Starting phenix.real_space_refine on Mon Sep 14 22:43:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdg_4817/09_2026/6rdg_4817.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21567 2.51 5 N 5801 2.21 5 O 6462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 227 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33964 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3649 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 461} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 7.23, per 1000 atoms: 0.21 Number of scatterers: 33964 At special positions: 0 Unit cell: (164.268, 135.837, 207.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6462 8.00 N 5801 7.00 C 21567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8170 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 25 sheets defined 52.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 54 through 67 removed outlier: 4.158A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 4.208A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 125 removed outlier: 3.671A pdb=" N VAL A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.967A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.112A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 3.635A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 3.549A pdb=" N SER C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.778A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.742A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.855A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.822A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.691A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.668A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 removed outlier: 3.846A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG E 91 " --> pdb=" O ASN E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 109 removed outlier: 3.752A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 126 removed outlier: 3.592A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.929A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 90 removed outlier: 4.278A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.762A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 69 removed outlier: 4.062A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.236A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.616A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 111 " --> pdb=" O PHE G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 126 Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.741A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.126A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.544A pdb=" N LEU H 99 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.849A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.826A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 92 removed outlier: 3.938A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 removed outlier: 3.518A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'I' and resid 97 through 127 removed outlier: 3.715A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.658A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.292A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 126 removed outlier: 3.691A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU J 111 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 121 " --> pdb=" O SER J 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.776A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.768A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR P 75 " --> pdb=" O GLN P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.732A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 4.443A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 149 removed outlier: 4.086A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'R' and resid 29 through 38 removed outlier: 3.920A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.590A pdb=" N THR R 55 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 159 through 165 removed outlier: 3.642A pdb=" N ALA R 163 " --> pdb=" O ALA R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 197 removed outlier: 3.502A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.815A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 removed outlier: 3.635A pdb=" N VAL S 75 " --> pdb=" O ALA S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 89 removed outlier: 3.682A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 128 removed outlier: 3.536A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 181 Processing helix chain 'S' and resid 227 through 231 removed outlier: 3.771A pdb=" N ALA S 230 " --> pdb=" O SER S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 274 removed outlier: 3.648A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 274 through 313 removed outlier: 3.899A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.949A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 removed outlier: 3.630A pdb=" N LEU T 160 " --> pdb=" O PRO T 157 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.673A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.513A pdb=" N ALA T 238 " --> pdb=" O VAL T 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.363A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.655A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 353 No H-bonds generated for 'chain 'T' and resid 351 through 353' Processing helix chain 'T' and resid 354 through 363 removed outlier: 3.519A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.575A pdb=" N PHE T 413 " --> pdb=" O GLU T 409 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS T 415 " --> pdb=" O GLU T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.703A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.578A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 456 removed outlier: 3.514A pdb=" N LEU T 446 " --> pdb=" O VAL T 442 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 removed outlier: 3.555A pdb=" N GLN T 461 " --> pdb=" O ALA T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 482 removed outlier: 3.566A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.658A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.537A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 546 through 556 removed outlier: 3.580A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 48 Processing helix chain 'U' and resid 58 through 71 removed outlier: 3.791A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 134 through 138 removed outlier: 4.049A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 Processing helix chain 'U' and resid 206 through 213 removed outlier: 3.604A pdb=" N LEU U 212 " --> pdb=" O ALA U 208 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.543A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 280 removed outlier: 3.639A pdb=" N LEU U 275 " --> pdb=" O GLN U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 295 through 315 Proline residue: U 303 - end of helix removed outlier: 3.552A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.732A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 414 removed outlier: 3.699A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 443 removed outlier: 3.659A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) Processing helix chain 'U' and resid 443 through 455 removed outlier: 3.870A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN U 452 " --> pdb=" O LEU U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.933A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 4.247A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 485 removed outlier: 3.632A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 removed outlier: 3.561A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 506 removed outlier: 3.557A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 520 through 527 Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.868A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 553 removed outlier: 3.512A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 removed outlier: 3.861A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 67 removed outlier: 4.029A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.765A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.561A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 211 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.702A pdb=" N ASP V 237 " --> pdb=" O ALA V 233 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 315 Proline residue: V 303 - end of helix removed outlier: 4.590A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 removed outlier: 3.850A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER V 331 " --> pdb=" O LEU V 327 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.726A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.721A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.849A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.571A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 454 removed outlier: 3.600A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 470 through 485 removed outlier: 3.509A pdb=" N LEU V 474 " --> pdb=" O THR V 470 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.987A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.540A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.797A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 555 removed outlier: 3.860A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.265A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 275 removed outlier: 4.711A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 296 removed outlier: 3.645A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.738A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE X 355 " --> pdb=" O PRO X 351 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 418 removed outlier: 3.502A pdb=" N ASN X 398 " --> pdb=" O ALA X 394 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 443 removed outlier: 3.558A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 447 through 451 removed outlier: 3.896A pdb=" N GLU X 451 " --> pdb=" O GLN X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 removed outlier: 3.562A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 487 removed outlier: 3.651A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 507 removed outlier: 3.718A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 removed outlier: 3.641A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 149 through 153 removed outlier: 3.540A pdb=" N GLN Y 153 " --> pdb=" O PHE Y 150 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 170 Processing helix chain 'Y' and resid 188 through 203 removed outlier: 3.612A pdb=" N MET Y 194 " --> pdb=" O THR Y 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.920A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 4.970A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 removed outlier: 3.551A pdb=" N PHE Y 290 " --> pdb=" O ASN Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.556A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 Processing helix chain 'Y' and resid 348 through 356 removed outlier: 3.634A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 371 Processing helix chain 'Y' and resid 388 through 412 removed outlier: 7.518A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN Y 412 " --> pdb=" O GLN Y 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 420 removed outlier: 3.793A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 426 through 440 removed outlier: 3.535A pdb=" N LEU Y 431 " --> pdb=" O GLU Y 427 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.551A pdb=" N SER Y 468 " --> pdb=" O ALA Y 464 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 504 removed outlier: 4.011A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 526 through 531 removed outlier: 3.712A pdb=" N VAL Y 531 " --> pdb=" O LEU Y 527 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 555 removed outlier: 3.540A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.598A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 removed outlier: 3.581A pdb=" N LEU Z 170 " --> pdb=" O VAL Z 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 201 removed outlier: 3.544A pdb=" N ALA Z 201 " --> pdb=" O ILE Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.864A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.572A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.681A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 355 removed outlier: 3.569A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.560A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 413 removed outlier: 3.669A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 415 through 421 Processing helix chain 'Z' and resid 422 through 425 removed outlier: 3.572A pdb=" N LEU Z 425 " --> pdb=" O MET Z 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 422 through 425' Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.774A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.564A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 505 removed outlier: 3.877A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) Processing helix chain 'Z' and resid 507 through 511 removed outlier: 3.500A pdb=" N GLU Z 511 " --> pdb=" O SER Z 508 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 Processing sheet with id=AA1, first strand: chain 'Q' and resid 61 through 63 removed outlier: 10.508A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 82 removed outlier: 6.366A pdb=" N PHE R 74 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 80 through 82 removed outlier: 6.366A pdb=" N PHE R 74 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 111 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.572A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 116 through 122 removed outlier: 3.889A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU T 108 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS T 126 " --> pdb=" O LEU T 122 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU T 122 " --> pdb=" O HIS T 126 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA7, first strand: chain 'T' and resid 163 through 165 removed outlier: 3.552A pdb=" N VAL T 262 " --> pdb=" O ASP T 325 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 201 through 202 removed outlier: 4.246A pdb=" N ILE T 215 " --> pdb=" O LEU T 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 116 through 122 removed outlier: 3.773A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB2, first strand: chain 'U' and resid 163 through 164 Processing sheet with id=AB3, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.853A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG Z 51 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL Z 40 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB5, first strand: chain 'V' and resid 163 through 164 removed outlier: 3.772A pdb=" N VAL V 262 " --> pdb=" O ASP V 325 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 110 through 111 Processing sheet with id=AB7, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.966A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE X 207 " --> pdb=" O ASP X 279 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL X 280 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL X 336 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU X 282 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA X 338 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL X 284 " --> pdb=" O ALA X 338 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N TYR X 340 " --> pdb=" O VAL X 284 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.911A pdb=" N GLU X 158 " --> pdb=" O ARG X 175 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC1, first strand: chain 'Y' and resid 110 through 113 removed outlier: 3.510A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.054A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN Y 250 " --> pdb=" O MET Y 122 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE Y 179 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS Y 178 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N THR Y 361 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY Y 180 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL Y 363 " --> pdb=" O GLY Y 180 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE Y 182 " --> pdb=" O VAL Y 363 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.422A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AC5, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.319A pdb=" N MET Z 122 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE Z 207 " --> pdb=" O LEU Z 281 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE Z 283 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA Z 211 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL Z 339 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU Z 181 " --> pdb=" O VAL Z 339 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.104A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 559 through 561 1605 hydrogen bonds defined for protein. 4596 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: 7.40 Time building geometry restraints manager: 3.81 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: 11168 1.34 - 1.46: 5402 1.46 - 1.57: 17662 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34453 Sorted by residual: bond pdb=" C4 ADP X 601 " pdb=" C5 ADP X 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP Z 601 " pdb=" C5 ADP Z 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP Z 601 " pdb=" C6 ADP Z 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C5 ADP X 601 " pdb=" C6 ADP X 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N ARG Z 216 " pdb=" CA ARG Z 216 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.48e+00 ... (remaining 34448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 46061 2.83 - 5.67: 546 5.67 - 8.50: 63 8.50 - 11.33: 22 11.33 - 14.16: 4 Bond angle restraints: 46696 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 132.51 7.36 1.00e+00 1.00e+00 5.41e+01 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 132.52 7.35 1.00e+00 1.00e+00 5.40e+01 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.24e+01 angle pdb=" N GLU H 111 " pdb=" CA GLU H 111 " pdb=" C GLU H 111 " ideal model delta sigma weight residual 112.89 104.53 8.36 1.24e+00 6.50e-01 4.55e+01 angle pdb=" C GLY P 48 " pdb=" N THR P 49 " pdb=" CA THR P 49 " ideal model delta sigma weight residual 121.54 132.63 -11.09 1.91e+00 2.74e-01 3.37e+01 ... (remaining 46691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.00: 20166 31.00 - 61.99: 532 61.99 - 92.99: 52 92.99 - 123.99: 0 123.99 - 154.99: 3 Dihedral angle restraints: 20753 sinusoidal: 7981 harmonic: 12772 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -122.53 -57.47 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -129.08 -50.92 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -131.25 -48.75 0 5.00e+00 4.00e-02 9.50e+01 ... (remaining 20750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4440 0.063 - 0.126: 946 0.126 - 0.190: 125 0.190 - 0.253: 13 0.253 - 0.316: 3 Chirality restraints: 5527 Sorted by residual: chirality pdb=" CB ILE Y 524 " pdb=" CA ILE Y 524 " pdb=" CG1 ILE Y 524 " pdb=" CG2 ILE Y 524 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN Z 286 " pdb=" N ASN Z 286 " pdb=" C ASN Z 286 " pdb=" CB ASN Z 286 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 5524 not shown) Planarity restraints: 6004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.031 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C ALA X 503 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C ALA Z 503 " -0.104 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 110 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C THR J 110 " -0.052 2.00e-02 2.50e+03 pdb=" O THR J 110 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU J 111 " 0.018 2.00e-02 2.50e+03 ... (remaining 6001 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 256 2.54 - 3.13: 24202 3.13 - 3.72: 54055 3.72 - 4.31: 82094 4.31 - 4.90: 131425 Nonbonded interactions: 292032 Sorted by model distance: nonbonded pdb=" N LEU V 327 " pdb=" O VAL V 382 " model vdw 1.951 3.120 nonbonded pdb=" NH2 ARG U 227 " pdb=" OD1 ASP Z 381 " model vdw 2.088 3.120 nonbonded pdb=" OE2 GLU H 111 " pdb=" CB ALA H 114 " model vdw 2.097 3.460 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.141 2.170 nonbonded pdb=" O SER V 328 " pdb=" OG SER V 331 " model vdw 2.156 3.040 ... (remaining 292027 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 80 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 80 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } 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=1.00 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: 7.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 31.700 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.005 0.109 34453 Z= 0.242 Angle : 0.825 14.165 46696 Z= 0.452 Chirality : 0.053 0.316 5527 Planarity : 0.006 0.067 6004 Dihedral : 13.992 154.986 12583 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.24 % Rotamer: Outliers : 0.22 % Allowed : 5.83 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.09), residues: 4466 helix: -4.39 (0.05), residues: 2114 sheet: -1.50 (0.20), residues: 570 loop : -1.91 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 239 TYR 0.017 0.002 TYR U 502 PHE 0.025 0.002 PHE A 122 TRP 0.032 0.003 TRP Y 141 HIS 0.008 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (34453) covalent geometry : angle 0.82485 / 0.45 (46696) hydrogen bonds : bond 0.27991 / 18.18 ( 1604) hydrogen bonds : angle 10.73148 / 7.40 ( 4596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 684 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8344 (t0) cc_final: 0.8069 (t0) REVERT: C 74 VAL cc_start: 0.8871 (m) cc_final: 0.8555 (p) REVERT: E 61 MET cc_start: 0.8009 (mtm) cc_final: 0.7755 (mtp) REVERT: E 62 VAL cc_start: 0.8591 (p) cc_final: 0.8273 (t) REVERT: F 87 ASN cc_start: 0.8543 (m-40) cc_final: 0.8342 (m-40) REVERT: G 81 MET cc_start: 0.6898 (ttp) cc_final: 0.6628 (ttp) REVERT: I 61 MET cc_start: 0.5783 (mmt) cc_final: 0.5514 (mmt) REVERT: I 118 LEU cc_start: 0.6708 (mt) cc_final: 0.6333 (mp) REVERT: J 87 ASN cc_start: 0.8457 (m-40) cc_final: 0.7885 (m110) REVERT: P 73 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6883 (mt-10) REVERT: P 83 GLN cc_start: 0.8096 (mt0) cc_final: 0.7839 (mt0) REVERT: P 103 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7599 (tttt) REVERT: P 120 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8171 (mttt) REVERT: P 135 LEU cc_start: 0.9236 (tp) cc_final: 0.8998 (mt) REVERT: Q 10 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7031 (mmt180) REVERT: Q 38 LYS cc_start: 0.7702 (mttp) cc_final: 0.7452 (mmmm) REVERT: Q 48 ARG cc_start: 0.8275 (ptt-90) cc_final: 0.7865 (ptt90) REVERT: Q 49 GLN cc_start: 0.7443 (pt0) cc_final: 0.7090 (pt0) REVERT: Q 52 TYR cc_start: 0.7339 (m-80) cc_final: 0.6992 (m-80) REVERT: S 136 ASP cc_start: 0.6960 (t70) cc_final: 0.6710 (t0) REVERT: S 188 GLN cc_start: 0.8418 (mt0) cc_final: 0.8045 (mt0) REVERT: S 234 GLU cc_start: 0.7597 (tt0) cc_final: 0.7237 (tm-30) REVERT: S 241 ASP cc_start: 0.7481 (m-30) cc_final: 0.7222 (m-30) REVERT: S 291 ASP cc_start: 0.7910 (t70) cc_final: 0.7644 (t0) REVERT: T 447 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8409 (ptpp) REVERT: T 483 MET cc_start: 0.7952 (tpt) cc_final: 0.7721 (tpp) REVERT: T 525 ILE cc_start: 0.8475 (pt) cc_final: 0.8194 (mp) REVERT: U 74 GLU cc_start: 0.7865 (pp20) cc_final: 0.7603 (pm20) REVERT: U 282 MET cc_start: 0.8812 (tpt) cc_final: 0.8329 (tpt) REVERT: U 475 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7195 (mm-30) REVERT: V 411 GLU cc_start: 0.7660 (mp0) cc_final: 0.7418 (mp0) REVERT: X 168 ASP cc_start: 0.8195 (m-30) cc_final: 0.7985 (m-30) REVERT: X 422 MET cc_start: 0.7406 (tmm) cc_final: 0.7124 (ttp) REVERT: Y 292 GLN cc_start: 0.8265 (tt0) cc_final: 0.8027 (tt0) REVERT: Y 430 LYS cc_start: 0.6815 (ptpt) cc_final: 0.6281 (ptpp) REVERT: Y 441 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8407 (mmt90) REVERT: Z 82 ASP cc_start: 0.7679 (t0) cc_final: 0.7167 (t0) REVERT: Z 140 ILE cc_start: 0.9165 (mm) cc_final: 0.8826 (tp) outliers start: 8 outliers final: 1 residues processed: 691 average time/residue: 0.7225 time to fit residues: 597.1194 Evaluate side-chains 449 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN E 94 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 98 GLN I 94 ASN J 94 ASN J 98 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 73 ASN R 85 GLN R 119 HIS ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 262 ASN S 267 HIS T 126 HIS T 134 ASN T 241 HIS T 386 GLN T 435 GLN U 78 GLN U 134 ASN U 179 ASN U 242 GLN U 319 HIS V 121 ASN V 123 GLN V 134 ASN V 139 HIS V 152 ASN V 196 GLN V 241 HIS V 242 GLN V 248 GLN V 386 GLN V 435 GLN V 452 GLN V 486 GLN V 497 GLN X 198 ASN X 204 HIS X 390 ASN X 414 GLN Y 199 ASN Y 278 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 42 GLN Z 144 HIS Z 199 ASN Z 278 GLN Z 337 GLN Z 388 ASN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095635 restraints weight = 47607.801| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.84 r_work: 0.2980 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34453 Z= 0.140 Angle : 0.615 9.487 46696 Z= 0.318 Chirality : 0.044 0.177 5527 Planarity : 0.005 0.050 6004 Dihedral : 6.920 161.191 4831 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer: Outliers : 2.47 % Allowed : 13.00 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.11), residues: 4466 helix: -2.27 (0.09), residues: 2139 sheet: -1.14 (0.20), residues: 579 loop : -1.29 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG X 385 TYR 0.020 0.001 TYR U 57 PHE 0.024 0.001 PHE A 122 TRP 0.013 0.001 TRP Y 141 HIS 0.005 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (34453) covalent geometry : angle 0.61534 / 0.32 (46696) hydrogen bonds : bond 0.04732 / 3.06 ( 1604) hydrogen bonds : angle 5.60508 / 3.87 ( 4596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 493 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.8618 (ttp) cc_final: 0.8312 (ttp) REVERT: A 87 ASN cc_start: 0.8499 (t0) cc_final: 0.8242 (t0) REVERT: A 116 PHE cc_start: 0.7831 (m-80) cc_final: 0.7614 (m-80) REVERT: C 74 VAL cc_start: 0.8805 (m) cc_final: 0.8460 (p) REVERT: C 84 SER cc_start: 0.8733 (m) cc_final: 0.8471 (m) REVERT: E 61 MET cc_start: 0.8587 (mtm) cc_final: 0.7439 (mtt) REVERT: E 116 PHE cc_start: 0.7526 (m-10) cc_final: 0.7271 (m-80) REVERT: F 87 ASN cc_start: 0.8468 (m-40) cc_final: 0.8185 (m110) REVERT: F 123 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6371 (mp) REVERT: G 91 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8322 (ttt90) REVERT: H 102 TYR cc_start: 0.7855 (m-80) cc_final: 0.7397 (m-80) REVERT: I 61 MET cc_start: 0.6807 (mmt) cc_final: 0.6441 (mmt) REVERT: I 91 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7565 (ttm-80) REVERT: J 102 TYR cc_start: 0.8024 (m-10) cc_final: 0.7720 (m-10) REVERT: P 120 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8355 (mmtt) REVERT: Q 10 ARG cc_start: 0.7551 (tpp-160) cc_final: 0.7225 (mpt90) REVERT: Q 38 LYS cc_start: 0.7777 (mttp) cc_final: 0.7323 (mmmm) REVERT: Q 48 ARG cc_start: 0.8394 (ptt-90) cc_final: 0.8111 (ptt90) REVERT: Q 49 GLN cc_start: 0.7769 (pt0) cc_final: 0.7368 (pt0) REVERT: Q 52 TYR cc_start: 0.7096 (m-80) cc_final: 0.6528 (m-10) REVERT: R 143 ASP cc_start: 0.8748 (m-30) cc_final: 0.8545 (m-30) REVERT: S 153 ILE cc_start: 0.7259 (tt) cc_final: 0.6539 (pt) REVERT: S 234 GLU cc_start: 0.7920 (tt0) cc_final: 0.7177 (tm-30) REVERT: S 291 ASP cc_start: 0.8774 (t70) cc_final: 0.8511 (t0) REVERT: T 287 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8562 (tpp) REVERT: T 447 LYS cc_start: 0.8646 (ptpt) cc_final: 0.8445 (ptpp) REVERT: T 483 MET cc_start: 0.8603 (tpt) cc_final: 0.8375 (tpp) REVERT: T 525 ILE cc_start: 0.8561 (pt) cc_final: 0.8338 (mp) REVERT: U 43 LYS cc_start: 0.8415 (tptt) cc_final: 0.7701 (tmmt) REVERT: U 74 GLU cc_start: 0.8249 (pp20) cc_final: 0.7734 (pm20) REVERT: U 282 MET cc_start: 0.9119 (tpt) cc_final: 0.8668 (tpt) REVERT: U 475 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7381 (mm-30) REVERT: U 496 ARG cc_start: 0.8928 (mtt-85) cc_final: 0.8626 (mtt-85) REVERT: V 50 LYS cc_start: 0.7210 (pptt) cc_final: 0.6949 (ptpp) REVERT: V 411 GLU cc_start: 0.8276 (mp0) cc_final: 0.7922 (mp0) REVERT: V 449 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7562 (mt-10) REVERT: X 253 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: Y 292 GLN cc_start: 0.8656 (tt0) cc_final: 0.8288 (tt0) REVERT: Y 405 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8251 (ttpp) REVERT: Y 430 LYS cc_start: 0.6735 (ptpt) cc_final: 0.6155 (mtmm) REVERT: Y 488 MET cc_start: 0.8724 (mmm) cc_final: 0.8453 (tpt) REVERT: Z 82 ASP cc_start: 0.8807 (t0) cc_final: 0.8278 (t0) REVERT: Z 140 ILE cc_start: 0.9309 (mm) cc_final: 0.8869 (tp) REVERT: Z 419 ILE cc_start: 0.8537 (pt) cc_final: 0.8233 (mt) outliers start: 88 outliers final: 28 residues processed: 558 average time/residue: 0.6938 time to fit residues: 466.7086 Evaluate side-chains 461 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 429 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 253 GLU Chi-restraints excluded: chain X residue 411 LYS Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 406 VAL Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 183 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 88 optimal weight: 0.0770 chunk 328 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN J 87 ASN J 98 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN T 134 ASN T 497 GLN T 549 HIS U 134 ASN V 121 ASN V 134 ASN V 452 GLN Y 252 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.095411 restraints weight = 47496.436| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.86 r_work: 0.2975 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34453 Z= 0.132 Angle : 0.574 9.700 46696 Z= 0.292 Chirality : 0.044 0.163 5527 Planarity : 0.004 0.049 6004 Dihedral : 6.596 166.812 4830 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 2.44 % Allowed : 15.33 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.12), residues: 4466 helix: -1.12 (0.10), residues: 2151 sheet: -1.02 (0.20), residues: 604 loop : -0.97 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 366 TYR 0.022 0.001 TYR U 57 PHE 0.018 0.001 PHE A 122 TRP 0.008 0.001 TRP Y 141 HIS 0.006 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (34453) covalent geometry : angle 0.57355 / 0.29 (46696) hydrogen bonds : bond 0.04004 / 2.61 ( 1604) hydrogen bonds : angle 4.99894 / 3.46 ( 4596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 462 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8579 (ttp) cc_final: 0.8331 (ttp) REVERT: A 87 ASN cc_start: 0.8328 (t0) cc_final: 0.8114 (t0) REVERT: C 74 VAL cc_start: 0.8746 (m) cc_final: 0.8440 (p) REVERT: C 84 SER cc_start: 0.8832 (m) cc_final: 0.8213 (p) REVERT: E 61 MET cc_start: 0.8539 (mtm) cc_final: 0.7311 (mtt) REVERT: E 62 VAL cc_start: 0.8176 (p) cc_final: 0.7810 (t) REVERT: F 61 MET cc_start: 0.6918 (mtm) cc_final: 0.6715 (mtm) REVERT: I 61 MET cc_start: 0.6610 (mmt) cc_final: 0.6265 (mmt) REVERT: J 102 TYR cc_start: 0.8007 (m-10) cc_final: 0.7803 (m-10) REVERT: P 66 GLN cc_start: 0.8334 (tt0) cc_final: 0.7637 (mt0) REVERT: P 128 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7861 (mt-10) REVERT: Q 10 ARG cc_start: 0.7515 (tpp-160) cc_final: 0.7201 (mpt90) REVERT: Q 38 LYS cc_start: 0.7852 (mttp) cc_final: 0.7343 (mmmm) REVERT: Q 48 ARG cc_start: 0.8308 (ptt-90) cc_final: 0.8003 (ptt90) REVERT: Q 49 GLN cc_start: 0.7890 (pt0) cc_final: 0.7411 (tt0) REVERT: Q 52 TYR cc_start: 0.7026 (m-80) cc_final: 0.6471 (m-10) REVERT: R 143 ASP cc_start: 0.8810 (m-30) cc_final: 0.8596 (m-30) REVERT: S 62 MET cc_start: 0.8639 (mmm) cc_final: 0.8424 (mmm) REVERT: S 153 ILE cc_start: 0.7155 (tt) cc_final: 0.6465 (pt) REVERT: S 217 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: S 234 GLU cc_start: 0.7944 (tt0) cc_final: 0.7223 (tm-30) REVERT: S 284 MET cc_start: 0.8614 (mtp) cc_final: 0.8310 (mtm) REVERT: S 291 ASP cc_start: 0.8791 (t70) cc_final: 0.8516 (t0) REVERT: T 427 VAL cc_start: 0.8367 (t) cc_final: 0.8154 (p) REVERT: T 447 LYS cc_start: 0.8649 (ptpt) cc_final: 0.8445 (ptpp) REVERT: T 475 GLU cc_start: 0.6624 (tm-30) cc_final: 0.6408 (tm-30) REVERT: T 482 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8333 (mp0) REVERT: T 483 MET cc_start: 0.8663 (tpt) cc_final: 0.8408 (tpp) REVERT: U 43 LYS cc_start: 0.8507 (tptt) cc_final: 0.7757 (tmmt) REVERT: U 46 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6261 (m-30) REVERT: U 72 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8001 (tm-30) REVERT: U 74 GLU cc_start: 0.8163 (pp20) cc_final: 0.7595 (pm20) REVERT: U 282 MET cc_start: 0.9125 (tpt) cc_final: 0.8696 (tpt) REVERT: U 475 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7387 (mm-30) REVERT: V 50 LYS cc_start: 0.7229 (pptt) cc_final: 0.6961 (tppp) REVERT: V 56 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8119 (tptt) REVERT: V 411 GLU cc_start: 0.8314 (mp0) cc_final: 0.8044 (mp0) REVERT: X 484 MET cc_start: 0.7687 (tmt) cc_final: 0.7474 (tmt) REVERT: Y 292 GLN cc_start: 0.8620 (tt0) cc_final: 0.8276 (tt0) REVERT: Y 366 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7132 (ptp-110) REVERT: Y 405 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8307 (ttpp) REVERT: Y 422 MET cc_start: 0.6628 (mmm) cc_final: 0.6137 (mmm) REVERT: Y 430 LYS cc_start: 0.6617 (ptpt) cc_final: 0.6118 (mtmm) REVERT: Y 437 ARG cc_start: 0.8336 (mtp180) cc_final: 0.8114 (mtp85) REVERT: Y 453 PHE cc_start: 0.8277 (p90) cc_final: 0.7858 (p90) REVERT: Y 488 MET cc_start: 0.8797 (mmm) cc_final: 0.8521 (tpt) REVERT: Z 82 ASP cc_start: 0.8778 (t0) cc_final: 0.8247 (t0) REVERT: Z 140 ILE cc_start: 0.9337 (mm) cc_final: 0.8904 (tp) REVERT: Z 198 ASN cc_start: 0.9012 (t0) cc_final: 0.8564 (t0) outliers start: 87 outliers final: 39 residues processed: 527 average time/residue: 0.6664 time to fit residues: 425.3536 Evaluate side-chains 471 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 428 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 217 GLU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 411 LYS Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 272 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 329 optimal weight: 7.9990 chunk 292 optimal weight: 0.8980 chunk 413 optimal weight: 3.9990 chunk 405 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 361 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 98 GLN F 87 ASN F 94 ASN G 98 GLN I 87 ASN J 98 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN T 539 ASN U 134 ASN V 121 ASN V 134 ASN ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 294 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095719 restraints weight = 47358.822| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.72 r_work: 0.2986 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34453 Z= 0.138 Angle : 0.561 10.034 46696 Z= 0.285 Chirality : 0.044 0.153 5527 Planarity : 0.004 0.048 6004 Dihedral : 6.477 177.306 4830 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 3.00 % Allowed : 15.89 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.12), residues: 4466 helix: -0.54 (0.11), residues: 2150 sheet: -0.98 (0.21), residues: 605 loop : -0.76 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 86 TYR 0.022 0.001 TYR U 57 PHE 0.034 0.001 PHE E 107 TRP 0.005 0.001 TRP Y 141 HIS 0.005 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (34453) covalent geometry : angle 0.56068 / 0.29 (46696) hydrogen bonds : bond 0.03754 / 2.44 ( 1604) hydrogen bonds : angle 4.75922 / 3.29 ( 4596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 466 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8540 (ttp) cc_final: 0.8257 (ttp) REVERT: A 87 ASN cc_start: 0.8183 (t0) cc_final: 0.7964 (t0) REVERT: A 95 ILE cc_start: 0.8087 (pt) cc_final: 0.7660 (mp) REVERT: B 109 LEU cc_start: 0.7503 (mp) cc_final: 0.7220 (tp) REVERT: C 74 VAL cc_start: 0.8721 (m) cc_final: 0.8443 (p) REVERT: C 81 MET cc_start: 0.8543 (ttm) cc_final: 0.8100 (ttm) REVERT: C 84 SER cc_start: 0.8761 (m) cc_final: 0.8176 (p) REVERT: C 111 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: E 61 MET cc_start: 0.8618 (mtm) cc_final: 0.7462 (mtt) REVERT: F 61 MET cc_start: 0.7041 (mtm) cc_final: 0.6814 (mtm) REVERT: G 91 ARG cc_start: 0.8432 (ttt90) cc_final: 0.7970 (ttt-90) REVERT: I 61 MET cc_start: 0.6486 (mmt) cc_final: 0.6123 (mmt) REVERT: I 117 SER cc_start: 0.8567 (m) cc_final: 0.8284 (t) REVERT: P 66 GLN cc_start: 0.8294 (tt0) cc_final: 0.7573 (mt0) REVERT: Q 38 LYS cc_start: 0.7869 (mttp) cc_final: 0.7331 (mmmm) REVERT: Q 52 TYR cc_start: 0.7063 (m-80) cc_final: 0.6583 (m-10) REVERT: R 143 ASP cc_start: 0.8814 (m-30) cc_final: 0.8548 (m-30) REVERT: S 147 ARG cc_start: 0.7786 (tmm-80) cc_final: 0.7415 (tmm-80) REVERT: S 153 ILE cc_start: 0.7158 (tt) cc_final: 0.6464 (pt) REVERT: S 183 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7463 (mp) REVERT: S 217 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: S 275 GLU cc_start: 0.7680 (pp20) cc_final: 0.7465 (pp20) REVERT: S 291 ASP cc_start: 0.8739 (t70) cc_final: 0.8437 (t0) REVERT: T 427 VAL cc_start: 0.8412 (t) cc_final: 0.8178 (p) REVERT: T 471 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7096 (tm-30) REVERT: T 482 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8266 (mp0) REVERT: T 483 MET cc_start: 0.8638 (tpt) cc_final: 0.8404 (tpp) REVERT: U 43 LYS cc_start: 0.8502 (tptt) cc_final: 0.7722 (tmmt) REVERT: U 46 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6122 (m-30) REVERT: U 57 TYR cc_start: 0.7886 (p90) cc_final: 0.7332 (p90) REVERT: U 72 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7984 (tm-30) REVERT: U 74 GLU cc_start: 0.8163 (pp20) cc_final: 0.7579 (pm20) REVERT: U 449 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: U 475 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7456 (mm-30) REVERT: V 50 LYS cc_start: 0.7287 (pptt) cc_final: 0.6909 (tppp) REVERT: V 56 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8051 (tptt) REVERT: V 411 GLU cc_start: 0.8291 (mp0) cc_final: 0.8064 (mp0) REVERT: V 449 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7559 (mt-10) REVERT: X 195 GLU cc_start: 0.8283 (tp30) cc_final: 0.7978 (tp30) REVERT: Y 292 GLN cc_start: 0.8565 (tt0) cc_final: 0.8210 (tt0) REVERT: Y 366 ARG cc_start: 0.7500 (mtp85) cc_final: 0.7226 (ptp-110) REVERT: Y 405 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8261 (ttpp) REVERT: Y 430 LYS cc_start: 0.6695 (ptpt) cc_final: 0.6195 (mtmm) REVERT: Y 437 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7676 (mtp85) REVERT: Y 453 PHE cc_start: 0.8245 (p90) cc_final: 0.7802 (p90) REVERT: Y 488 MET cc_start: 0.8750 (mmm) cc_final: 0.8462 (tpt) REVERT: Y 529 LYS cc_start: 0.8103 (tmtm) cc_final: 0.7811 (tmtm) REVERT: Y 533 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: Z 82 ASP cc_start: 0.8738 (t0) cc_final: 0.8195 (t0) REVERT: Z 198 ASN cc_start: 0.8998 (t0) cc_final: 0.8531 (t0) outliers start: 107 outliers final: 52 residues processed: 543 average time/residue: 0.6807 time to fit residues: 447.6633 Evaluate side-chains 488 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 428 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 217 GLU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 293 SER Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 449 GLU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 480 ASP Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 1 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 98 GLN G 94 ASN G 98 GLN I 87 ASN J 98 GLN P 52 GLN P 59 GLN P 71 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN T 539 ASN U 134 ASN U 488 GLN V 121 ASN V 134 ASN V 358 HIS V 452 GLN X 414 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093090 restraints weight = 47659.049| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.66 r_work: 0.2950 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34453 Z= 0.192 Angle : 0.598 9.532 46696 Z= 0.305 Chirality : 0.046 0.173 5527 Planarity : 0.004 0.049 6004 Dihedral : 6.491 169.472 4830 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.33 % Allowed : 16.90 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4466 helix: -0.31 (0.11), residues: 2144 sheet: -0.90 (0.21), residues: 597 loop : -0.69 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 283 TYR 0.021 0.002 TYR U 57 PHE 0.033 0.002 PHE E 107 TRP 0.006 0.001 TRP R 37 HIS 0.005 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (34453) covalent geometry : angle 0.59846 / 0.30 (46696) hydrogen bonds : bond 0.03987 / 2.60 ( 1604) hydrogen bonds : angle 4.79416 / 3.32 ( 4596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 446 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8448 (ttp) cc_final: 0.8040 (ttp) REVERT: A 95 ILE cc_start: 0.8054 (pt) cc_final: 0.7690 (mm) REVERT: C 74 VAL cc_start: 0.8771 (m) cc_final: 0.8484 (p) REVERT: C 81 MET cc_start: 0.8617 (ttm) cc_final: 0.8159 (ttm) REVERT: C 84 SER cc_start: 0.8815 (m) cc_final: 0.8214 (p) REVERT: D 61 MET cc_start: 0.6737 (mmt) cc_final: 0.5916 (mmt) REVERT: E 61 MET cc_start: 0.8628 (mtm) cc_final: 0.7388 (mtt) REVERT: E 62 VAL cc_start: 0.8136 (p) cc_final: 0.7780 (t) REVERT: F 61 MET cc_start: 0.7073 (mtm) cc_final: 0.6870 (mtm) REVERT: G 91 ARG cc_start: 0.8531 (ttt90) cc_final: 0.8123 (ttt-90) REVERT: I 61 MET cc_start: 0.6162 (mmt) cc_final: 0.5731 (mmt) REVERT: I 81 MET cc_start: 0.8335 (ttp) cc_final: 0.7991 (ttp) REVERT: I 117 SER cc_start: 0.8550 (m) cc_final: 0.8271 (t) REVERT: P 66 GLN cc_start: 0.8319 (tt0) cc_final: 0.7591 (mt0) REVERT: P 69 LYS cc_start: 0.8033 (tttm) cc_final: 0.7679 (tptt) REVERT: P 128 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7856 (mt-10) REVERT: Q 38 LYS cc_start: 0.7889 (mttp) cc_final: 0.7347 (mmmm) REVERT: Q 52 TYR cc_start: 0.7158 (m-80) cc_final: 0.6705 (m-10) REVERT: R 54 TYR cc_start: 0.8132 (m-80) cc_final: 0.7918 (m-80) REVERT: R 143 ASP cc_start: 0.8846 (m-30) cc_final: 0.8559 (m-30) REVERT: S 124 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6900 (ptm-80) REVERT: S 147 ARG cc_start: 0.7816 (tmm-80) cc_final: 0.7414 (tmm-80) REVERT: S 153 ILE cc_start: 0.7294 (tt) cc_final: 0.6644 (pt) REVERT: S 183 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7540 (mp) REVERT: S 275 GLU cc_start: 0.7737 (pp20) cc_final: 0.7242 (pp20) REVERT: S 291 ASP cc_start: 0.8774 (t70) cc_final: 0.8449 (t0) REVERT: T 179 ASN cc_start: 0.8713 (t0) cc_final: 0.8407 (t0) REVERT: T 411 GLU cc_start: 0.8028 (mp0) cc_final: 0.7715 (mm-30) REVERT: T 471 GLN cc_start: 0.7414 (tm-30) cc_final: 0.7186 (tm-30) REVERT: T 483 MET cc_start: 0.8677 (tpt) cc_final: 0.8441 (tpp) REVERT: U 43 LYS cc_start: 0.8536 (tptt) cc_final: 0.7734 (tmmt) REVERT: U 46 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6281 (m-30) REVERT: U 57 TYR cc_start: 0.7861 (p90) cc_final: 0.7274 (p90) REVERT: U 72 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8066 (tm-30) REVERT: U 74 GLU cc_start: 0.8216 (pp20) cc_final: 0.7626 (pm20) REVERT: U 282 MET cc_start: 0.9119 (tpt) cc_final: 0.8687 (tpt) REVERT: U 475 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7515 (mm-30) REVERT: V 50 LYS cc_start: 0.7339 (pptt) cc_final: 0.6957 (tppp) REVERT: V 56 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8063 (tptt) REVERT: V 411 GLU cc_start: 0.8303 (mp0) cc_final: 0.8068 (mp0) REVERT: X 195 GLU cc_start: 0.8400 (tp30) cc_final: 0.8130 (tp30) REVERT: X 303 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8853 (mtt180) REVERT: X 535 LYS cc_start: 0.7524 (mppt) cc_final: 0.7182 (mtpm) REVERT: Y 292 GLN cc_start: 0.8566 (tt0) cc_final: 0.8181 (tt0) REVERT: Y 366 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7268 (ptp-110) REVERT: Y 371 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8252 (mp) REVERT: Y 405 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8261 (ttpp) REVERT: Y 430 LYS cc_start: 0.6769 (ptpt) cc_final: 0.6262 (mtmm) REVERT: Y 453 PHE cc_start: 0.8295 (p90) cc_final: 0.7934 (p90) REVERT: Y 488 MET cc_start: 0.8738 (mmm) cc_final: 0.8518 (mmm) REVERT: Z 82 ASP cc_start: 0.8768 (t0) cc_final: 0.8216 (t0) REVERT: Z 198 ASN cc_start: 0.9034 (t0) cc_final: 0.8566 (t0) REVERT: Z 480 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7778 (m-30) outliers start: 119 outliers final: 60 residues processed: 531 average time/residue: 0.6856 time to fit residues: 439.6700 Evaluate side-chains 492 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 424 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 293 SER Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 76 SER Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 303 ARG Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 371 LEU Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 296 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 365 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 258 optimal weight: 0.9980 chunk 350 optimal weight: 0.0770 chunk 382 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 330 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN B 98 GLN G 98 GLN I 87 ASN P 52 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN U 134 ASN U 386 GLN V 121 ASN V 134 ASN V 452 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099236 restraints weight = 47452.479| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.85 r_work: 0.2971 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34453 Z= 0.117 Angle : 0.553 9.690 46696 Z= 0.281 Chirality : 0.043 0.147 5527 Planarity : 0.004 0.054 6004 Dihedral : 6.114 148.489 4830 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 2.83 % Allowed : 17.88 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4466 helix: 0.00 (0.11), residues: 2141 sheet: -0.88 (0.21), residues: 607 loop : -0.55 (0.16), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 86 TYR 0.019 0.001 TYR U 57 PHE 0.036 0.001 PHE E 107 TRP 0.005 0.001 TRP U 73 HIS 0.005 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (34453) covalent geometry : angle 0.55344 / 0.28 (46696) hydrogen bonds : bond 0.03502 / 2.29 ( 1604) hydrogen bonds : angle 4.59978 / 3.19 ( 4596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 463 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 66 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8003 (t) REVERT: A 81 MET cc_start: 0.8493 (ttp) cc_final: 0.8204 (ttp) REVERT: A 95 ILE cc_start: 0.8095 (pt) cc_final: 0.7677 (mm) REVERT: A 107 PHE cc_start: 0.8313 (t80) cc_final: 0.8010 (t80) REVERT: B 95 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8233 (mp) REVERT: C 74 VAL cc_start: 0.8778 (m) cc_final: 0.8560 (p) REVERT: C 81 MET cc_start: 0.8571 (ttm) cc_final: 0.8158 (ttm) REVERT: C 84 SER cc_start: 0.8837 (m) cc_final: 0.8282 (p) REVERT: D 61 MET cc_start: 0.6733 (mmt) cc_final: 0.5916 (mmt) REVERT: E 61 MET cc_start: 0.8656 (mtm) cc_final: 0.7391 (mtt) REVERT: F 61 MET cc_start: 0.7037 (mtm) cc_final: 0.6831 (mtm) REVERT: F 81 MET cc_start: 0.8461 (ttp) cc_final: 0.8189 (ppp) REVERT: G 91 ARG cc_start: 0.8555 (ttt90) cc_final: 0.8182 (ttt-90) REVERT: G 98 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: G 102 TYR cc_start: 0.7746 (m-10) cc_final: 0.7526 (m-10) REVERT: H 84 SER cc_start: 0.8637 (m) cc_final: 0.8196 (t) REVERT: I 61 MET cc_start: 0.6395 (mmt) cc_final: 0.5943 (mmt) REVERT: I 81 MET cc_start: 0.8397 (ttp) cc_final: 0.8053 (ttp) REVERT: I 117 SER cc_start: 0.8525 (m) cc_final: 0.8282 (t) REVERT: P 66 GLN cc_start: 0.8316 (tt0) cc_final: 0.7586 (mt0) REVERT: P 69 LYS cc_start: 0.8048 (tttm) cc_final: 0.7632 (tptt) REVERT: P 73 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6961 (mt-10) REVERT: P 84 HIS cc_start: 0.7749 (m-70) cc_final: 0.7535 (m-70) REVERT: P 128 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7876 (mt-10) REVERT: Q 38 LYS cc_start: 0.7883 (mttp) cc_final: 0.7346 (mmmm) REVERT: Q 48 ARG cc_start: 0.8257 (ptt-90) cc_final: 0.8010 (ptt90) REVERT: Q 52 TYR cc_start: 0.7161 (m-80) cc_final: 0.6680 (m-10) REVERT: R 54 TYR cc_start: 0.8148 (m-80) cc_final: 0.7918 (m-80) REVERT: R 127 PHE cc_start: 0.8324 (m-80) cc_final: 0.8111 (m-80) REVERT: R 143 ASP cc_start: 0.8820 (m-30) cc_final: 0.8576 (m-30) REVERT: S 147 ARG cc_start: 0.7795 (tmm-80) cc_final: 0.7394 (tmm-80) REVERT: S 153 ILE cc_start: 0.7294 (tt) cc_final: 0.6444 (pt) REVERT: S 183 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7437 (mp) REVERT: S 275 GLU cc_start: 0.7722 (pp20) cc_final: 0.7318 (pp20) REVERT: S 291 ASP cc_start: 0.8804 (t70) cc_final: 0.8513 (t0) REVERT: T 179 ASN cc_start: 0.8691 (t0) cc_final: 0.8445 (t0) REVERT: T 411 GLU cc_start: 0.8037 (mp0) cc_final: 0.7708 (mm-30) REVERT: T 471 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7145 (tm-30) REVERT: T 483 MET cc_start: 0.8728 (tpt) cc_final: 0.8503 (tpp) REVERT: U 43 LYS cc_start: 0.8493 (tptt) cc_final: 0.7704 (tmmt) REVERT: U 46 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6312 (m-30) REVERT: U 57 TYR cc_start: 0.7905 (p90) cc_final: 0.7402 (p90) REVERT: U 72 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8078 (tm-30) REVERT: U 74 GLU cc_start: 0.8205 (pp20) cc_final: 0.7601 (pm20) REVERT: U 282 MET cc_start: 0.9138 (tpt) cc_final: 0.8756 (tpt) REVERT: U 474 LEU cc_start: 0.7870 (tp) cc_final: 0.7541 (mt) REVERT: U 475 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7640 (mm-30) REVERT: V 50 LYS cc_start: 0.7312 (pptt) cc_final: 0.6896 (tppp) REVERT: V 56 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8041 (tptt) REVERT: V 411 GLU cc_start: 0.8258 (mp0) cc_final: 0.8054 (mp0) REVERT: X 195 GLU cc_start: 0.8402 (tp30) cc_final: 0.8147 (tp30) REVERT: X 285 ASP cc_start: 0.7942 (t0) cc_final: 0.7697 (t0) REVERT: X 303 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8795 (mtt180) REVERT: X 535 LYS cc_start: 0.7514 (mppt) cc_final: 0.7249 (mtpm) REVERT: Y 292 GLN cc_start: 0.8634 (tt0) cc_final: 0.8284 (tt0) REVERT: Y 366 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7275 (ptp-110) REVERT: Y 405 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8365 (ttpp) REVERT: Y 430 LYS cc_start: 0.6779 (ptpt) cc_final: 0.6271 (mtmm) REVERT: Y 437 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7863 (mtp85) REVERT: Y 453 PHE cc_start: 0.8217 (p90) cc_final: 0.7766 (p90) REVERT: Y 488 MET cc_start: 0.8757 (mmm) cc_final: 0.8542 (mmm) REVERT: Y 529 LYS cc_start: 0.8122 (tmtm) cc_final: 0.7811 (tmtm) REVERT: Y 533 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: Z 82 ASP cc_start: 0.8780 (t0) cc_final: 0.8237 (t0) REVERT: Z 198 ASN cc_start: 0.9025 (t0) cc_final: 0.8541 (t0) REVERT: Z 480 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7908 (m-30) outliers start: 101 outliers final: 55 residues processed: 542 average time/residue: 0.6683 time to fit residues: 439.5138 Evaluate side-chains 503 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 438 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 293 SER Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 303 ARG Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 385 ARG Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 480 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 130 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 414 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 395 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 426 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 211 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 98 GLN G 98 GLN I 87 ASN P 52 GLN P 59 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN U 134 ASN U 529 ASN V 121 ASN V 134 ASN V 452 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.095554 restraints weight = 47523.683| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.81 r_work: 0.2978 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34453 Z= 0.135 Angle : 0.560 9.824 46696 Z= 0.284 Chirality : 0.044 0.211 5527 Planarity : 0.004 0.064 6004 Dihedral : 5.952 129.771 4830 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 3.05 % Allowed : 18.10 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4466 helix: 0.13 (0.11), residues: 2142 sheet: -0.81 (0.21), residues: 607 loop : -0.51 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 86 TYR 0.019 0.001 TYR U 57 PHE 0.037 0.001 PHE E 107 TRP 0.004 0.001 TRP R 37 HIS 0.005 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (34453) covalent geometry : angle 0.56017 / 0.28 (46696) hydrogen bonds : bond 0.03534 / 2.31 ( 1604) hydrogen bonds : angle 4.56440 / 3.16 ( 4596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 458 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 66 CYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7994 (t) REVERT: A 81 MET cc_start: 0.8467 (ttp) cc_final: 0.8108 (ttp) REVERT: A 95 ILE cc_start: 0.8075 (pt) cc_final: 0.7742 (mm) REVERT: A 107 PHE cc_start: 0.8334 (t80) cc_final: 0.8018 (t80) REVERT: B 95 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8150 (mp) REVERT: C 74 VAL cc_start: 0.8759 (m) cc_final: 0.8549 (p) REVERT: C 81 MET cc_start: 0.8555 (ttm) cc_final: 0.8141 (ttm) REVERT: C 84 SER cc_start: 0.8804 (m) cc_final: 0.8258 (p) REVERT: D 61 MET cc_start: 0.6701 (mmt) cc_final: 0.5930 (mmt) REVERT: E 61 MET cc_start: 0.8656 (mtm) cc_final: 0.7399 (mtt) REVERT: F 61 MET cc_start: 0.7060 (mtm) cc_final: 0.6848 (mtm) REVERT: F 81 MET cc_start: 0.8382 (ttp) cc_final: 0.8115 (ppp) REVERT: G 98 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: G 102 TYR cc_start: 0.7780 (m-10) cc_final: 0.7569 (m-10) REVERT: H 84 SER cc_start: 0.8640 (m) cc_final: 0.8262 (t) REVERT: I 61 MET cc_start: 0.6379 (mmt) cc_final: 0.6036 (mmt) REVERT: I 81 MET cc_start: 0.8380 (ttp) cc_final: 0.8095 (ttp) REVERT: I 117 SER cc_start: 0.8443 (m) cc_final: 0.8223 (t) REVERT: J 102 TYR cc_start: 0.7835 (m-80) cc_final: 0.7620 (m-10) REVERT: P 66 GLN cc_start: 0.8301 (tt0) cc_final: 0.7581 (mt0) REVERT: P 69 LYS cc_start: 0.8014 (tttm) cc_final: 0.7641 (tptt) REVERT: P 84 HIS cc_start: 0.7652 (m-70) cc_final: 0.7428 (m-70) REVERT: P 128 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7875 (mt-10) REVERT: Q 10 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6233 (mpt90) REVERT: Q 38 LYS cc_start: 0.7879 (mttp) cc_final: 0.7332 (mmmm) REVERT: Q 48 ARG cc_start: 0.8235 (ptt-90) cc_final: 0.7986 (ptt90) REVERT: Q 52 TYR cc_start: 0.7154 (m-80) cc_final: 0.6681 (m-10) REVERT: R 54 TYR cc_start: 0.8138 (m-80) cc_final: 0.7904 (m-80) REVERT: R 143 ASP cc_start: 0.8818 (m-30) cc_final: 0.8543 (m-30) REVERT: S 147 ARG cc_start: 0.7774 (tmm-80) cc_final: 0.7364 (tmm-80) REVERT: S 153 ILE cc_start: 0.7276 (tt) cc_final: 0.6648 (pt) REVERT: S 183 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7379 (mp) REVERT: S 217 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: S 220 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7701 (mm) REVERT: S 275 GLU cc_start: 0.7680 (pp20) cc_final: 0.7411 (pp20) REVERT: S 291 ASP cc_start: 0.8769 (t70) cc_final: 0.8461 (t0) REVERT: T 179 ASN cc_start: 0.8649 (t0) cc_final: 0.8402 (t0) REVERT: T 411 GLU cc_start: 0.8027 (mp0) cc_final: 0.7702 (mm-30) REVERT: T 479 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6301 (mpt180) REVERT: T 483 MET cc_start: 0.8678 (tpt) cc_final: 0.8416 (tpp) REVERT: U 46 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6450 (m-30) REVERT: U 57 TYR cc_start: 0.7864 (p90) cc_final: 0.7396 (p90) REVERT: U 72 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8065 (tm-30) REVERT: U 74 GLU cc_start: 0.8196 (pp20) cc_final: 0.7566 (pm20) REVERT: U 150 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8827 (mm) REVERT: U 282 MET cc_start: 0.9114 (tpt) cc_final: 0.8717 (tpt) REVERT: U 474 LEU cc_start: 0.7805 (tp) cc_final: 0.7479 (mt) REVERT: U 475 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7699 (mm-30) REVERT: V 43 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6741 (mmmt) REVERT: V 50 LYS cc_start: 0.7364 (pptt) cc_final: 0.6923 (tppp) REVERT: V 56 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8067 (tptt) REVERT: V 169 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: V 411 GLU cc_start: 0.8233 (mp0) cc_final: 0.7986 (mp0) REVERT: V 515 GLN cc_start: 0.8117 (mt0) cc_final: 0.7780 (pt0) REVERT: X 195 GLU cc_start: 0.8394 (tp30) cc_final: 0.8133 (tp30) REVERT: X 303 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8818 (mtt180) REVERT: X 535 LYS cc_start: 0.7473 (mppt) cc_final: 0.7220 (mtpm) REVERT: Y 292 GLN cc_start: 0.8562 (tt0) cc_final: 0.8188 (tt0) REVERT: Y 366 ARG cc_start: 0.7470 (mtp85) cc_final: 0.7269 (ptp-110) REVERT: Y 405 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8347 (ttpp) REVERT: Y 430 LYS cc_start: 0.6754 (ptpt) cc_final: 0.6258 (mtmm) REVERT: Y 437 ARG cc_start: 0.8409 (mtp180) cc_final: 0.7809 (mtp85) REVERT: Y 453 PHE cc_start: 0.8224 (p90) cc_final: 0.7785 (p90) REVERT: Y 501 LYS cc_start: 0.7556 (tmmm) cc_final: 0.7353 (tmmm) REVERT: Y 504 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6619 (mtpt) REVERT: Y 529 LYS cc_start: 0.8122 (tmtm) cc_final: 0.7802 (tmtm) REVERT: Y 533 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: Z 82 ASP cc_start: 0.8756 (t0) cc_final: 0.8211 (t0) REVERT: Z 198 ASN cc_start: 0.9015 (t0) cc_final: 0.8526 (t0) outliers start: 109 outliers final: 58 residues processed: 540 average time/residue: 0.6881 time to fit residues: 447.7129 Evaluate side-chains 518 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 444 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 10 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 217 GLU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 293 SER Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 150 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 56 LYS Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 303 ARG Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 385 ARG Chi-restraints excluded: chain Z residue 473 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 381 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 294 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 98 GLN G 98 GLN I 87 ASN J 98 GLN P 52 GLN P 59 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN U 134 ASN U 529 ASN V 121 ASN V 134 ASN V 452 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094666 restraints weight = 47431.957| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.66 r_work: 0.2974 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34453 Z= 0.152 Angle : 0.574 10.388 46696 Z= 0.291 Chirality : 0.044 0.177 5527 Planarity : 0.004 0.057 6004 Dihedral : 5.868 113.561 4830 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 4466 helix: 0.18 (0.11), residues: 2143 sheet: -0.75 (0.21), residues: 607 loop : -0.50 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG V 86 TYR 0.019 0.002 TYR C 102 PHE 0.039 0.001 PHE E 107 TRP 0.005 0.001 TRP R 37 HIS 0.008 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (34453) covalent geometry : angle 0.57413 / 0.29 (46696) hydrogen bonds : bond 0.03612 / 2.36 ( 1604) hydrogen bonds : angle 4.58286 / 3.17 ( 4596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 445 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 66 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7996 (t) REVERT: A 81 MET cc_start: 0.8453 (ttp) cc_final: 0.8076 (ttp) REVERT: A 95 ILE cc_start: 0.8076 (pt) cc_final: 0.7751 (mm) REVERT: A 107 PHE cc_start: 0.8394 (t80) cc_final: 0.7962 (t80) REVERT: B 61 MET cc_start: 0.6995 (mtt) cc_final: 0.6767 (ttt) REVERT: B 95 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 81 MET cc_start: 0.8555 (ttm) cc_final: 0.8133 (ttm) REVERT: C 84 SER cc_start: 0.8813 (m) cc_final: 0.8275 (p) REVERT: D 61 MET cc_start: 0.6695 (mmt) cc_final: 0.5914 (mmt) REVERT: E 61 MET cc_start: 0.8631 (mtm) cc_final: 0.7422 (mtt) REVERT: F 61 MET cc_start: 0.7046 (mtm) cc_final: 0.6835 (mtm) REVERT: F 81 MET cc_start: 0.8469 (ttp) cc_final: 0.7887 (ppp) REVERT: F 119 LEU cc_start: 0.7689 (tt) cc_final: 0.7437 (tp) REVERT: G 86 ILE cc_start: 0.8675 (mt) cc_final: 0.8430 (mp) REVERT: G 98 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: G 102 TYR cc_start: 0.7786 (m-10) cc_final: 0.7541 (m-10) REVERT: H 84 SER cc_start: 0.8639 (m) cc_final: 0.8256 (t) REVERT: I 61 MET cc_start: 0.6358 (mmt) cc_final: 0.6011 (mmt) REVERT: I 81 MET cc_start: 0.8366 (ttp) cc_final: 0.8074 (ttp) REVERT: I 117 SER cc_start: 0.8415 (m) cc_final: 0.8194 (t) REVERT: J 102 TYR cc_start: 0.7936 (m-80) cc_final: 0.7667 (m-10) REVERT: P 66 GLN cc_start: 0.8321 (tt0) cc_final: 0.7607 (mt0) REVERT: P 69 LYS cc_start: 0.8002 (tttm) cc_final: 0.7713 (tptt) REVERT: P 84 HIS cc_start: 0.7650 (m-70) cc_final: 0.7416 (m-70) REVERT: P 128 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7709 (mt-10) REVERT: P 146 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8205 (tm) REVERT: Q 10 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6199 (mpt90) REVERT: Q 27 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8547 (tm) REVERT: Q 38 LYS cc_start: 0.7883 (mttp) cc_final: 0.7342 (mmmm) REVERT: Q 48 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7966 (ptt90) REVERT: Q 52 TYR cc_start: 0.7158 (m-80) cc_final: 0.6683 (m-10) REVERT: R 54 TYR cc_start: 0.8134 (m-80) cc_final: 0.7895 (m-80) REVERT: R 143 ASP cc_start: 0.8810 (m-30) cc_final: 0.8560 (m-30) REVERT: S 147 ARG cc_start: 0.7777 (tmm-80) cc_final: 0.7371 (tmm-80) REVERT: S 153 ILE cc_start: 0.7334 (tt) cc_final: 0.6664 (pt) REVERT: S 183 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7410 (mp) REVERT: S 220 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7720 (mm) REVERT: S 275 GLU cc_start: 0.7668 (pp20) cc_final: 0.7422 (pp20) REVERT: S 291 ASP cc_start: 0.8754 (t70) cc_final: 0.8449 (t0) REVERT: T 179 ASN cc_start: 0.8644 (t0) cc_final: 0.8392 (t0) REVERT: T 411 GLU cc_start: 0.8034 (mp0) cc_final: 0.7702 (mm-30) REVERT: T 479 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6290 (mpt180) REVERT: U 46 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: U 57 TYR cc_start: 0.7841 (p90) cc_final: 0.7334 (p90) REVERT: U 59 ILE cc_start: 0.8143 (mt) cc_final: 0.7859 (mt) REVERT: U 72 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8065 (tm-30) REVERT: U 74 GLU cc_start: 0.8062 (pp20) cc_final: 0.7511 (pm20) REVERT: U 150 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8824 (mm) REVERT: U 474 LEU cc_start: 0.7794 (tp) cc_final: 0.7462 (mt) REVERT: U 475 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7714 (mm-30) REVERT: V 43 LYS cc_start: 0.7051 (mmmt) cc_final: 0.6833 (mmmt) REVERT: V 50 LYS cc_start: 0.7366 (pptt) cc_final: 0.7002 (tppt) REVERT: V 169 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: V 411 GLU cc_start: 0.8238 (mp0) cc_final: 0.7999 (mp0) REVERT: V 515 GLN cc_start: 0.8123 (mt0) cc_final: 0.7779 (pt0) REVERT: X 195 GLU cc_start: 0.8294 (tp30) cc_final: 0.8022 (tp30) REVERT: X 303 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8823 (mtt180) REVERT: Y 292 GLN cc_start: 0.8569 (tt0) cc_final: 0.8169 (tt0) REVERT: Y 366 ARG cc_start: 0.7463 (mtp85) cc_final: 0.7255 (ptp-110) REVERT: Y 405 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8531 (ttmt) REVERT: Y 430 LYS cc_start: 0.6777 (ptpt) cc_final: 0.6277 (mtmm) REVERT: Y 437 ARG cc_start: 0.8396 (mtp180) cc_final: 0.8040 (mtp85) REVERT: Y 453 PHE cc_start: 0.8241 (p90) cc_final: 0.7803 (p90) REVERT: Y 488 MET cc_start: 0.8787 (mmm) cc_final: 0.8575 (tpt) REVERT: Y 529 LYS cc_start: 0.8132 (tmtm) cc_final: 0.7781 (tmtm) REVERT: Y 533 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: Z 82 ASP cc_start: 0.8745 (t0) cc_final: 0.8200 (t0) REVERT: Z 198 ASN cc_start: 0.9010 (t0) cc_final: 0.8531 (t0) outliers start: 105 outliers final: 66 residues processed: 516 average time/residue: 0.6814 time to fit residues: 425.9027 Evaluate side-chains 515 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 434 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 10 ARG Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 293 SER Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 150 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 303 ARG Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 405 LYS Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 385 ARG Chi-restraints excluded: chain Z residue 473 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 51 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 440 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 354 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 chunk 249 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 98 GLN G 98 GLN I 87 ASN J 98 GLN P 52 GLN P 59 GLN T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN T 539 ASN U 61 HIS U 134 ASN U 529 ASN V 121 ASN V 134 ASN V 452 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095188 restraints weight = 47369.443| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.67 r_work: 0.2984 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34453 Z= 0.138 Angle : 0.579 11.305 46696 Z= 0.291 Chirality : 0.044 0.163 5527 Planarity : 0.004 0.058 6004 Dihedral : 5.757 102.616 4830 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 2.83 % Allowed : 18.91 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 4466 helix: 0.27 (0.11), residues: 2144 sheet: -0.72 (0.21), residues: 601 loop : -0.46 (0.16), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 86 TYR 0.021 0.001 TYR C 102 PHE 0.041 0.001 PHE E 107 TRP 0.005 0.001 TRP R 37 HIS 0.006 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (34453) covalent geometry : angle 0.57885 / 0.29 (46696) hydrogen bonds : bond 0.03523 / 2.31 ( 1604) hydrogen bonds : angle 4.55230 / 3.15 ( 4596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 442 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 66 CYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 81 MET cc_start: 0.8451 (ttp) cc_final: 0.8093 (ttp) REVERT: A 95 ILE cc_start: 0.8087 (pt) cc_final: 0.7769 (mm) REVERT: A 107 PHE cc_start: 0.8391 (t80) cc_final: 0.7959 (t80) REVERT: C 81 MET cc_start: 0.8565 (ttm) cc_final: 0.8152 (ttm) REVERT: C 84 SER cc_start: 0.8807 (m) cc_final: 0.8278 (p) REVERT: D 61 MET cc_start: 0.6716 (mmt) cc_final: 0.5991 (mmt) REVERT: E 61 MET cc_start: 0.8630 (mtm) cc_final: 0.7407 (mtt) REVERT: F 61 MET cc_start: 0.6955 (mtm) cc_final: 0.6745 (mtm) REVERT: F 81 MET cc_start: 0.8431 (ttp) cc_final: 0.7829 (ppp) REVERT: F 119 LEU cc_start: 0.7663 (tt) cc_final: 0.7404 (tp) REVERT: G 86 ILE cc_start: 0.8677 (mt) cc_final: 0.8457 (mp) REVERT: G 98 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: G 102 TYR cc_start: 0.7799 (m-10) cc_final: 0.7582 (m-10) REVERT: H 61 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7366 (mtp) REVERT: H 84 SER cc_start: 0.8634 (m) cc_final: 0.8258 (t) REVERT: I 61 MET cc_start: 0.6198 (mmt) cc_final: 0.5849 (mmt) REVERT: I 81 MET cc_start: 0.8369 (ttp) cc_final: 0.8067 (ttp) REVERT: I 117 SER cc_start: 0.8415 (m) cc_final: 0.8204 (t) REVERT: J 102 TYR cc_start: 0.7942 (m-80) cc_final: 0.7720 (m-10) REVERT: P 69 LYS cc_start: 0.8002 (tttm) cc_final: 0.7785 (tptt) REVERT: P 84 HIS cc_start: 0.7648 (m-70) cc_final: 0.7324 (m-70) REVERT: P 128 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7614 (mt-10) REVERT: P 146 LEU cc_start: 0.8516 (tp) cc_final: 0.8254 (tm) REVERT: Q 10 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6157 (mpt90) REVERT: Q 38 LYS cc_start: 0.7884 (mttp) cc_final: 0.7344 (mmmm) REVERT: Q 48 ARG cc_start: 0.8219 (ptt-90) cc_final: 0.7954 (ptt90) REVERT: Q 52 TYR cc_start: 0.7155 (m-80) cc_final: 0.6601 (m-10) REVERT: R 54 TYR cc_start: 0.8123 (m-80) cc_final: 0.7883 (m-80) REVERT: R 143 ASP cc_start: 0.8801 (m-30) cc_final: 0.8558 (m-30) REVERT: S 147 ARG cc_start: 0.7764 (tmm-80) cc_final: 0.7360 (tmm-80) REVERT: S 153 ILE cc_start: 0.7344 (tt) cc_final: 0.6636 (pt) REVERT: S 183 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7554 (mp) REVERT: S 220 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7724 (mm) REVERT: S 275 GLU cc_start: 0.7662 (pp20) cc_final: 0.7268 (pp20) REVERT: S 291 ASP cc_start: 0.8747 (t70) cc_final: 0.8446 (t0) REVERT: T 179 ASN cc_start: 0.8674 (t0) cc_final: 0.8422 (t0) REVERT: T 411 GLU cc_start: 0.8050 (mp0) cc_final: 0.7712 (mm-30) REVERT: T 479 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6355 (mpt180) REVERT: U 46 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: U 57 TYR cc_start: 0.7829 (p90) cc_final: 0.7393 (p90) REVERT: U 59 ILE cc_start: 0.8117 (mt) cc_final: 0.7871 (mt) REVERT: U 72 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8059 (tm-30) REVERT: U 74 GLU cc_start: 0.8063 (pp20) cc_final: 0.7517 (pm20) REVERT: U 150 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8815 (mm) REVERT: U 474 LEU cc_start: 0.7792 (tp) cc_final: 0.7457 (mt) REVERT: U 475 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7712 (mm-30) REVERT: V 43 LYS cc_start: 0.7035 (mmmt) cc_final: 0.6810 (mmmt) REVERT: V 50 LYS cc_start: 0.7391 (pptt) cc_final: 0.7017 (tppt) REVERT: V 169 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: V 411 GLU cc_start: 0.8259 (mp0) cc_final: 0.8037 (mp0) REVERT: V 471 GLN cc_start: 0.6796 (tm-30) cc_final: 0.6533 (tp40) REVERT: V 515 GLN cc_start: 0.8153 (mt0) cc_final: 0.7815 (pt0) REVERT: X 195 GLU cc_start: 0.8287 (tp30) cc_final: 0.8014 (tp30) REVERT: X 285 ASP cc_start: 0.7862 (t0) cc_final: 0.7640 (t0) REVERT: X 303 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8814 (mtt180) REVERT: Y 292 GLN cc_start: 0.8564 (tt0) cc_final: 0.8172 (tt0) REVERT: Y 430 LYS cc_start: 0.6801 (ptpt) cc_final: 0.6306 (mtmm) REVERT: Y 437 ARG cc_start: 0.8385 (mtp180) cc_final: 0.8043 (mtp85) REVERT: Y 453 PHE cc_start: 0.8238 (p90) cc_final: 0.7802 (p90) REVERT: Y 488 MET cc_start: 0.8786 (mmm) cc_final: 0.8569 (tpt) REVERT: Z 82 ASP cc_start: 0.8737 (t0) cc_final: 0.8196 (t0) REVERT: Z 198 ASN cc_start: 0.8995 (t0) cc_final: 0.8525 (t0) REVERT: Z 202 LYS cc_start: 0.8393 (mmtp) cc_final: 0.8163 (mmtp) outliers start: 101 outliers final: 65 residues processed: 512 average time/residue: 0.6561 time to fit residues: 406.5388 Evaluate side-chains 500 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 424 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 10 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 293 SER Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 150 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 303 ARG Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 385 ARG Chi-restraints excluded: chain Z residue 473 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 68 optimal weight: 10.0000 chunk 371 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 419 optimal weight: 0.0470 chunk 275 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 348 optimal weight: 0.9990 chunk 373 optimal weight: 0.0570 chunk 345 optimal weight: 0.9980 chunk 308 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN J 98 GLN P 52 GLN P 59 GLN R 154 GLN T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN U 134 ASN U 529 ASN V 121 ASN V 134 ASN V 452 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096697 restraints weight = 47751.665| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.80 r_work: 0.2993 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34453 Z= 0.118 Angle : 0.571 11.009 46696 Z= 0.287 Chirality : 0.043 0.159 5527 Planarity : 0.004 0.061 6004 Dihedral : 5.636 93.328 4830 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 2.33 % Allowed : 19.78 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4466 helix: 0.35 (0.12), residues: 2152 sheet: -0.73 (0.21), residues: 607 loop : -0.42 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 86 TYR 0.025 0.001 TYR C 102 PHE 0.044 0.001 PHE E 107 TRP 0.004 0.001 TRP R 37 HIS 0.006 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (34453) covalent geometry : angle 0.57094 / 0.29 (46696) hydrogen bonds : bond 0.03388 / 2.22 ( 1604) hydrogen bonds : angle 4.50304 / 3.11 ( 4596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 448 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 66 CYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7845 (t) REVERT: A 81 MET cc_start: 0.8458 (ttp) cc_final: 0.8093 (ttp) REVERT: A 95 ILE cc_start: 0.8012 (pt) cc_final: 0.7723 (mm) REVERT: A 107 PHE cc_start: 0.8396 (t80) cc_final: 0.7933 (t80) REVERT: B 95 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7970 (mp) REVERT: C 81 MET cc_start: 0.8566 (ttm) cc_final: 0.8156 (ttm) REVERT: C 84 SER cc_start: 0.8809 (m) cc_final: 0.8295 (p) REVERT: C 98 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: D 61 MET cc_start: 0.6691 (mmt) cc_final: 0.5918 (mmt) REVERT: E 61 MET cc_start: 0.8673 (mtm) cc_final: 0.7423 (mtt) REVERT: F 61 MET cc_start: 0.6902 (mtm) cc_final: 0.6699 (mtm) REVERT: F 81 MET cc_start: 0.8459 (ttp) cc_final: 0.8078 (ppp) REVERT: F 119 LEU cc_start: 0.7654 (tt) cc_final: 0.7377 (tp) REVERT: G 86 ILE cc_start: 0.8685 (mt) cc_final: 0.8433 (mp) REVERT: G 98 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: H 61 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7342 (mtp) REVERT: H 84 SER cc_start: 0.8586 (m) cc_final: 0.8239 (t) REVERT: I 61 MET cc_start: 0.6367 (mmt) cc_final: 0.6016 (mmt) REVERT: I 81 MET cc_start: 0.8387 (ttp) cc_final: 0.8077 (ttp) REVERT: I 117 SER cc_start: 0.8392 (m) cc_final: 0.8192 (t) REVERT: J 100 VAL cc_start: 0.7598 (t) cc_final: 0.7207 (m) REVERT: J 102 TYR cc_start: 0.7962 (m-80) cc_final: 0.7720 (m-10) REVERT: P 66 GLN cc_start: 0.8325 (tt0) cc_final: 0.7597 (mt0) REVERT: P 69 LYS cc_start: 0.7993 (tttm) cc_final: 0.7697 (tptt) REVERT: P 73 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7311 (mt-10) REVERT: P 84 HIS cc_start: 0.7667 (m-70) cc_final: 0.7398 (m-70) REVERT: P 146 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8262 (tm) REVERT: Q 10 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6139 (mpt90) REVERT: Q 38 LYS cc_start: 0.7903 (mttp) cc_final: 0.7359 (mmmm) REVERT: Q 52 TYR cc_start: 0.7139 (m-80) cc_final: 0.6623 (m-10) REVERT: R 54 TYR cc_start: 0.8114 (m-80) cc_final: 0.7858 (m-80) REVERT: R 143 ASP cc_start: 0.8800 (m-30) cc_final: 0.8526 (m-30) REVERT: R 175 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5370 (pp20) REVERT: S 62 MET cc_start: 0.8574 (mmm) cc_final: 0.8354 (mmm) REVERT: S 147 ARG cc_start: 0.7691 (tmm-80) cc_final: 0.7284 (tmm-80) REVERT: S 153 ILE cc_start: 0.7246 (tt) cc_final: 0.6659 (pt) REVERT: S 183 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7517 (mp) REVERT: S 220 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7736 (mm) REVERT: S 275 GLU cc_start: 0.7668 (pp20) cc_final: 0.7274 (pp20) REVERT: S 291 ASP cc_start: 0.8753 (t70) cc_final: 0.8471 (t0) REVERT: T 179 ASN cc_start: 0.8756 (t0) cc_final: 0.8496 (t0) REVERT: T 411 GLU cc_start: 0.8127 (mp0) cc_final: 0.7769 (mm-30) REVERT: T 479 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6367 (mpt180) REVERT: U 46 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: U 57 TYR cc_start: 0.7880 (p90) cc_final: 0.7415 (p90) REVERT: U 72 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8060 (tm-30) REVERT: U 74 GLU cc_start: 0.8048 (pp20) cc_final: 0.7496 (pm20) REVERT: U 282 MET cc_start: 0.9119 (tpt) cc_final: 0.8754 (tpt) REVERT: U 474 LEU cc_start: 0.7779 (tp) cc_final: 0.7463 (mt) REVERT: U 475 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7728 (mm-30) REVERT: U 496 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.8322 (mtt-85) REVERT: V 43 LYS cc_start: 0.7031 (mmmt) cc_final: 0.6802 (mmmt) REVERT: V 50 LYS cc_start: 0.7362 (pptt) cc_final: 0.7051 (tppt) REVERT: V 169 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: V 411 GLU cc_start: 0.8246 (mp0) cc_final: 0.7922 (mp0) REVERT: V 471 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6682 (tp40) REVERT: V 515 GLN cc_start: 0.8089 (mt0) cc_final: 0.7729 (pt0) REVERT: X 195 GLU cc_start: 0.8276 (tp30) cc_final: 0.8073 (tp30) REVERT: X 285 ASP cc_start: 0.7883 (t0) cc_final: 0.7646 (t0) REVERT: X 303 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8783 (mtt180) REVERT: Y 292 GLN cc_start: 0.8585 (tt0) cc_final: 0.8217 (tt0) REVERT: Y 430 LYS cc_start: 0.6789 (ptpt) cc_final: 0.6311 (mtmm) REVERT: Y 437 ARG cc_start: 0.8376 (mtp180) cc_final: 0.7900 (mtp85) REVERT: Y 453 PHE cc_start: 0.8212 (p90) cc_final: 0.7821 (p90) REVERT: Z 82 ASP cc_start: 0.8734 (t0) cc_final: 0.8197 (t0) REVERT: Z 198 ASN cc_start: 0.9003 (t0) cc_final: 0.8533 (t0) REVERT: Z 202 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8145 (mmtp) outliers start: 83 outliers final: 54 residues processed: 505 average time/residue: 0.6497 time to fit residues: 398.8064 Evaluate side-chains 489 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 421 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 10 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 293 SER Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 479 ARG Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 303 ARG Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 492 ILE Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 385 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 385 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 392 optimal weight: 0.0050 chunk 15 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 325 optimal weight: 0.5980 chunk 386 optimal weight: 0.9990 chunk 412 optimal weight: 0.0670 overall best weight: 0.5332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 GLN I 87 ASN J 98 GLN P 52 GLN P 59 GLN T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN T 539 ASN U 134 ASN U 149 GLN U 529 ASN V 121 ASN V 134 ASN V 452 GLN V 549 HIS Y 83 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 440 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096402 restraints weight = 47456.155| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.87 r_work: 0.2986 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34453 Z= 0.116 Angle : 0.572 10.716 46696 Z= 0.287 Chirality : 0.043 0.169 5527 Planarity : 0.004 0.060 6004 Dihedral : 5.542 87.451 4830 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 2.16 % Allowed : 20.09 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4466 helix: 0.43 (0.12), residues: 2150 sheet: -0.65 (0.21), residues: 601 loop : -0.39 (0.16), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 86 TYR 0.021 0.001 TYR G 102 PHE 0.044 0.001 PHE E 107 TRP 0.004 0.001 TRP R 37 HIS 0.006 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (34453) covalent geometry : angle 0.57243 / 0.29 (46696) hydrogen bonds : bond 0.03327 / 2.18 ( 1604) hydrogen bonds : angle 4.47942 / 3.10 ( 4596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13998.45 seconds wall clock time: 238 minutes 50.40 seconds (14330.40 seconds total)