pt0) REVERT: W 122 GLU cc_start: 0.8298 (tp30) cc_final: 0.8013 (tp30) REVERT: g 106 ASP cc_start: 0.8521 (p0) cc_final: 0.8248 (p0) REVERT: g 115 GLU cc_start: 0.8273 (tt0) cc_final: 0.7915 (tt0) REVERT: g 504 SER cc_start: 0.9077 (t) cc_final: 0.8712 (p) REVERT: g 537 GLN cc_start: 0.7527 (mp10) cc_final: 0.7176 (mp10) outliers start: 214 outliers final: 159 residues processed: 1397 average time/residue: 0.5777 time to fit residues: 1398.0666 Evaluate side-chains 1380 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1212 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 542 VAL Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 157 THR Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 103 THR Chi-restraints excluded: chain Y residue 154 GLN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 489 VAL Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 516 SER Chi-restraints excluded: chain P residue 546 LEU Chi-restraints excluded: chain Z residue 95 LEU Chi-restraints excluded: chain Z residue 154 GLN Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 173 PHE Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 457 THR Chi-restraints excluded: chain Q residue 476 SER Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain a residue 471 ILE Chi-restraints excluded: chain a residue 503 GLN Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 154 GLN Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 466 ASP Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 144 MET Chi-restraints excluded: chain b residue 481 VAL Chi-restraints excluded: chain b residue 497 THR Chi-restraints excluded: chain b residue 542 VAL Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 52 ASN Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 154 GLN Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 57 ASN Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 461 LEU Chi-restraints excluded: chain c residue 492 LEU Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 542 VAL Chi-restraints excluded: chain c residue 545 LEU Chi-restraints excluded: chain c residue 547 GLN Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 155 THR Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 464 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain d residue 534 LYS Chi-restraints excluded: chain d residue 545 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 513 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 504 SER Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 489 VAL Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 108 ASP Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 543 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 279 optimal weight: 5.9990 chunk 746 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 486 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 830 optimal weight: 0.9980 chunk 689 optimal weight: 0.0570 chunk 384 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 435 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 3 GLN C 69 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN N 98 GLN X 48 GLN E 21 ASN O 540 GLN F 22 GLN F 147 GLN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 16 ASN G 16 ASN a 525 GLN a 529 ASN H 154 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN b 537 GLN S 52 ASN S 547 GLN T 86 ASN d 76 GLN d 526 GLN U 21 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 113 GLN e 16 ASN L 154 GLN V 21 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 522 GLN M 494 ASN ** M 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 6 ASN W 171 ASN g 69 ASN g 147 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 66210 Z= 0.179 Angle : 0.534 13.284 89568 Z= 0.293 Chirality : 0.037 0.317 10995 Planarity : 0.003 0.060 12150 Dihedral : 3.870 36.090 9216 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.24 % Allowed : 18.24 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.43 (0.09), residues: 8769 helix: 3.55 (0.06), residues: 6330 sheet: 0.67 (0.22), residues: 462 loop : -2.00 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE c 474 TYR 0.018 0.001 TYR S 511 ARG 0.009 0.000 ARG W 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1528 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1365 time to evaluate : 5.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.5390 (OUTLIER) cc_final: 0.2825 (tp40) REVERT: A 36 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8038 (pp) REVERT: A 459 ASP cc_start: 0.8064 (p0) cc_final: 0.7655 (p0) REVERT: A 486 ASP cc_start: 0.8213 (p0) cc_final: 0.8012 (p0) REVERT: A 492 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7412 (mp) REVERT: B 459 ASP cc_start: 0.8050 (m-30) cc_final: 0.7710 (t70) REVERT: B 486 ASP cc_start: 0.7764 (p0) cc_final: 0.7344 (p0) REVERT: B 536 ASN cc_start: 0.8394 (m110) cc_final: 0.7731 (p0) REVERT: C 30 GLU cc_start: 0.8337 (tt0) cc_final: 0.7886 (tm-30) REVERT: C 122 GLU cc_start: 0.7957 (tp30) cc_final: 0.7729 (tp30) REVERT: D 21 ASN cc_start: 0.8955 (t0) cc_final: 0.8664 (t0) REVERT: D 32 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7138 (mm) REVERT: D 37 ARG cc_start: 0.7377 (ttp80) cc_final: 0.7014 (ttp80) REVERT: D 117 LYS cc_start: 0.8760 (tptp) cc_final: 0.8531 (tptp) REVERT: D 493 ASN cc_start: 0.8604 (m110) cc_final: 0.7909 (m110) REVERT: N 145 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7413 (mmmt) REVERT: N 518 MET cc_start: 0.7595 (tmm) cc_final: 0.7141 (tmm) REVERT: X 94 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8083 (tm-30) REVERT: X 114 ASP cc_start: 0.8859 (m-30) cc_final: 0.8489 (m-30) REVERT: X 176 ASN cc_start: 0.8834 (p0) cc_final: 0.8576 (p0) REVERT: E 21 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8289 (t0) REVERT: E 459 ASP cc_start: 0.7624 (p0) cc_final: 0.7113 (p0) REVERT: E 461 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7998 (mm) REVERT: E 466 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: O 79 GLU cc_start: 0.8281 (tt0) cc_final: 0.7712 (mt-10) REVERT: O 459 ASP cc_start: 0.6696 (p0) cc_final: 0.6359 (p0) REVERT: Y 472 ASP cc_start: 0.8076 (m-30) cc_final: 0.7717 (m-30) REVERT: P 30 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7414 (tm-30) REVERT: P 122 GLU cc_start: 0.9028 (tp30) cc_final: 0.8697 (tp30) REVERT: P 141 ASP cc_start: 0.7494 (p0) cc_final: 0.6927 (t0) REVERT: P 174 ASN cc_start: 0.7977 (t0) cc_final: 0.7747 (t0) REVERT: Z 72 ILE cc_start: 0.8997 (mt) cc_final: 0.8741 (mt) REVERT: Z 114 ASP cc_start: 0.7991 (m-30) cc_final: 0.7741 (m-30) REVERT: Z 117 LYS cc_start: 0.8870 (tppt) cc_final: 0.8491 (tppt) REVERT: Z 121 ASP cc_start: 0.8641 (m-30) cc_final: 0.8265 (m-30) REVERT: Z 173 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: G 534 LYS cc_start: 0.8841 (mttm) cc_final: 0.8568 (mtpt) REVERT: Q 22 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7794 (tm-30) REVERT: Q 30 GLU cc_start: 0.8264 (tt0) cc_final: 0.7978 (tt0) REVERT: Q 117 LYS cc_start: 0.8968 (tptp) cc_final: 0.8762 (tptt) REVERT: Q 140 LYS cc_start: 0.8220 (tttm) cc_final: 0.7967 (ttmm) REVERT: Q 161 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8926 (mttt) REVERT: a 30 GLU cc_start: 0.8621 (tm-30) cc_final: 0.7896 (tt0) REVERT: a 31 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8543 (ttm170) REVERT: a 140 LYS cc_start: 0.7694 (pttt) cc_final: 0.7339 (pttp) REVERT: H 157 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8893 (m) REVERT: H 473 LYS cc_start: 0.8534 (ptmm) cc_final: 0.8178 (ptpt) REVERT: H 501 GLU cc_start: 0.7875 (tt0) cc_final: 0.7634 (tt0) REVERT: R 70 ASP cc_start: 0.7135 (m-30) cc_final: 0.6872 (m-30) REVERT: R 486 ASP cc_start: 0.7835 (p0) cc_final: 0.7590 (p0) REVERT: R 501 GLU cc_start: 0.8084 (tt0) cc_final: 0.7841 (tt0) REVERT: b 94 GLU cc_start: 0.7271 (tt0) cc_final: 0.6846 (tt0) REVERT: b 117 LYS cc_start: 0.8823 (tptt) cc_final: 0.8128 (tppt) REVERT: b 121 ASP cc_start: 0.8260 (m-30) cc_final: 0.7902 (m-30) REVERT: I 122 GLU cc_start: 0.9119 (tp30) cc_final: 0.8893 (tp30) REVERT: S 140 LYS cc_start: 0.8307 (tptt) cc_final: 0.7988 (tppt) REVERT: c 70 ASP cc_start: 0.7826 (m-30) cc_final: 0.7612 (m-30) REVERT: c 79 GLU cc_start: 0.8286 (tp30) cc_final: 0.7999 (tp30) REVERT: c 84 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7878 (mm-30) REVERT: c 129 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.5802 (mp10) REVERT: T 30 GLU cc_start: 0.7944 (tp30) cc_final: 0.7733 (tp30) REVERT: d 52 ASN cc_start: 0.7773 (t0) cc_final: 0.7412 (t0) REVERT: d 70 ASP cc_start: 0.7894 (m-30) cc_final: 0.7569 (m-30) REVERT: d 84 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8394 (mm-30) REVERT: K 154 GLN cc_start: 0.7286 (pt0) cc_final: 0.6588 (tt0) REVERT: K 455 GLU cc_start: 0.7258 (tp30) cc_final: 0.6815 (pm20) REVERT: U 82 LEU cc_start: 0.8941 (mm) cc_final: 0.8545 (mm) REVERT: e 94 GLU cc_start: 0.8463 (tt0) cc_final: 0.7995 (mm-30) REVERT: e 115 GLU cc_start: 0.8353 (tp30) cc_final: 0.8108 (tp30) REVERT: e 144 MET cc_start: 0.8691 (ttm) cc_final: 0.8438 (ttm) REVERT: L 70 ASP cc_start: 0.7927 (m-30) cc_final: 0.7474 (m-30) REVERT: L 507 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.5769 (pp30) REVERT: f 122 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8231 (tm-30) REVERT: f 520 LYS cc_start: 0.7511 (mttt) cc_final: 0.7057 (mmtt) REVERT: M 42 LYS cc_start: 0.7692 (ptmm) cc_final: 0.6760 (tptt) REVERT: M 122 GLU cc_start: 0.8579 (tp30) cc_final: 0.8372 (tp30) REVERT: M 466 ASP cc_start: 0.8169 (t70) cc_final: 0.7798 (t0) REVERT: M 534 LYS cc_start: 0.8703 (ptmt) cc_final: 0.8444 (mtmt) REVERT: W 122 GLU cc_start: 0.8233 (tp30) cc_final: 0.7929 (tp30) REVERT: g 106 ASP cc_start: 0.8402 (p0) cc_final: 0.8139 (p0) REVERT: g 115 GLU cc_start: 0.8287 (tt0) cc_final: 0.8019 (tt0) REVERT: g 504 SER cc_start: 0.9044 (t) cc_final: 0.8663 (p) REVERT: g 537 GLN cc_start: 0.7501 (mp10) cc_final: 0.7233 (mp10) outliers start: 163 outliers final: 109 residues processed: 1452 average time/residue: 0.5897 time to fit residues: 1483.4180 Evaluate side-chains 1374 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1254 time to evaluate : 5.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 166 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 546 LEU Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 154 GLN Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 173 PHE Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 457 THR Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 141 ASP Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain a residue 471 ILE Chi-restraints excluded: chain a residue 503 GLN Chi-restraints excluded: chain a residue 525 GLN Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 466 ASP Chi-restraints excluded: chain H residue 546 LEU Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 155 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 52 ASN Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 129 GLN Chi-restraints excluded: chain c residue 492 LEU Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 155 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 464 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 155 THR Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 504 SER Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 489 VAL Chi-restraints excluded: chain L residue 507 GLN Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 543 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 800 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 472 optimal weight: 6.9990 chunk 606 optimal weight: 4.9990 chunk 469 optimal weight: 0.7980 chunk 698 optimal weight: 1.9990 chunk 463 optimal weight: 0.9990 chunk 826 optimal weight: 2.9990 chunk 517 optimal weight: 6.9990 chunk 504 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 174 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 526 GLN X 17 ASN O 57 ASN O 540 GLN F 21 ASN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 498 ASN a 503 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 52 ASN ** c 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 21 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN V 21 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 171 ASN g 147 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 66210 Z= 0.252 Angle : 0.568 13.620 89568 Z= 0.310 Chirality : 0.039 0.322 10995 Planarity : 0.003 0.062 12150 Dihedral : 3.910 36.542 9216 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.05 % Favored : 95.94 % Rotamer: Outliers : 2.49 % Allowed : 18.72 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.36 (0.09), residues: 8769 helix: 3.48 (0.06), residues: 6330 sheet: 0.67 (0.22), residues: 462 loop : -1.99 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE M 173 TYR 0.024 0.002 TYR S 511 ARG 0.007 0.000 ARG H 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1272 time to evaluate : 5.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8020 (pp) REVERT: A 459 ASP cc_start: 0.8148 (p0) cc_final: 0.7709 (p0) REVERT: A 492 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7527 (mp) REVERT: B 84 GLU cc_start: 0.8141 (tp30) cc_final: 0.7854 (tp30) REVERT: B 459 ASP cc_start: 0.8003 (m-30) cc_final: 0.7667 (t70) REVERT: B 486 ASP cc_start: 0.7755 (p0) cc_final: 0.7315 (p0) REVERT: B 536 ASN cc_start: 0.8432 (m110) cc_final: 0.7749 (p0) REVERT: C 122 GLU cc_start: 0.8071 (tp30) cc_final: 0.7741 (tp30) REVERT: D 20 LYS cc_start: 0.8903 (mttm) cc_final: 0.8509 (mttp) REVERT: D 21 ASN cc_start: 0.8968 (t0) cc_final: 0.8672 (t0) REVERT: D 32 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7216 (mm) REVERT: D 117 LYS cc_start: 0.8738 (tptp) cc_final: 0.8422 (tptp) REVERT: D 121 ASP cc_start: 0.7869 (m-30) cc_final: 0.7631 (m-30) REVERT: D 493 ASN cc_start: 0.8598 (m110) cc_final: 0.7909 (m110) REVERT: D 520 LYS cc_start: 0.8985 (ptmm) cc_final: 0.8772 (ptmm) REVERT: N 145 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7539 (mmmt) REVERT: N 170 LEU cc_start: 0.7572 (pp) cc_final: 0.7306 (pp) REVERT: N 518 MET cc_start: 0.7626 (tmm) cc_final: 0.7147 (tmm) REVERT: N 529 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7938 (m110) REVERT: X 6 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8353 (m-40) REVERT: X 21 ASN cc_start: 0.8719 (t0) cc_final: 0.8381 (t0) REVERT: X 94 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8077 (tm-30) REVERT: X 114 ASP cc_start: 0.8900 (m-30) cc_final: 0.8528 (m-30) REVERT: X 176 ASN cc_start: 0.8816 (p0) cc_final: 0.8576 (p0) REVERT: E 459 ASP cc_start: 0.7736 (p0) cc_final: 0.7400 (p0) REVERT: E 461 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8025 (mm) REVERT: E 466 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: O 79 GLU cc_start: 0.8300 (tt0) cc_final: 0.7726 (mt-10) REVERT: O 459 ASP cc_start: 0.6803 (p0) cc_final: 0.6464 (p0) REVERT: Y 472 ASP cc_start: 0.8121 (m-30) cc_final: 0.7759 (m-30) REVERT: P 30 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7384 (tm-30) REVERT: P 141 ASP cc_start: 0.7594 (p0) cc_final: 0.7111 (t0) REVERT: P 174 ASN cc_start: 0.8093 (t0) cc_final: 0.7863 (t0) REVERT: Z 72 ILE cc_start: 0.9037 (mt) cc_final: 0.8793 (mt) REVERT: Z 114 ASP cc_start: 0.8025 (m-30) cc_final: 0.7520 (m-30) REVERT: Z 117 LYS cc_start: 0.8901 (tppt) cc_final: 0.8547 (tppt) REVERT: Z 121 ASP cc_start: 0.8692 (m-30) cc_final: 0.8340 (m-30) REVERT: Z 173 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7227 (m-10) REVERT: G 94 GLU cc_start: 0.7800 (tp30) cc_final: 0.7338 (tp30) REVERT: G 173 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7889 (t80) REVERT: G 534 LYS cc_start: 0.8892 (mttm) cc_final: 0.8588 (mtpt) REVERT: Q 22 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7875 (tm-30) REVERT: Q 30 GLU cc_start: 0.8323 (tt0) cc_final: 0.8028 (tt0) REVERT: Q 140 LYS cc_start: 0.8260 (tttm) cc_final: 0.8007 (ttmm) REVERT: a 30 GLU cc_start: 0.8637 (tm-30) cc_final: 0.7869 (tt0) REVERT: a 140 LYS cc_start: 0.7772 (pttt) cc_final: 0.7414 (pttp) REVERT: H 473 LYS cc_start: 0.8576 (ptmm) cc_final: 0.8236 (ptpt) REVERT: H 501 GLU cc_start: 0.7941 (tt0) cc_final: 0.7668 (tt0) REVERT: R 70 ASP cc_start: 0.7119 (m-30) cc_final: 0.6836 (m-30) REVERT: R 486 ASP cc_start: 0.7897 (p0) cc_final: 0.7663 (p0) REVERT: R 501 GLU cc_start: 0.8100 (tt0) cc_final: 0.7850 (tt0) REVERT: b 94 GLU cc_start: 0.7154 (tt0) cc_final: 0.6745 (tt0) REVERT: b 117 LYS cc_start: 0.8845 (tptt) cc_final: 0.8183 (tppt) REVERT: b 121 ASP cc_start: 0.8280 (m-30) cc_final: 0.7944 (m-30) REVERT: I 122 GLU cc_start: 0.9150 (tp30) cc_final: 0.8943 (tp30) REVERT: S 140 LYS cc_start: 0.8283 (tptt) cc_final: 0.8000 (tppt) REVERT: c 70 ASP cc_start: 0.7876 (m-30) cc_final: 0.7643 (m-30) REVERT: c 79 GLU cc_start: 0.8300 (tp30) cc_final: 0.8007 (tp30) REVERT: c 129 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.5766 (mp10) REVERT: J 154 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6344 (tp40) REVERT: T 30 GLU cc_start: 0.8031 (tp30) cc_final: 0.7775 (tp30) REVERT: T 537 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7825 (tp40) REVERT: d 52 ASN cc_start: 0.7859 (t0) cc_final: 0.7499 (t0) REVERT: d 70 ASP cc_start: 0.8001 (m-30) cc_final: 0.7667 (m-30) REVERT: d 131 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: d 154 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: K 154 GLN cc_start: 0.7371 (pt0) cc_final: 0.6557 (tt0) REVERT: K 455 GLU cc_start: 0.7371 (tp30) cc_final: 0.6834 (pm20) REVERT: U 82 LEU cc_start: 0.8945 (mm) cc_final: 0.8542 (mm) REVERT: e 94 GLU cc_start: 0.8484 (tt0) cc_final: 0.8005 (mm-30) REVERT: e 115 GLU cc_start: 0.8365 (tp30) cc_final: 0.8104 (tp30) REVERT: e 144 MET cc_start: 0.8669 (ttm) cc_final: 0.8410 (ttm) REVERT: L 70 ASP cc_start: 0.7939 (m-30) cc_final: 0.7487 (m-30) REVERT: L 459 ASP cc_start: 0.7828 (m-30) cc_final: 0.7559 (m-30) REVERT: L 507 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.5788 (pp30) REVERT: f 117 LYS cc_start: 0.9014 (tppt) cc_final: 0.8279 (tppt) REVERT: f 122 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8228 (tm-30) REVERT: f 520 LYS cc_start: 0.7559 (mttt) cc_final: 0.7100 (mmtt) REVERT: M 42 LYS cc_start: 0.7724 (ptmm) cc_final: 0.6736 (tptt) REVERT: M 131 GLN cc_start: 0.8556 (pm20) cc_final: 0.8093 (pt0) REVERT: M 534 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8430 (mtmt) REVERT: W 122 GLU cc_start: 0.8264 (tp30) cc_final: 0.7980 (tp30) REVERT: g 106 ASP cc_start: 0.8393 (p0) cc_final: 0.8166 (p0) REVERT: g 115 GLU cc_start: 0.8254 (tt0) cc_final: 0.7930 (tt0) REVERT: g 504 SER cc_start: 0.9064 (t) cc_final: 0.8696 (p) REVERT: g 514 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: g 537 GLN cc_start: 0.7565 (mp10) cc_final: 0.7328 (mp10) outliers start: 182 outliers final: 133 residues processed: 1379 average time/residue: 0.5860 time to fit residues: 1398.6027 Evaluate side-chains 1382 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1234 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 529 ASN Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 516 SER Chi-restraints excluded: chain P residue 546 LEU Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 154 GLN Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 173 PHE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 174 ASN Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 457 THR Chi-restraints excluded: chain Q residue 476 SER Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 141 ASP Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain a residue 471 ILE Chi-restraints excluded: chain a residue 503 GLN Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain R residue 155 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 52 ASN Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 154 GLN Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 57 ASN Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 129 GLN Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 461 LEU Chi-restraints excluded: chain c residue 492 LEU Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 510 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 155 THR Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 154 GLN Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 464 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 513 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 155 THR Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 504 SER Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 489 VAL Chi-restraints excluded: chain L residue 507 GLN Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 108 ASP Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 458 SER Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 514 GLU Chi-restraints excluded: chain g residue 529 ASN Chi-restraints excluded: chain g residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 511 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 chunk 493 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 525 optimal weight: 3.9990 chunk 563 optimal weight: 10.0000 chunk 408 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 650 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 522 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 526 GLN N 537 GLN X 21 ASN X 547 GLN E 21 ASN E 154 GLN O 540 GLN F 21 ASN F 22 GLN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 503 GLN a 529 ASN H 498 ASN H 537 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 537 GLN S 52 ASN ** c 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN d 526 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 133 ASN e 16 ASN L 48 GLN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 6 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 66210 Z= 0.371 Angle : 0.642 13.419 89568 Z= 0.349 Chirality : 0.042 0.317 10995 Planarity : 0.003 0.063 12150 Dihedral : 4.184 36.553 9216 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.33 % Favored : 95.66 % Rotamer: Outliers : 2.80 % Allowed : 18.82 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.03 (0.09), residues: 8769 helix: 3.25 (0.06), residues: 6315 sheet: 0.49 (0.22), residues: 462 loop : -2.10 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE c 474 TYR 0.027 0.002 TYR O 511 ARG 0.007 0.001 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1212 time to evaluate : 5.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.5247 (OUTLIER) cc_final: 0.2812 (tp-100) REVERT: A 36 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8070 (pp) REVERT: A 459 ASP cc_start: 0.8206 (p0) cc_final: 0.7793 (p0) REVERT: A 492 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 42 LYS cc_start: 0.8800 (tptm) cc_final: 0.8599 (tptm) REVERT: B 459 ASP cc_start: 0.8043 (m-30) cc_final: 0.7692 (t70) REVERT: B 486 ASP cc_start: 0.7923 (p0) cc_final: 0.7494 (p0) REVERT: B 536 ASN cc_start: 0.8465 (m110) cc_final: 0.7888 (p0) REVERT: C 30 GLU cc_start: 0.8311 (tt0) cc_final: 0.7844 (tm-30) REVERT: C 122 GLU cc_start: 0.8183 (tp30) cc_final: 0.7731 (tp30) REVERT: D 21 ASN cc_start: 0.8997 (t0) cc_final: 0.8695 (t0) REVERT: D 32 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7304 (mm) REVERT: D 493 ASN cc_start: 0.8585 (m110) cc_final: 0.7913 (m110) REVERT: D 501 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7846 (mm-30) REVERT: N 145 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7450 (mmmt) REVERT: N 518 MET cc_start: 0.7660 (tmm) cc_final: 0.7167 (tmm) REVERT: N 529 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7958 (m110) REVERT: X 6 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8397 (m-40) REVERT: X 94 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7871 (tm-30) REVERT: X 114 ASP cc_start: 0.8940 (m-30) cc_final: 0.8584 (m-30) REVERT: X 176 ASN cc_start: 0.8784 (p0) cc_final: 0.8549 (p0) REVERT: E 459 ASP cc_start: 0.7739 (p0) cc_final: 0.7423 (p0) REVERT: E 461 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8161 (mm) REVERT: E 466 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: O 79 GLU cc_start: 0.8277 (tt0) cc_final: 0.7714 (mt-10) REVERT: O 459 ASP cc_start: 0.7020 (p0) cc_final: 0.6678 (p0) REVERT: Y 472 ASP cc_start: 0.8200 (m-30) cc_final: 0.7864 (m-30) REVERT: F 21 ASN cc_start: 0.8422 (t0) cc_final: 0.8153 (t0) REVERT: P 30 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7476 (tm-30) REVERT: P 122 GLU cc_start: 0.9032 (tp30) cc_final: 0.8832 (tp30) REVERT: P 141 ASP cc_start: 0.7689 (p0) cc_final: 0.7234 (t0) REVERT: P 174 ASN cc_start: 0.8223 (t0) cc_final: 0.7964 (t0) REVERT: Z 72 ILE cc_start: 0.9043 (mt) cc_final: 0.8820 (mt) REVERT: Z 114 ASP cc_start: 0.8168 (m-30) cc_final: 0.7670 (m-30) REVERT: Z 117 LYS cc_start: 0.8877 (tppt) cc_final: 0.8501 (tppt) REVERT: Z 121 ASP cc_start: 0.8790 (m-30) cc_final: 0.8431 (m-30) REVERT: Z 173 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7025 (m-10) REVERT: G 94 GLU cc_start: 0.7951 (tp30) cc_final: 0.7477 (tp30) REVERT: G 173 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7852 (t80) REVERT: G 534 LYS cc_start: 0.8951 (mttm) cc_final: 0.8627 (mtpt) REVERT: Q 22 GLN cc_start: 0.8238 (tm-30) cc_final: 0.8008 (tm-30) REVERT: Q 30 GLU cc_start: 0.8412 (tt0) cc_final: 0.8123 (tt0) REVERT: Q 140 LYS cc_start: 0.8279 (tttm) cc_final: 0.8043 (ttmm) REVERT: a 140 LYS cc_start: 0.7845 (pttt) cc_final: 0.7480 (pttp) REVERT: H 473 LYS cc_start: 0.8685 (ptmm) cc_final: 0.8300 (ptpt) REVERT: H 501 GLU cc_start: 0.7969 (tt0) cc_final: 0.7655 (tt0) REVERT: R 70 ASP cc_start: 0.7121 (m-30) cc_final: 0.6821 (m-30) REVERT: R 140 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8423 (pttt) REVERT: R 486 ASP cc_start: 0.7985 (p0) cc_final: 0.7779 (p0) REVERT: R 501 GLU cc_start: 0.8035 (tt0) cc_final: 0.7786 (tt0) REVERT: b 59 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8187 (mtmt) REVERT: b 94 GLU cc_start: 0.6824 (tt0) cc_final: 0.6494 (tt0) REVERT: b 117 LYS cc_start: 0.8876 (tptt) cc_final: 0.8286 (tppt) REVERT: b 121 ASP cc_start: 0.8337 (m-30) cc_final: 0.7967 (m-30) REVERT: b 501 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: I 140 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8400 (mmmm) REVERT: S 10 LEU cc_start: 0.9236 (mp) cc_final: 0.9019 (mt) REVERT: S 140 LYS cc_start: 0.8363 (tptt) cc_final: 0.8078 (tppt) REVERT: c 70 ASP cc_start: 0.7927 (m-30) cc_final: 0.7686 (m-30) REVERT: c 129 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.5978 (mp10) REVERT: J 154 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6427 (tp40) REVERT: T 30 GLU cc_start: 0.8282 (tp30) cc_final: 0.8016 (tp30) REVERT: T 466 ASP cc_start: 0.8229 (m-30) cc_final: 0.7533 (m-30) REVERT: T 537 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7875 (tp40) REVERT: d 30 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6814 (tp30) REVERT: d 70 ASP cc_start: 0.7998 (m-30) cc_final: 0.7729 (m-30) REVERT: d 117 LYS cc_start: 0.8575 (tppt) cc_final: 0.8052 (tppt) REVERT: d 131 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: d 154 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: K 455 GLU cc_start: 0.7375 (tp30) cc_final: 0.6873 (pm20) REVERT: U 82 LEU cc_start: 0.9022 (mm) cc_final: 0.8665 (mm) REVERT: e 94 GLU cc_start: 0.8569 (tt0) cc_final: 0.8099 (mm-30) REVERT: L 459 ASP cc_start: 0.7801 (m-30) cc_final: 0.7553 (m-30) REVERT: L 507 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.5498 (pp30) REVERT: L 508 ASP cc_start: 0.8438 (m-30) cc_final: 0.8226 (m-30) REVERT: f 117 LYS cc_start: 0.9018 (tppt) cc_final: 0.8291 (tppt) REVERT: f 122 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8148 (tm-30) REVERT: f 520 LYS cc_start: 0.7661 (mttt) cc_final: 0.7167 (mmtt) REVERT: M 42 LYS cc_start: 0.7742 (ptmm) cc_final: 0.6763 (tptt) REVERT: M 131 GLN cc_start: 0.8587 (pm20) cc_final: 0.8157 (pt0) REVERT: M 534 LYS cc_start: 0.8719 (ptmt) cc_final: 0.8470 (mtmt) REVERT: g 84 GLU cc_start: 0.7879 (tp30) cc_final: 0.7653 (tp30) REVERT: g 115 GLU cc_start: 0.8309 (tt0) cc_final: 0.7973 (tt0) REVERT: g 486 ASP cc_start: 0.7641 (m-30) cc_final: 0.7220 (m-30) REVERT: g 504 SER cc_start: 0.9119 (t) cc_final: 0.8756 (p) REVERT: g 537 GLN cc_start: 0.7534 (mp10) cc_final: 0.7229 (mp10) outliers start: 205 outliers final: 153 residues processed: 1338 average time/residue: 0.5728 time to fit residues: 1330.3283 Evaluate side-chains 1339 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1169 time to evaluate : 5.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 457 THR Chi-restraints excluded: chain N residue 529 ASN Chi-restraints excluded: chain N residue 542 VAL Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 157 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 541 GLN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 489 VAL Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 516 SER Chi-restraints excluded: chain P residue 546 LEU Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 154 GLN Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 173 PHE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 174 ASN Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 476 SER Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 141 ASP Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain a residue 471 ILE Chi-restraints excluded: chain a residue 503 GLN Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 466 ASP Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 175 VAL Chi-restraints excluded: chain b residue 481 VAL Chi-restraints excluded: chain b residue 501 GLU Chi-restraints excluded: chain b residue 513 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 52 ASN Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 154 GLN Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 57 ASN Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 129 GLN Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 461 LEU Chi-restraints excluded: chain c residue 492 LEU Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 510 ASP Chi-restraints excluded: chain c residue 545 LEU Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 155 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain d residue 154 GLN Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 513 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 155 THR Chi-restraints excluded: chain e residue 161 LYS Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 504 SER Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 489 VAL Chi-restraints excluded: chain L residue 507 GLN Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 108 ASP Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 458 SER Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 752 optimal weight: 2.9990 chunk 792 optimal weight: 0.9990 chunk 722 optimal weight: 0.9990 chunk 770 optimal weight: 7.9990 chunk 463 optimal weight: 0.9980 chunk 335 optimal weight: 0.7980 chunk 605 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 696 optimal weight: 0.9990 chunk 728 optimal weight: 0.9990 chunk 767 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 537 GLN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 537 GLN X 547 GLN E 21 ASN E 22 GLN ** E 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 525 GLN O 540 GLN Y 154 GLN F 22 GLN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN a 503 GLN H 537 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN S 536 ASN S 547 GLN c 541 GLN d 22 GLN d 526 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN V 21 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN ** f 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 6 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 66210 Z= 0.195 Angle : 0.572 13.541 89568 Z= 0.312 Chirality : 0.038 0.313 10995 Planarity : 0.003 0.133 12150 Dihedral : 3.968 36.100 9216 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 2.20 % Allowed : 19.83 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.34 (0.09), residues: 8769 helix: 3.47 (0.06), residues: 6330 sheet: 0.66 (0.22), residues: 462 loop : -2.00 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE S 54 TYR 0.022 0.002 TYR V 511 ARG 0.009 0.000 ARG b 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1457 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 1297 time to evaluate : 5.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 122 GLU cc_start: 0.8372 (tp30) cc_final: 0.8151 (tp30) REVERT: A 459 ASP cc_start: 0.8076 (p0) cc_final: 0.7639 (p0) REVERT: A 492 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7418 (mp) REVERT: B 84 GLU cc_start: 0.8123 (tp30) cc_final: 0.7853 (tp30) REVERT: B 459 ASP cc_start: 0.8007 (m-30) cc_final: 0.7674 (t70) REVERT: B 486 ASP cc_start: 0.7785 (p0) cc_final: 0.7385 (p0) REVERT: B 536 ASN cc_start: 0.8408 (m110) cc_final: 0.7882 (p0) REVERT: C 30 GLU cc_start: 0.8323 (tt0) cc_final: 0.7860 (tm-30) REVERT: C 122 GLU cc_start: 0.8073 (tp30) cc_final: 0.7682 (tp30) REVERT: C 131 GLN cc_start: 0.8634 (pp30) cc_final: 0.8391 (pp30) REVERT: D 20 LYS cc_start: 0.8845 (mttm) cc_final: 0.8542 (mttp) REVERT: D 21 ASN cc_start: 0.8918 (t0) cc_final: 0.8620 (t0) REVERT: D 32 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7208 (mm) REVERT: D 117 LYS cc_start: 0.8767 (tptp) cc_final: 0.8495 (tptp) REVERT: N 145 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7448 (mmmt) REVERT: N 159 ASP cc_start: 0.8218 (t0) cc_final: 0.7923 (t0) REVERT: N 518 MET cc_start: 0.7665 (tmm) cc_final: 0.7173 (tmm) REVERT: N 525 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7827 (tm-30) REVERT: N 529 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7816 (m110) REVERT: X 94 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7909 (tm-30) REVERT: X 114 ASP cc_start: 0.8885 (m-30) cc_final: 0.8499 (m-30) REVERT: E 459 ASP cc_start: 0.7658 (p0) cc_final: 0.7147 (p0) REVERT: E 461 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8026 (mm) REVERT: E 466 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: O 79 GLU cc_start: 0.8298 (tt0) cc_final: 0.7769 (mt-10) REVERT: O 459 ASP cc_start: 0.6798 (p0) cc_final: 0.6468 (p0) REVERT: O 541 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8338 (tm-30) REVERT: Y 472 ASP cc_start: 0.8111 (m-30) cc_final: 0.7753 (m-30) REVERT: P 122 GLU cc_start: 0.9010 (tp30) cc_final: 0.8740 (tp30) REVERT: P 141 ASP cc_start: 0.7561 (p0) cc_final: 0.7148 (t0) REVERT: P 174 ASN cc_start: 0.7951 (t0) cc_final: 0.7715 (t0) REVERT: Z 72 ILE cc_start: 0.9001 (mt) cc_final: 0.8747 (mt) REVERT: Z 114 ASP cc_start: 0.8079 (m-30) cc_final: 0.7555 (m-30) REVERT: Z 117 LYS cc_start: 0.8868 (tppt) cc_final: 0.8497 (tppt) REVERT: Z 121 ASP cc_start: 0.8709 (m-30) cc_final: 0.8342 (m-30) REVERT: Z 173 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: G 94 GLU cc_start: 0.7797 (tp30) cc_final: 0.7244 (tp30) REVERT: G 173 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7884 (t80) REVERT: G 534 LYS cc_start: 0.8899 (mttm) cc_final: 0.8584 (mtpt) REVERT: Q 30 GLU cc_start: 0.8289 (tt0) cc_final: 0.8001 (tt0) REVERT: Q 140 LYS cc_start: 0.8265 (tttm) cc_final: 0.8031 (ttmm) REVERT: a 30 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7905 (tt0) REVERT: a 31 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8563 (ttm170) REVERT: a 140 LYS cc_start: 0.7698 (pttt) cc_final: 0.7342 (pttp) REVERT: a 503 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8971 (tt0) REVERT: H 42 LYS cc_start: 0.8694 (ttpp) cc_final: 0.7526 (tptt) REVERT: H 473 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8233 (ptpt) REVERT: H 501 GLU cc_start: 0.7871 (tt0) cc_final: 0.7568 (tt0) REVERT: R 70 ASP cc_start: 0.7129 (m-30) cc_final: 0.6863 (m-30) REVERT: R 486 ASP cc_start: 0.7862 (p0) cc_final: 0.7617 (p0) REVERT: R 501 GLU cc_start: 0.8074 (tt0) cc_final: 0.7834 (tt0) REVERT: b 94 GLU cc_start: 0.6883 (tt0) cc_final: 0.6432 (tt0) REVERT: b 117 LYS cc_start: 0.8848 (tptt) cc_final: 0.8188 (tppt) REVERT: b 121 ASP cc_start: 0.8287 (m-30) cc_final: 0.7925 (m-30) REVERT: b 501 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: I 8 ASN cc_start: 0.7678 (t0) cc_final: 0.7285 (t0) REVERT: I 140 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8359 (mmmm) REVERT: S 36 LEU cc_start: 0.8580 (mp) cc_final: 0.8364 (mm) REVERT: S 140 LYS cc_start: 0.8286 (tptt) cc_final: 0.8010 (tppt) REVERT: c 70 ASP cc_start: 0.7815 (m-30) cc_final: 0.7601 (m-30) REVERT: c 79 GLU cc_start: 0.8322 (tp30) cc_final: 0.8087 (tp30) REVERT: c 129 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.5821 (mp10) REVERT: J 154 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.6307 (tp40) REVERT: T 537 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7846 (tp40) REVERT: d 52 ASN cc_start: 0.7823 (t0) cc_final: 0.7445 (t0) REVERT: d 70 ASP cc_start: 0.7917 (m-30) cc_final: 0.7615 (m-30) REVERT: d 117 LYS cc_start: 0.8528 (tppt) cc_final: 0.8038 (tppt) REVERT: d 537 GLN cc_start: 0.8364 (mm110) cc_final: 0.8063 (tp-100) REVERT: K 154 GLN cc_start: 0.7258 (pt0) cc_final: 0.6513 (tt0) REVERT: K 455 GLU cc_start: 0.7431 (tp30) cc_final: 0.6907 (pm20) REVERT: U 82 LEU cc_start: 0.8935 (mm) cc_final: 0.8555 (mm) REVERT: e 94 GLU cc_start: 0.8504 (tt0) cc_final: 0.8018 (mm-30) REVERT: e 540 GLN cc_start: 0.8496 (pt0) cc_final: 0.8208 (mt0) REVERT: L 70 ASP cc_start: 0.7925 (m-30) cc_final: 0.7459 (m-30) REVERT: L 507 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.5635 (pp30) REVERT: V 113 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8382 (mm-40) REVERT: f 117 LYS cc_start: 0.9008 (tppt) cc_final: 0.8236 (tppt) REVERT: f 122 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8180 (tm-30) REVERT: f 520 LYS cc_start: 0.7549 (mttt) cc_final: 0.7090 (mmtt) REVERT: M 42 LYS cc_start: 0.7685 (ptmm) cc_final: 0.6714 (tptt) REVERT: M 131 GLN cc_start: 0.8498 (pm20) cc_final: 0.8109 (pt0) REVERT: M 534 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8472 (mtmt) REVERT: W 122 GLU cc_start: 0.8379 (tp30) cc_final: 0.8173 (tp30) REVERT: W 473 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8771 (mtmt) REVERT: g 84 GLU cc_start: 0.7809 (tp30) cc_final: 0.7587 (tp30) REVERT: g 115 GLU cc_start: 0.8238 (tt0) cc_final: 0.7903 (tt0) REVERT: g 504 SER cc_start: 0.9087 (t) cc_final: 0.8686 (p) REVERT: g 537 GLN cc_start: 0.7522 (mp10) cc_final: 0.7183 (mp10) outliers start: 160 outliers final: 127 residues processed: 1392 average time/residue: 0.5864 time to fit residues: 1413.0542 Evaluate side-chains 1381 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1240 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 457 THR Chi-restraints excluded: chain N residue 529 ASN Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 157 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain Y residue 154 GLN Chi-restraints excluded: chain Y residue 541 GLN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 546 LEU Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 154 GLN Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 173 PHE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 457 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 141 ASP Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain a residue 173 PHE Chi-restraints excluded: chain a residue 471 ILE Chi-restraints excluded: chain a residue 503 GLN Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 466 ASP Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 501 GLU Chi-restraints excluded: chain b residue 513 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 497 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 52 ASN Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 57 ASN Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 129 GLN Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 492 LEU Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 510 ASP Chi-restraints excluded: chain c residue 545 LEU Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 155 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 513 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 155 THR Chi-restraints excluded: chain e residue 161 LYS Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 504 SER Chi-restraints excluded: chain e residue 531 VAL Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 507 GLN Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 108 ASP Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain M residue 534 LYS Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 506 optimal weight: 9.9990 chunk 814 optimal weight: 0.8980 chunk 497 optimal weight: 5.9990 chunk 386 optimal weight: 0.7980 chunk 566 optimal weight: 2.9990 chunk 854 optimal weight: 0.5980 chunk 786 optimal weight: 0.8980 chunk 680 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 525 optimal weight: 1.9990 chunk 417 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 537 GLN X 493 ASN X 547 GLN ** E 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 540 GLN Y 154 GLN P 6 ASN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 498 ASN a 503 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN S 536 ASN c 541 GLN T 86 ASN d 22 GLN d 76 GLN U 21 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN L 21 ASN L 154 GLN V 21 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 66210 Z= 0.186 Angle : 0.573 13.757 89568 Z= 0.311 Chirality : 0.038 0.353 10995 Planarity : 0.003 0.132 12150 Dihedral : 3.874 35.646 9216 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.02 % Favored : 95.97 % Rotamer: Outliers : 2.14 % Allowed : 20.14 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.45 (0.09), residues: 8769 helix: 3.54 (0.06), residues: 6330 sheet: 0.80 (0.22), residues: 462 loop : -1.97 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.057 0.001 PHE c 173 TYR 0.023 0.001 TYR V 511 ARG 0.009 0.000 ARG H 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1278 time to evaluate : 5.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7896 (pp) REVERT: A 459 ASP cc_start: 0.7981 (p0) cc_final: 0.7547 (p0) REVERT: A 492 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7409 (mp) REVERT: B 459 ASP cc_start: 0.7967 (m-30) cc_final: 0.7664 (t70) REVERT: B 486 ASP cc_start: 0.7806 (p0) cc_final: 0.7457 (p0) REVERT: B 536 ASN cc_start: 0.8399 (m110) cc_final: 0.7862 (p0) REVERT: C 30 GLU cc_start: 0.8324 (tt0) cc_final: 0.7850 (tm-30) REVERT: C 122 GLU cc_start: 0.8066 (tp30) cc_final: 0.7738 (tp30) REVERT: C 131 GLN cc_start: 0.8584 (pp30) cc_final: 0.8380 (pp30) REVERT: D 21 ASN cc_start: 0.8919 (t0) cc_final: 0.8586 (t0) REVERT: D 32 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7117 (mm) REVERT: D 155 THR cc_start: 0.8463 (p) cc_final: 0.8191 (t) REVERT: N 145 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7445 (mmmt) REVERT: N 159 ASP cc_start: 0.8210 (t0) cc_final: 0.7939 (t0) REVERT: N 518 MET cc_start: 0.7663 (tmm) cc_final: 0.7162 (tmm) REVERT: N 525 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7832 (tm-30) REVERT: N 529 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7810 (m110) REVERT: X 94 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8071 (tm-30) REVERT: X 114 ASP cc_start: 0.8919 (m-30) cc_final: 0.8544 (m-30) REVERT: X 173 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: E 459 ASP cc_start: 0.7613 (p0) cc_final: 0.7289 (p0) REVERT: E 461 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (mm) REVERT: E 466 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: O 79 GLU cc_start: 0.8301 (tt0) cc_final: 0.7748 (mt-10) REVERT: O 459 ASP cc_start: 0.6699 (p0) cc_final: 0.6424 (p0) REVERT: O 541 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8025 (tm-30) REVERT: Y 472 ASP cc_start: 0.7973 (m-30) cc_final: 0.7648 (m-30) REVERT: P 23 SER cc_start: 0.9012 (t) cc_final: 0.8663 (p) REVERT: P 122 GLU cc_start: 0.8991 (tp30) cc_final: 0.8708 (tp30) REVERT: P 141 ASP cc_start: 0.7547 (p0) cc_final: 0.7131 (t0) REVERT: P 174 ASN cc_start: 0.7936 (t0) cc_final: 0.7707 (t0) REVERT: Z 72 ILE cc_start: 0.8983 (mt) cc_final: 0.8726 (mt) REVERT: Z 114 ASP cc_start: 0.8065 (m-30) cc_final: 0.7533 (m-30) REVERT: Z 117 LYS cc_start: 0.8872 (tppt) cc_final: 0.8494 (tppt) REVERT: Z 121 ASP cc_start: 0.8633 (m-30) cc_final: 0.8259 (m-30) REVERT: Z 173 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7152 (m-10) REVERT: G 94 GLU cc_start: 0.7752 (tp30) cc_final: 0.7239 (tp30) REVERT: G 173 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7680 (t80) REVERT: G 534 LYS cc_start: 0.8869 (mttm) cc_final: 0.8570 (mtpt) REVERT: Q 30 GLU cc_start: 0.8272 (tt0) cc_final: 0.7977 (tt0) REVERT: Q 113 GLN cc_start: 0.8954 (tp40) cc_final: 0.8336 (tp40) REVERT: Q 140 LYS cc_start: 0.8273 (tttm) cc_final: 0.8018 (ttmm) REVERT: a 30 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7931 (tt0) REVERT: a 31 ARG cc_start: 0.8819 (ttm170) cc_final: 0.8535 (ttm170) REVERT: a 140 LYS cc_start: 0.7717 (pttt) cc_final: 0.7357 (pttp) REVERT: H 42 LYS cc_start: 0.8673 (ttpp) cc_final: 0.7391 (tptt) REVERT: H 473 LYS cc_start: 0.8488 (ptmm) cc_final: 0.8128 (ptpt) REVERT: R 70 ASP cc_start: 0.7141 (m-30) cc_final: 0.6880 (m-30) REVERT: R 140 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8439 (pttt) REVERT: R 486 ASP cc_start: 0.7832 (p0) cc_final: 0.7583 (p0) REVERT: R 501 GLU cc_start: 0.8073 (tt0) cc_final: 0.7837 (tt0) REVERT: b 94 GLU cc_start: 0.6855 (tt0) cc_final: 0.6389 (tt0) REVERT: b 117 LYS cc_start: 0.8835 (tptt) cc_final: 0.8165 (tppt) REVERT: b 121 ASP cc_start: 0.8270 (m-30) cc_final: 0.7906 (m-30) REVERT: b 501 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: I 140 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8368 (mmmm) REVERT: S 36 LEU cc_start: 0.8487 (mp) cc_final: 0.8269 (mm) REVERT: S 140 LYS cc_start: 0.8313 (tptt) cc_final: 0.8015 (tppt) REVERT: c 70 ASP cc_start: 0.7803 (m-30) cc_final: 0.7587 (m-30) REVERT: c 79 GLU cc_start: 0.8318 (tp30) cc_final: 0.8068 (tp30) REVERT: c 129 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.5806 (mp10) REVERT: J 154 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6307 (tp40) REVERT: d 30 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: d 52 ASN cc_start: 0.7772 (t0) cc_final: 0.7409 (t0) REVERT: d 70 ASP cc_start: 0.7872 (m-30) cc_final: 0.7551 (m-30) REVERT: d 117 LYS cc_start: 0.8485 (tppt) cc_final: 0.7984 (tppt) REVERT: d 537 GLN cc_start: 0.8336 (mm110) cc_final: 0.8017 (tp-100) REVERT: K 154 GLN cc_start: 0.7285 (pt0) cc_final: 0.6555 (tt0) REVERT: K 455 GLU cc_start: 0.7310 (tp30) cc_final: 0.6913 (pm20) REVERT: U 82 LEU cc_start: 0.8950 (mm) cc_final: 0.8634 (mm) REVERT: e 94 GLU cc_start: 0.8489 (tt0) cc_final: 0.8019 (mm-30) REVERT: e 540 GLN cc_start: 0.8414 (pt0) cc_final: 0.8164 (mt0) REVERT: L 70 ASP cc_start: 0.7932 (m-30) cc_final: 0.7465 (m-30) REVERT: L 459 ASP cc_start: 0.7575 (m-30) cc_final: 0.7331 (m-30) REVERT: L 507 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.5681 (pp30) REVERT: V 113 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8364 (mm-40) REVERT: f 117 LYS cc_start: 0.8996 (tppt) cc_final: 0.8257 (tppt) REVERT: f 122 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8141 (tm-30) REVERT: f 520 LYS cc_start: 0.7512 (mttt) cc_final: 0.7047 (mmtt) REVERT: M 42 LYS cc_start: 0.7683 (ptmm) cc_final: 0.6706 (tptt) REVERT: M 131 GLN cc_start: 0.8497 (pm20) cc_final: 0.8141 (pt0) REVERT: M 466 ASP cc_start: 0.8160 (t70) cc_final: 0.7753 (t0) REVERT: M 534 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8456 (mtmt) REVERT: W 473 LYS cc_start: 0.8984 (mtmt) cc_final: 0.8782 (mtmt) REVERT: g 84 GLU cc_start: 0.7750 (tp30) cc_final: 0.7520 (tp30) REVERT: g 115 GLU cc_start: 0.8236 (tt0) cc_final: 0.7990 (tt0) REVERT: g 504 SER cc_start: 0.9060 (t) cc_final: 0.8609 (p) REVERT: g 514 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: g 537 GLN cc_start: 0.7489 (mp10) cc_final: 0.7139 (mp10) outliers start: 156 outliers final: 120 residues processed: 1369 average time/residue: 0.5845 time to fit residues: 1385.4102 Evaluate side-chains 1384 residues out of total 7440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1249 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 457 THR Chi-restraints excluded: chain N residue 529 ASN Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 157 THR Chi-restraints excluded: chain X residue 173 PHE Chi-restraints excluded: chain X residue 547 GLN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 544 SER Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain Y residue 44 ASP Chi-restraints excluded: chain Y residue 541 GLN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 546 LEU Chi-restraints excluded: chain Z residue 38 ILE Chi-restraints excluded: chain Z residue 154 GLN Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 173 PHE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 158 ILE Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 457 THR Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 141 ASP Chi-restraints excluded: chain a residue 170 LEU Chi-restraints excluded: chain a residue 173 PHE Chi-restraints excluded: chain a residue 471 ILE Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 466 ASP Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 501 GLU Chi-restraints excluded: chain b residue 513 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 497 THR Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 543 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 154 GLN Chi-restraints excluded: chain S residue 508 ASP Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 57 ASN Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 129 GLN Chi-restraints excluded: chain c residue 492 LEU Chi-restraints excluded: chain c residue 496 THR Chi-restraints excluded: chain c residue 510 ASP Chi-restraints excluded: chain c residue 541 GLN Chi-restraints excluded: chain c residue 545 LEU Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 481 VAL Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 496 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 513 THR Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 124 ASP Chi-restraints excluded: chain e residue 155 THR Chi-restraints excluded: chain e residue 161 LYS Chi-restraints excluded: chain e residue 167 THR Chi-restraints excluded: chain e residue 504 SER Chi-restraints excluded: chain e residue 531 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 507 GLN Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain W residue 20 LYS Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain W residue 504 SER Chi-restraints excluded: chain W residue 543 LEU Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 540 optimal weight: 0.8980 chunk 725 optimal weight: 0.0770 chunk 208 optimal weight: 5.9990 chunk 627 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 681 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 700 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN B 76 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 537 GLN X 493 ASN X 547 GLN E 22 GLN ** E 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 540 GLN ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 ASN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 498 ASN a 503 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN S 536 ASN c 88 ASN T 16 ASN ** T 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** U 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN L 21 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN ** f 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.099859 restraints weight = 367356.268| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.18 r_work: 0.3217 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 66210 Z= 0.188 Angle : 0.574 13.947 89568 Z= 0.312 Chirality : 0.038 0.393 10995 Planarity : 0.003 0.130 12150 Dihedral : 3.863 35.432 9216 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.00 % Favored : 95.99 % Rotamer: Outliers : 1.94 % Allowed : 20.48 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.46 (0.09), residues: 8769 helix: 3.55 (0.06), residues: 6330 sheet: 0.86 (0.22), residues: 462 loop : -1.97 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.051 0.001 PHE c 173 TYR 0.021 0.001 TYR V 511 ARG 0.009 0.000 ARG H 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20273.76 seconds wall clock time: 352 minutes 40.42 seconds (21160.42 seconds total)