Starting phenix.real_space_refine on Mon Sep 14 22:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rdj_4820/09_2026/6rdj_4820.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdj_4820/09_2026/6rdj_4820.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/6rdj_4820/09_2026/6rdj_4820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdj_4820/09_2026/6rdj_4820.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rdj_4820/09_2026/6rdj_4820.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rdj_4820/09_2026/6rdj_4820.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rdj_4820/09_2026/6rdj_4820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdj_4820/09_2026/6rdj_4820.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 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 255 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: 33891 Number of models: 1 Model: "" Number of chains: 25 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: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} 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: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} 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: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} 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: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} 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: "Y" 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} Time building chain proxies: 7.37, per 1000 atoms: 0.22 Number of scatterers: 33891 At special positions: 0 Unit cell: (159.003, 132.678, 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 6421 8.00 N 5795 7.00 C 21541 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 26 sheets defined 52.0% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.640A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.627A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.693A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 removed outlier: 3.727A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.603A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.020A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.841A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.793A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.645A pdb=" N VAL C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 4.205A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.111A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.508A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.533A pdb=" N CYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 removed outlier: 4.010A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 126 removed outlier: 3.609A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.524A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.032A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 119 removed outlier: 3.564A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.111A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.716A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 4.310A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.818A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.484A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 127 removed outlier: 3.964A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 67 Processing helix chain 'I' and resid 69 through 92 removed outlier: 3.970A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 125 removed outlier: 3.515A pdb=" N VAL I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.580A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 90 removed outlier: 4.408A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.594A pdb=" N LEU J 99 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 62 Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.708A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.557A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 107 removed outlier: 4.025A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 127 removed outlier: 3.589A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.315A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 129 through 132' Processing helix chain 'P' and resid 133 through 146 removed outlier: 4.053A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 3.578A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 37 removed outlier: 3.760A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 40 No H-bonds generated for 'chain 'R' and resid 38 through 40' 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 158 through 168 removed outlier: 3.927A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 194 Processing helix chain 'S' and resid 41 through 79 removed outlier: 3.612A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.360A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.526A pdb=" N ASN S 118 " --> pdb=" O GLY S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 4.111A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 148' Processing helix chain 'S' and resid 149 through 154 Processing helix chain 'S' and resid 171 through 184 Processing helix chain 'S' and resid 216 through 222 Processing helix chain 'S' and resid 238 through 312 removed outlier: 3.579A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.839A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 removed outlier: 3.582A pdb=" N THR T 159 " --> pdb=" O GLY T 156 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU T 160 " --> pdb=" O PRO T 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 156 through 160' Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.551A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.508A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 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 300 Processing helix chain 'T' and resid 301 through 315 removed outlier: 3.688A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 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: 3.619A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 removed outlier: 3.687A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.600A pdb=" N LYS T 415 " --> pdb=" O GLU T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.605A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.654A 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: 3.806A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 460 removed outlier: 3.621A pdb=" N ALA T 451 " --> pdb=" O LYS T 447 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.827A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 506 removed outlier: 3.525A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 516 through 528 removed outlier: 4.122A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL T 528 " --> pdb=" O VAL T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.694A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 554 removed outlier: 4.249A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 47 Processing helix chain 'U' and resid 58 through 63 Processing helix chain 'U' and resid 65 through 73 removed outlier: 3.655A pdb=" N ALA U 69 " --> pdb=" O LYS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.928A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.599A 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 removed outlier: 3.756A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.566A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 284 removed outlier: 3.711A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.638A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.600A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.665A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 removed outlier: 3.539A pdb=" N GLY U 373 " --> pdb=" O LYS U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 400 Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 459 removed outlier: 3.631A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 4.159A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.523A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.892A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 556 removed outlier: 3.970A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS U 556 " --> pdb=" O ALA U 552 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.553A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.877A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 212 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.862A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) 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 316 Proline residue: V 303 - end of helix removed outlier: 3.724A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 Processing helix chain 'V' and resid 353 through 363 Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.552A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 415 Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.725A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 439 through 456 removed outlier: 3.880A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.935A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 507 removed outlier: 3.779A pdb=" N GLY V 507 " --> pdb=" O ALA V 503 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 517 removed outlier: 3.783A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 526 Processing helix chain 'V' and resid 531 through 540 Processing helix chain 'V' and resid 545 through 554 removed outlier: 4.318A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.666A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 201 Processing helix chain 'X' and resid 216 through 229 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.054A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.602A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.907A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 355 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 removed outlier: 3.568A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 421 removed outlier: 4.691A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 425 Processing helix chain 'X' and resid 426 through 444 removed outlier: 3.919A pdb=" N SER X 444 " --> pdb=" O GLN X 440 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 removed outlier: 3.558A pdb=" N GLY X 455 " --> pdb=" O GLU X 451 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 491 through 506 removed outlier: 3.783A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 removed outlier: 3.573A 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 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.871A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 Processing helix chain 'Y' and resid 287 through 296 removed outlier: 3.872A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 370 removed outlier: 3.507A pdb=" N ALA Y 369 " --> pdb=" O SER Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 421 removed outlier: 3.578A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 444 removed outlier: 3.678A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER Y 444 " --> pdb=" O GLN Y 440 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 Processing helix chain 'Y' and resid 482 through 486 removed outlier: 3.617A pdb=" N PHE Y 486 " --> pdb=" O GLU Y 483 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 507 removed outlier: 3.593A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Y' and resid 544 through 555 Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.594A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.715A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.517A pdb=" N PHE Z 290 " --> pdb=" O ASN Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 3.827A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 365 through 370 Processing helix chain 'Z' and resid 392 through 411 removed outlier: 4.385A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 4.610A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 426 through 443 removed outlier: 3.611A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 447 through 449 No H-bonds generated for 'chain 'Z' and resid 447 through 449' Processing helix chain 'Z' and resid 450 through 455 removed outlier: 3.613A pdb=" N GLY Z 455 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 Processing helix chain 'Z' and resid 483 through 487 removed outlier: 3.641A pdb=" N TYR Z 487 " --> pdb=" O MET Z 484 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 505 removed outlier: 3.790A pdb=" N VAL Z 495 " --> pdb=" O ASP Z 491 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 506 through 509 removed outlier: 3.545A pdb=" N ARG Z 509 " --> pdb=" O ILE Z 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 506 through 509' Processing helix chain 'Z' and resid 526 through 532 removed outlier: 3.762A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 61 through 65 removed outlier: 10.152A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N PHE S 197 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'R' and resid 80 through 82 removed outlier: 3.900A pdb=" N VAL R 146 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.957A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.612A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA6, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.612A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 62 through 65 removed outlier: 4.666A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA7, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA8, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.508A pdb=" N THR T 164 " --> pdb=" O SER T 289 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 116 through 122 removed outlier: 3.858A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL U 87 " --> pdb=" O TYR U 98 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR U 98 " --> pdb=" O VAL U 87 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER X 62 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER X 61 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (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 removed outlier: 6.449A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.544A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 38 through 44 current: chain 'V' and resid 144 through 150 Processing sheet with id=AB4, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.544A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 116 through 122 current: chain 'Z' and resid 62 through 65 removed outlier: 6.666A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 38 through 44 current: chain 'V' and resid 144 through 150 Processing sheet with id=AB5, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.745A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.516A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.469A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.302A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC2, first strand: chain 'Y' and resid 110 through 111 Processing sheet with id=AC3, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.537A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.025A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AC6, first strand: chain 'Z' and resid 121 through 122 removed outlier: 7.044A pdb=" N VAL Z 209 " --> pdb=" O PHE Z 283 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP Z 285 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA Z 211 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS Z 178 " --> pdb=" O ALA Z 360 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR Z 362 " --> pdb=" O LYS Z 178 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY Z 180 " --> pdb=" O THR Z 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.313A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 559 through 561 1741 hydrogen bonds defined for protein. 5055 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: 7.96 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9920 1.33 - 1.45: 5365 1.45 - 1.57: 18906 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.82e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.80e+01 bond pdb=" C ILE V 67 " pdb=" N PRO V 68 " ideal model delta sigma weight residual 1.331 1.382 -0.051 7.90e-03 1.60e+04 4.14e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.46e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 46240 4.08 - 8.16: 358 8.16 - 12.24: 34 12.24 - 16.31: 3 16.31 - 20.39: 3 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.58 18.29 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 123.31 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.51 13.32 1.00e+00 1.00e+00 1.77e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 125.43 11.40 1.00e+00 1.00e+00 1.30e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.73: 20251 33.73 - 67.46: 446 67.46 - 101.18: 30 101.18 - 134.91: 1 134.91 - 168.64: 2 Dihedral angle restraints: 20730 sinusoidal: 7973 harmonic: 12757 Sorted by residual: 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 -120.82 -59.18 0 5.00e+00 4.00e-02 1.40e+02 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 -124.13 -55.87 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLU V 348 " pdb=" C GLU V 348 " pdb=" N ALA V 349 " pdb=" CA ALA V 349 " ideal model delta harmonic sigma weight residual 180.00 124.85 55.15 0 5.00e+00 4.00e-02 1.22e+02 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4169 0.070 - 0.141: 1179 0.141 - 0.211: 147 0.211 - 0.282: 19 0.282 - 0.352: 5 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL Z 113 " pdb=" CA VAL Z 113 " pdb=" CG1 VAL Z 113 " pdb=" CG2 VAL Z 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PRO U 201 " pdb=" N PRO U 201 " pdb=" C PRO U 201 " pdb=" CB PRO U 201 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.02e-02 3.62e+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=" C ALA U 296 " 0.062 5.00e-02 4.00e+02 9.30e-02 1.39e+01 pdb=" N PRO U 297 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL X 341 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO X 342 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO X 342 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO X 342 " -0.045 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 361 2.60 - 3.17: 27810 3.17 - 3.75: 54542 3.75 - 4.32: 80420 4.32 - 4.90: 130615 Nonbonded interactions: 293748 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.025 2.170 nonbonded pdb=" O2B ATP T1001 " pdb="MG MG T1002 " model vdw 2.025 2.170 nonbonded pdb=" OE1 GLN U 228 " pdb=" NH1 ARG Z 385 " model vdw 2.044 3.120 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.056 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.085 2.170 ... (remaining 293743 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 85 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 85 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 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 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: 7.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.820 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.011 0.135 34412 Z= 0.463 Angle : 1.039 20.392 46638 Z= 0.596 Chirality : 0.064 0.352 5519 Planarity : 0.008 0.093 5997 Dihedral : 14.389 168.639 12570 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.95 % Favored : 94.75 % Rotamer: Outliers : 0.31 % Allowed : 7.94 % Favored : 91.75 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.75 (0.10), residues: 4461 helix: -2.93 (0.08), residues: 2184 sheet: -1.34 (0.20), residues: 596 loop : -1.97 (0.13), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 98 TYR 0.021 0.003 TYR X 340 PHE 0.036 0.003 PHE S 249 TRP 0.018 0.003 TRP X 141 HIS 0.013 0.002 HIS Y 79 Details of bonding type rmsd/Z covalent geometry : bond 0.01069 / 0.46 (34412) covalent geometry : angle 1.03854 / 0.60 (46638) hydrogen bonds : bond 0.18039 / 11.97 ( 1721) hydrogen bonds : angle 7.68124 / 5.51 ( 5055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 675 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8444 (mp) cc_final: 0.8213 (mt) REVERT: C 107 PHE cc_start: 0.8281 (t80) cc_final: 0.8063 (t80) REVERT: D 123 LEU cc_start: 0.7367 (tt) cc_final: 0.7114 (mm) REVERT: E 95 ILE cc_start: 0.8871 (tp) cc_final: 0.8517 (tp) REVERT: H 56 LEU cc_start: 0.7739 (tt) cc_final: 0.7465 (tm) REVERT: I 61 MET cc_start: 0.8014 (mmt) cc_final: 0.7640 (mmm) REVERT: J 56 LEU cc_start: 0.6617 (tt) cc_final: 0.6350 (mp) REVERT: J 107 PHE cc_start: 0.8577 (t80) cc_final: 0.8056 (t80) REVERT: J 115 LEU cc_start: 0.6296 (mt) cc_final: 0.5852 (pp) REVERT: P 59 GLN cc_start: 0.8367 (mt0) cc_final: 0.8006 (mm-40) REVERT: P 63 LYS cc_start: 0.8562 (tppt) cc_final: 0.8084 (tttm) REVERT: P 76 GLN cc_start: 0.8558 (mt0) cc_final: 0.8140 (mt0) REVERT: P 150 LYS cc_start: 0.6743 (mttm) cc_final: 0.6440 (tptt) REVERT: Q 19 TYR cc_start: 0.8754 (t80) cc_final: 0.8397 (t80) REVERT: R 58 LYS cc_start: 0.7770 (mptt) cc_final: 0.7496 (mmtm) REVERT: R 117 GLU cc_start: 0.7194 (pm20) cc_final: 0.6985 (pm20) REVERT: S 68 MET cc_start: 0.8150 (ttp) cc_final: 0.7822 (tmm) REVERT: S 218 LYS cc_start: 0.8629 (tmtt) cc_final: 0.8323 (tmtm) REVERT: S 275 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7553 (tm-30) REVERT: T 237 ASP cc_start: 0.7237 (m-30) cc_final: 0.7009 (m-30) REVERT: T 440 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7969 (ttmt) REVERT: T 467 ASP cc_start: 0.7111 (m-30) cc_final: 0.5918 (t0) REVERT: T 471 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7286 (tm-30) REVERT: T 482 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7966 (mp0) REVERT: T 535 ILE cc_start: 0.8779 (mt) cc_final: 0.8530 (mp) REVERT: T 555 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7170 (mmt90) REVERT: U 118 MET cc_start: 0.8901 (ttt) cc_final: 0.8629 (ttp) REVERT: U 472 TYR cc_start: 0.7307 (t80) cc_final: 0.6928 (t80) REVERT: U 553 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7633 (mm-30) REVERT: V 50 LYS cc_start: 0.7758 (tppt) cc_final: 0.7481 (tptt) REVERT: V 447 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8151 (mtpt) REVERT: V 461 GLN cc_start: 0.8196 (mp-120) cc_final: 0.7996 (mm-40) REVERT: V 535 ILE cc_start: 0.8999 (mt) cc_final: 0.8777 (mm) REVERT: X 484 MET cc_start: 0.8310 (mmt) cc_final: 0.8065 (mmm) REVERT: Y 227 MET cc_start: 0.8723 (mtp) cc_final: 0.8451 (mtt) REVERT: Y 424 GLU cc_start: 0.7111 (mp0) cc_final: 0.6904 (pm20) REVERT: Y 548 ASP cc_start: 0.7665 (t0) cc_final: 0.7461 (t0) REVERT: Z 292 GLN cc_start: 0.7879 (mt0) cc_final: 0.7672 (mt0) REVERT: Z 430 LYS cc_start: 0.7143 (tppp) cc_final: 0.6844 (mttt) outliers start: 11 outliers final: 7 residues processed: 685 average time/residue: 0.6878 time to fit residues: 566.8253 Evaluate side-chains 456 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 449 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 431 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN C 94 ASN H 98 GLN I 98 GLN J 92 ASN J 98 GLN P 71 GLN P 140 ASN Q 40 GLN Q 46 HIS ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS R 137 HIS ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN T 104 GLN T 196 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 435 GLN T 441 GLN T 461 GLN T 497 GLN T 539 ASN U 83 HIS U 123 GLN U 134 ASN U 149 GLN U 241 HIS U 246 ASN U 319 HIS U 386 GLN U 441 GLN U 497 GLN U 539 ASN U 549 HIS V 60 GLN V 78 GLN V 126 HIS V 139 HIS V 152 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 242 GLN V 244 ASN V 246 ASN V 271 GLN V 486 GLN V 488 GLN X 157 GLN X 199 ASN X 241 ASN X 278 GLN X 322 GLN X 337 GLN X 414 GLN Y 123 ASN Y 144 HIS Y 174 GLN Y 204 HIS Y 278 GLN Y 440 GLN Z 144 HIS Z 199 ASN Z 250 GLN Z 278 GLN Z 294 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105784 restraints weight = 48157.240| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.76 r_work: 0.3114 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34412 Z= 0.146 Angle : 0.614 10.866 46638 Z= 0.319 Chirality : 0.044 0.258 5519 Planarity : 0.005 0.065 5997 Dihedral : 7.191 179.396 4836 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.52 % Favored : 96.26 % Rotamer: Outliers : 2.72 % Allowed : 14.76 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.93 (0.12), residues: 4461 helix: -1.08 (0.10), residues: 2194 sheet: -1.21 (0.21), residues: 599 loop : -1.33 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 124 TYR 0.018 0.001 TYR C 102 PHE 0.026 0.001 PHE F 107 TRP 0.006 0.001 TRP R 37 HIS 0.004 0.001 HIS S 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (34412) covalent geometry : angle 0.61386 / 0.32 (46638) hydrogen bonds : bond 0.03980 / 2.67 ( 1721) hydrogen bonds : angle 5.05788 / 3.61 ( 5055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 538 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7633 (mp) REVERT: C 107 PHE cc_start: 0.8091 (t80) cc_final: 0.7711 (t80) REVERT: E 95 ILE cc_start: 0.8887 (tp) cc_final: 0.8665 (tp) REVERT: F 81 MET cc_start: 0.7980 (ttp) cc_final: 0.7688 (ttp) REVERT: H 56 LEU cc_start: 0.7705 (tt) cc_final: 0.7481 (tm) REVERT: H 61 MET cc_start: 0.7930 (mmm) cc_final: 0.6936 (tpp) REVERT: H 82 PHE cc_start: 0.8088 (m-80) cc_final: 0.7871 (m-10) REVERT: I 61 MET cc_start: 0.8003 (mmt) cc_final: 0.7654 (mmm) REVERT: I 81 MET cc_start: 0.8444 (ttp) cc_final: 0.8088 (ttp) REVERT: J 56 LEU cc_start: 0.6446 (tt) cc_final: 0.6040 (mp) REVERT: J 61 MET cc_start: 0.7702 (mmm) cc_final: 0.7260 (mpm) REVERT: J 95 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7797 (tt) REVERT: J 107 PHE cc_start: 0.8658 (t80) cc_final: 0.8450 (t80) REVERT: P 38 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7493 (ttmm) REVERT: P 59 GLN cc_start: 0.8593 (mt0) cc_final: 0.8271 (mm-40) REVERT: P 63 LYS cc_start: 0.8320 (tppt) cc_final: 0.8000 (ttpp) REVERT: P 83 GLN cc_start: 0.7975 (pp30) cc_final: 0.7763 (pp30) REVERT: P 141 TYR cc_start: 0.8721 (t80) cc_final: 0.8506 (t80) REVERT: P 142 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8028 (mt-10) REVERT: P 150 LYS cc_start: 0.6798 (mttm) cc_final: 0.6412 (tptt) REVERT: Q 19 TYR cc_start: 0.8861 (t80) cc_final: 0.8466 (t80) REVERT: R 58 LYS cc_start: 0.7948 (mptt) cc_final: 0.7725 (mmtm) REVERT: S 68 MET cc_start: 0.8560 (ttp) cc_final: 0.8114 (tmm) REVERT: S 82 VAL cc_start: 0.8831 (t) cc_final: 0.8579 (m) REVERT: T 237 ASP cc_start: 0.7816 (m-30) cc_final: 0.7613 (m-30) REVERT: T 300 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.9040 (t80) REVERT: T 405 GLN cc_start: 0.7663 (tt0) cc_final: 0.7407 (tt0) REVERT: T 411 GLU cc_start: 0.8527 (pm20) cc_final: 0.8277 (mp0) REVERT: T 440 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8230 (ttmt) REVERT: T 471 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7358 (tm-30) REVERT: T 487 LYS cc_start: 0.8896 (ptmt) cc_final: 0.8595 (mtpp) REVERT: T 489 PHE cc_start: 0.7965 (m-80) cc_final: 0.7715 (m-80) REVERT: T 496 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8374 (mtt90) REVERT: T 502 TYR cc_start: 0.8164 (t80) cc_final: 0.7754 (t80) REVERT: T 549 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6891 (t70) REVERT: T 555 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7209 (mmt90) REVERT: U 553 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7943 (mm-30) REVERT: V 50 LYS cc_start: 0.7867 (tppt) cc_final: 0.7207 (mmtm) REVERT: V 429 ARG cc_start: 0.8341 (mtt-85) cc_final: 0.7613 (mtt-85) REVERT: V 509 LEU cc_start: 0.8511 (mm) cc_final: 0.8145 (mp) REVERT: X 158 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: Y 215 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8459 (mm-30) REVERT: Y 227 MET cc_start: 0.8906 (mtp) cc_final: 0.8601 (mtt) REVERT: Y 414 GLN cc_start: 0.8180 (tt0) cc_final: 0.7951 (mt0) REVERT: Y 424 GLU cc_start: 0.6918 (mp0) cc_final: 0.6564 (pm20) REVERT: Z 140 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8678 (mp) REVERT: Z 429 ASP cc_start: 0.7114 (m-30) cc_final: 0.6750 (m-30) outliers start: 97 outliers final: 38 residues processed: 599 average time/residue: 0.6518 time to fit residues: 475.9631 Evaluate side-chains 491 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 445 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 107 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 422 optimal weight: 0.3980 chunk 307 optimal weight: 3.9990 chunk 396 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 98 GLN I 94 ASN J 92 ASN J 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 ASN Q 40 GLN Q 43 GLN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS S 262 ASN T 140 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 264 GLN T 358 HIS T 539 ASN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 64 GLN V 78 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 271 GLN ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN V 471 GLN V 515 GLN X 83 ASN X 414 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103959 restraints weight = 48199.850| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.71 r_work: 0.3076 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34412 Z= 0.163 Angle : 0.601 10.601 46638 Z= 0.310 Chirality : 0.045 0.249 5519 Planarity : 0.005 0.058 5997 Dihedral : 6.781 161.996 4830 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.92 % Favored : 95.85 % Rotamer: Outliers : 3.20 % Allowed : 16.50 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.15 (0.13), residues: 4461 helix: -0.27 (0.11), residues: 2216 sheet: -1.14 (0.21), residues: 604 loop : -1.10 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 437 TYR 0.018 0.002 TYR J 102 PHE 0.032 0.002 PHE E 107 TRP 0.007 0.001 TRP R 37 HIS 0.010 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (34412) covalent geometry : angle 0.60056 / 0.31 (46638) hydrogen bonds : bond 0.03863 / 2.59 ( 1721) hydrogen bonds : angle 4.76855 / 3.41 ( 5055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 473 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.7035 (m-80) cc_final: 0.6748 (m-10) REVERT: B 123 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7580 (mp) REVERT: C 102 TYR cc_start: 0.7585 (m-10) cc_final: 0.7283 (m-10) REVERT: C 109 LEU cc_start: 0.8402 (mt) cc_final: 0.8200 (mp) REVERT: C 111 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: E 61 MET cc_start: 0.7294 (mtt) cc_final: 0.6973 (mtt) REVERT: E 87 ASN cc_start: 0.8007 (m-40) cc_final: 0.7317 (t0) REVERT: E 95 ILE cc_start: 0.8888 (tp) cc_final: 0.8618 (tp) REVERT: F 81 MET cc_start: 0.7941 (ttp) cc_final: 0.7636 (ttp) REVERT: G 82 PHE cc_start: 0.8218 (m-10) cc_final: 0.7772 (m-10) REVERT: H 61 MET cc_start: 0.7910 (mmm) cc_final: 0.6979 (tpp) REVERT: H 107 PHE cc_start: 0.8078 (t80) cc_final: 0.7869 (t80) REVERT: I 61 MET cc_start: 0.7964 (mmt) cc_final: 0.7634 (mmm) REVERT: I 81 MET cc_start: 0.8445 (ttp) cc_final: 0.8177 (ttp) REVERT: J 56 LEU cc_start: 0.6439 (tt) cc_final: 0.6001 (mp) REVERT: J 61 MET cc_start: 0.7524 (mmm) cc_final: 0.7297 (mpm) REVERT: J 107 PHE cc_start: 0.8744 (t80) cc_final: 0.8530 (t80) REVERT: P 38 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7524 (ttmm) REVERT: P 59 GLN cc_start: 0.8571 (mt0) cc_final: 0.8225 (mm-40) REVERT: P 63 LYS cc_start: 0.8331 (tppt) cc_final: 0.8070 (ttpp) REVERT: P 83 GLN cc_start: 0.8076 (pp30) cc_final: 0.7840 (pp30) REVERT: P 142 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8073 (mt-10) REVERT: Q 19 TYR cc_start: 0.8792 (t80) cc_final: 0.8420 (t80) REVERT: R 58 LYS cc_start: 0.7892 (mptt) cc_final: 0.7675 (mmtm) REVERT: R 117 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: R 178 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: S 68 MET cc_start: 0.8537 (ttp) cc_final: 0.8092 (tmm) REVERT: S 220 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7650 (mm) REVERT: T 149 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: T 237 ASP cc_start: 0.7920 (m-30) cc_final: 0.7707 (m-30) REVERT: T 353 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7928 (t0) REVERT: T 405 GLN cc_start: 0.7648 (tt0) cc_final: 0.7368 (tt0) REVERT: T 411 GLU cc_start: 0.8574 (pm20) cc_final: 0.8266 (mp0) REVERT: T 440 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8235 (ttmt) REVERT: T 471 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7503 (tm-30) REVERT: T 487 LYS cc_start: 0.8900 (ptmt) cc_final: 0.8673 (mtmt) REVERT: T 496 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8486 (mtt90) REVERT: T 522 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7272 (mp0) REVERT: T 549 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6789 (t70) REVERT: T 555 ARG cc_start: 0.7691 (mtt-85) cc_final: 0.7338 (mmt90) REVERT: U 448 LEU cc_start: 0.7532 (mt) cc_final: 0.7313 (tt) REVERT: U 472 TYR cc_start: 0.7344 (t80) cc_final: 0.7040 (t80) REVERT: U 553 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7935 (mm-30) REVERT: V 50 LYS cc_start: 0.7932 (tppt) cc_final: 0.7500 (tptt) REVERT: V 135 ASP cc_start: 0.8179 (p0) cc_final: 0.7972 (p0) REVERT: V 287 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8701 (mtp) REVERT: V 429 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.7723 (mtt-85) REVERT: V 509 LEU cc_start: 0.8591 (mm) cc_final: 0.8201 (mp) REVERT: V 539 ASN cc_start: 0.8570 (t0) cc_final: 0.8369 (t0) REVERT: X 424 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7489 (tp30) REVERT: X 500 ASP cc_start: 0.7338 (m-30) cc_final: 0.7096 (m-30) REVERT: Y 55 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: Y 227 MET cc_start: 0.8918 (mtp) cc_final: 0.8638 (mtt) REVERT: Y 409 ASP cc_start: 0.8229 (m-30) cc_final: 0.7870 (m-30) REVERT: Y 424 GLU cc_start: 0.6940 (mp0) cc_final: 0.6685 (pm20) REVERT: Y 441 ARG cc_start: 0.8391 (mmt-90) cc_final: 0.8183 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7093 (m-30) cc_final: 0.6743 (m-30) outliers start: 114 outliers final: 50 residues processed: 547 average time/residue: 0.6196 time to fit residues: 418.2276 Evaluate side-chains 485 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 424 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 171 optimal weight: 0.9990 chunk 295 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN E 94 ASN G 94 ASN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 43 GLN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 121 ASN U 134 ASN U 242 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 104 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN V 515 GLN X 198 ASN X 414 GLN Y 204 HIS Z 448 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098825 restraints weight = 49131.097| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.70 r_work: 0.3029 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34412 Z= 0.191 Angle : 0.613 10.384 46638 Z= 0.315 Chirality : 0.046 0.255 5519 Planarity : 0.005 0.056 5997 Dihedral : 6.458 124.833 4828 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.67 % Rotamer: Outliers : 3.62 % Allowed : 17.82 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.79 (0.13), residues: 4461 helix: 0.09 (0.11), residues: 2219 sheet: -1.06 (0.21), residues: 597 loop : -0.99 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 199 TYR 0.020 0.002 TYR X 487 PHE 0.037 0.002 PHE E 107 TRP 0.008 0.001 TRP R 37 HIS 0.008 0.001 HIS Y 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (34412) covalent geometry : angle 0.61298 / 0.32 (46638) hydrogen bonds : bond 0.03874 / 2.60 ( 1721) hydrogen bonds : angle 4.70614 / 3.36 ( 5055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 456 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7571 (mp) REVERT: C 95 ILE cc_start: 0.8946 (tt) cc_final: 0.8623 (tt) REVERT: E 61 MET cc_start: 0.7293 (mtt) cc_final: 0.6794 (mtt) REVERT: E 87 ASN cc_start: 0.7943 (m-40) cc_final: 0.7164 (t0) REVERT: E 95 ILE cc_start: 0.8980 (tp) cc_final: 0.8699 (tp) REVERT: F 81 MET cc_start: 0.8034 (ttp) cc_final: 0.7783 (ttp) REVERT: G 82 PHE cc_start: 0.8313 (m-10) cc_final: 0.7764 (m-10) REVERT: G 111 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8075 (mm-30) REVERT: H 60 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7169 (mtpp) REVERT: H 61 MET cc_start: 0.7921 (mmm) cc_final: 0.7031 (tpp) REVERT: H 107 PHE cc_start: 0.8118 (t80) cc_final: 0.7853 (t80) REVERT: I 61 MET cc_start: 0.7828 (mmt) cc_final: 0.7490 (mmm) REVERT: I 81 MET cc_start: 0.8467 (ttp) cc_final: 0.8201 (ttp) REVERT: J 56 LEU cc_start: 0.6447 (tt) cc_final: 0.5994 (mt) REVERT: J 107 PHE cc_start: 0.8743 (t80) cc_final: 0.8541 (t80) REVERT: P 38 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7589 (ttmm) REVERT: P 59 GLN cc_start: 0.8606 (mt0) cc_final: 0.8169 (mm-40) REVERT: P 63 LYS cc_start: 0.8333 (tppt) cc_final: 0.8022 (ttmm) REVERT: P 83 GLN cc_start: 0.8084 (pp30) cc_final: 0.7836 (pp30) REVERT: P 142 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7925 (mt-10) REVERT: P 150 LYS cc_start: 0.4830 (tptt) cc_final: 0.3574 (mmmt) REVERT: Q 49 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8302 (pt0) REVERT: R 117 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: R 178 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: S 68 MET cc_start: 0.8465 (ttp) cc_final: 0.8019 (tmm) REVERT: S 220 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7558 (mm) REVERT: T 149 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: T 353 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7937 (t0) REVERT: T 405 GLN cc_start: 0.7669 (tt0) cc_final: 0.7453 (tt0) REVERT: T 411 GLU cc_start: 0.8499 (pm20) cc_final: 0.8221 (mp0) REVERT: T 440 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8170 (ttmt) REVERT: T 471 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7503 (tm-30) REVERT: T 487 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8630 (mtmt) REVERT: T 496 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8424 (mtt90) REVERT: T 549 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6833 (t70) REVERT: T 555 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7280 (mmt90) REVERT: U 472 TYR cc_start: 0.7369 (t80) cc_final: 0.7053 (t80) REVERT: U 553 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7790 (mm-30) REVERT: V 50 LYS cc_start: 0.7990 (tppt) cc_final: 0.7558 (tptt) REVERT: V 429 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.7629 (mtt-85) REVERT: V 471 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6922 (mt0) REVERT: V 509 LEU cc_start: 0.8620 (mm) cc_final: 0.8250 (mp) REVERT: V 518 VAL cc_start: 0.8835 (p) cc_final: 0.8483 (t) REVERT: V 539 ASN cc_start: 0.8577 (t0) cc_final: 0.8325 (t0) REVERT: X 158 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8034 (mm-30) REVERT: X 276 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: X 424 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7436 (tp30) REVERT: X 531 VAL cc_start: 0.7649 (t) cc_final: 0.7067 (p) REVERT: Y 215 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8325 (mm-30) REVERT: Y 411 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8323 (ttpt) REVERT: Y 424 GLU cc_start: 0.6921 (mp0) cc_final: 0.6504 (pm20) REVERT: Y 441 ARG cc_start: 0.8350 (mmt-90) cc_final: 0.8108 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7040 (m-30) cc_final: 0.6682 (m-30) outliers start: 129 outliers final: 62 residues processed: 544 average time/residue: 0.6351 time to fit residues: 423.2550 Evaluate side-chains 499 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 423 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 481 THR Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 471 GLN Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 411 LYS Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 241 optimal weight: 0.9980 chunk 290 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 424 optimal weight: 0.0370 chunk 113 optimal weight: 0.9990 chunk 406 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 300 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN G 94 ASN I 98 GLN J 92 ASN Q 40 GLN Q 43 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104420 restraints weight = 49321.226| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.78 r_work: 0.3099 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34412 Z= 0.123 Angle : 0.564 10.389 46638 Z= 0.288 Chirality : 0.044 0.259 5519 Planarity : 0.004 0.053 5997 Dihedral : 5.930 104.449 4828 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.21 % Rotamer: Outliers : 3.56 % Allowed : 18.66 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.38 (0.13), residues: 4461 helix: 0.45 (0.11), residues: 2210 sheet: -0.92 (0.22), residues: 581 loop : -0.80 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 199 TYR 0.016 0.001 TYR J 102 PHE 0.038 0.001 PHE E 107 TRP 0.006 0.001 TRP R 37 HIS 0.005 0.001 HIS S 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (34412) covalent geometry : angle 0.56380 / 0.29 (46638) hydrogen bonds : bond 0.03385 / 2.28 ( 1721) hydrogen bonds : angle 4.50579 / 3.22 ( 5055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 490 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7504 (mp) REVERT: E 61 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: E 87 ASN cc_start: 0.7793 (m-40) cc_final: 0.7172 (t0) REVERT: E 95 ILE cc_start: 0.8981 (tp) cc_final: 0.8743 (tp) REVERT: F 81 MET cc_start: 0.7964 (ttp) cc_final: 0.7721 (ttp) REVERT: G 82 PHE cc_start: 0.8248 (m-10) cc_final: 0.7654 (m-10) REVERT: G 111 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7990 (mt-10) REVERT: H 60 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7184 (mtpp) REVERT: H 61 MET cc_start: 0.7824 (mmm) cc_final: 0.6913 (tpp) REVERT: H 107 PHE cc_start: 0.8166 (t80) cc_final: 0.7944 (t80) REVERT: I 61 MET cc_start: 0.7885 (mmt) cc_final: 0.7532 (mmm) REVERT: I 81 MET cc_start: 0.8494 (ttp) cc_final: 0.8140 (ttp) REVERT: J 56 LEU cc_start: 0.6367 (tt) cc_final: 0.5919 (mt) REVERT: P 38 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7620 (ttmm) REVERT: P 142 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7941 (mt-10) REVERT: P 150 LYS cc_start: 0.5091 (tptt) cc_final: 0.3901 (mmmt) REVERT: R 58 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7784 (mmtm) REVERT: R 178 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: S 68 MET cc_start: 0.8457 (ttp) cc_final: 0.7996 (tmm) REVERT: S 220 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7589 (mm) REVERT: T 149 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: T 169 GLN cc_start: 0.8511 (mt0) cc_final: 0.8190 (mp10) REVERT: T 411 GLU cc_start: 0.8501 (pm20) cc_final: 0.8220 (mp0) REVERT: T 440 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8124 (ttmt) REVERT: T 496 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8402 (mtt90) REVERT: T 502 TYR cc_start: 0.8214 (t80) cc_final: 0.7988 (t80) REVERT: T 549 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6581 (t70) REVERT: T 555 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7303 (mmt90) REVERT: U 472 TYR cc_start: 0.7271 (t80) cc_final: 0.6992 (t80) REVERT: U 553 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7789 (mm-30) REVERT: V 50 LYS cc_start: 0.7971 (tppt) cc_final: 0.7539 (tptt) REVERT: V 429 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.7630 (mtt-85) REVERT: V 471 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6777 (mt0) REVERT: V 518 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8376 (t) REVERT: V 539 ASN cc_start: 0.8591 (t0) cc_final: 0.8340 (t0) REVERT: X 158 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8006 (mm-30) REVERT: X 424 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7455 (tp30) REVERT: X 531 VAL cc_start: 0.7453 (t) cc_final: 0.6909 (p) REVERT: Y 215 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: Y 409 ASP cc_start: 0.8161 (m-30) cc_final: 0.7696 (m-30) REVERT: Y 424 GLU cc_start: 0.6648 (mp0) cc_final: 0.6323 (pm20) REVERT: Y 441 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7989 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7055 (m-30) cc_final: 0.6690 (m-30) outliers start: 127 outliers final: 60 residues processed: 577 average time/residue: 0.6020 time to fit residues: 429.1557 Evaluate side-chains 508 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 438 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 251 LYS Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 471 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 127 optimal weight: 0.9990 chunk 269 optimal weight: 0.2980 chunk 407 optimal weight: 2.9990 chunk 426 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 382 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN I 98 GLN J 92 ASN Q 40 GLN Q 43 GLN R 66 HIS ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN X 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103254 restraints weight = 48891.526| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.67 r_work: 0.3065 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34412 Z= 0.148 Angle : 0.587 10.733 46638 Z= 0.298 Chirality : 0.045 0.298 5519 Planarity : 0.004 0.053 5997 Dihedral : 5.797 108.328 4828 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.72 % Favored : 96.05 % Rotamer: Outliers : 3.65 % Allowed : 19.78 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.28 (0.13), residues: 4461 helix: 0.56 (0.12), residues: 2220 sheet: -0.91 (0.22), residues: 584 loop : -0.78 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 199 TYR 0.016 0.001 TYR X 487 PHE 0.032 0.002 PHE E 107 TRP 0.007 0.001 TRP R 37 HIS 0.006 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (34412) covalent geometry : angle 0.58697 / 0.30 (46638) hydrogen bonds : bond 0.03509 / 2.36 ( 1721) hydrogen bonds : angle 4.50982 / 3.22 ( 5055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 455 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7040 (mm) REVERT: B 107 PHE cc_start: 0.7952 (t80) cc_final: 0.7431 (t80) REVERT: C 109 LEU cc_start: 0.8660 (mt) cc_final: 0.8373 (mt) REVERT: E 61 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6977 (mtt) REVERT: E 87 ASN cc_start: 0.7845 (m-40) cc_final: 0.7190 (t0) REVERT: G 82 PHE cc_start: 0.8126 (m-10) cc_final: 0.7646 (m-10) REVERT: G 111 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8129 (mt-10) REVERT: H 60 LYS cc_start: 0.7892 (mtpt) cc_final: 0.7253 (mtpp) REVERT: H 61 MET cc_start: 0.7746 (mmm) cc_final: 0.6879 (tpp) REVERT: H 81 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8059 (ptm) REVERT: H 107 PHE cc_start: 0.8204 (t80) cc_final: 0.7946 (t80) REVERT: I 61 MET cc_start: 0.7917 (mmt) cc_final: 0.7585 (mmm) REVERT: I 81 MET cc_start: 0.8522 (ttp) cc_final: 0.8217 (ttp) REVERT: I 107 PHE cc_start: 0.8006 (t80) cc_final: 0.7672 (t80) REVERT: J 56 LEU cc_start: 0.6483 (tt) cc_final: 0.6054 (mt) REVERT: J 111 GLU cc_start: 0.8052 (tp30) cc_final: 0.7848 (tp30) REVERT: P 142 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7922 (mt-10) REVERT: P 150 LYS cc_start: 0.5055 (tptt) cc_final: 0.3977 (mmmt) REVERT: R 65 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6897 (t) REVERT: R 178 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: S 68 MET cc_start: 0.8505 (ttp) cc_final: 0.8059 (tmm) REVERT: S 220 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7615 (mm) REVERT: T 149 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: T 169 GLN cc_start: 0.8546 (mt0) cc_final: 0.8226 (mp10) REVERT: T 411 GLU cc_start: 0.8491 (pm20) cc_final: 0.8233 (mp0) REVERT: T 440 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8139 (ttmt) REVERT: T 471 GLN cc_start: 0.8216 (tp40) cc_final: 0.7902 (tp40) REVERT: T 496 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8396 (mtt90) REVERT: T 549 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6466 (t70) REVERT: T 555 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.7381 (mmt90) REVERT: U 472 TYR cc_start: 0.7363 (t80) cc_final: 0.7048 (t80) REVERT: U 553 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7830 (mm-30) REVERT: V 50 LYS cc_start: 0.7957 (tppt) cc_final: 0.7542 (tptt) REVERT: V 471 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6906 (mt0) REVERT: V 518 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8379 (t) REVERT: X 158 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: X 276 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: X 424 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7464 (tp30) REVERT: X 531 VAL cc_start: 0.7462 (t) cc_final: 0.6928 (p) REVERT: Y 314 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8920 (tp) REVERT: Y 409 ASP cc_start: 0.8221 (m-30) cc_final: 0.7783 (m-30) REVERT: Y 424 GLU cc_start: 0.6643 (mp0) cc_final: 0.6356 (pm20) REVERT: Y 441 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.8071 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7082 (m-30) cc_final: 0.6748 (m-30) outliers start: 130 outliers final: 67 residues processed: 539 average time/residue: 0.5865 time to fit residues: 392.2412 Evaluate side-chains 512 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 431 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 475 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 471 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 59 optimal weight: 3.9990 chunk 433 optimal weight: 2.9990 chunk 424 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 436 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN I 98 GLN J 92 ASN Q 40 GLN Q 43 GLN R 73 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 GLN X 414 GLN Y 198 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101801 restraints weight = 49356.728| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.74 r_work: 0.3081 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34412 Z= 0.134 Angle : 0.581 11.903 46638 Z= 0.294 Chirality : 0.044 0.320 5519 Planarity : 0.004 0.055 5997 Dihedral : 5.657 107.149 4828 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.77 % Favored : 96.01 % Rotamer: Outliers : 3.73 % Allowed : 20.48 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.12 (0.13), residues: 4461 helix: 0.68 (0.12), residues: 2221 sheet: -0.83 (0.22), residues: 567 loop : -0.70 (0.16), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 199 TYR 0.016 0.001 TYR X 487 PHE 0.033 0.001 PHE J 107 TRP 0.006 0.001 TRP R 37 HIS 0.006 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (34412) covalent geometry : angle 0.58088 / 0.29 (46638) hydrogen bonds : bond 0.03394 / 2.28 ( 1721) hydrogen bonds : angle 4.44756 / 3.18 ( 5055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 467 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8429 (t0) cc_final: 0.8174 (t0) REVERT: B 104 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6918 (mm) REVERT: B 107 PHE cc_start: 0.8012 (t80) cc_final: 0.7752 (t80) REVERT: C 109 LEU cc_start: 0.8616 (mt) cc_final: 0.8289 (mp) REVERT: E 61 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7030 (mtt) REVERT: E 87 ASN cc_start: 0.7841 (m-40) cc_final: 0.7150 (t0) REVERT: G 82 PHE cc_start: 0.8036 (m-10) cc_final: 0.7538 (m-10) REVERT: G 111 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8051 (mt-10) REVERT: H 60 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7143 (mttm) REVERT: H 61 MET cc_start: 0.7691 (mmm) cc_final: 0.6845 (tpp) REVERT: H 107 PHE cc_start: 0.8172 (t80) cc_final: 0.7922 (t80) REVERT: I 61 MET cc_start: 0.7805 (mmt) cc_final: 0.7488 (mmm) REVERT: I 81 MET cc_start: 0.8482 (ttp) cc_final: 0.8252 (ttm) REVERT: J 56 LEU cc_start: 0.6400 (tt) cc_final: 0.5950 (mt) REVERT: P 142 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7725 (mt-10) REVERT: P 150 LYS cc_start: 0.4649 (tptt) cc_final: 0.3795 (mmmt) REVERT: R 178 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: S 68 MET cc_start: 0.8444 (ttp) cc_final: 0.7990 (tmm) REVERT: S 220 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7601 (mm) REVERT: T 149 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: T 169 GLN cc_start: 0.8519 (mt0) cc_final: 0.8137 (mp10) REVERT: T 405 GLN cc_start: 0.7611 (tt0) cc_final: 0.7409 (tt0) REVERT: T 411 GLU cc_start: 0.8482 (pm20) cc_final: 0.8195 (mp0) REVERT: T 440 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8089 (ttmt) REVERT: T 471 GLN cc_start: 0.8228 (tp40) cc_final: 0.7682 (tp40) REVERT: T 549 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6433 (t70) REVERT: T 555 ARG cc_start: 0.7737 (mtt-85) cc_final: 0.7391 (mmt90) REVERT: U 472 TYR cc_start: 0.7354 (t80) cc_final: 0.7085 (t80) REVERT: U 553 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7760 (mm-30) REVERT: V 50 LYS cc_start: 0.8003 (tppt) cc_final: 0.7580 (tptt) REVERT: V 471 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6783 (mt0) REVERT: V 509 LEU cc_start: 0.8503 (mt) cc_final: 0.8162 (mp) REVERT: V 518 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8372 (t) REVERT: X 158 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: X 276 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: X 424 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7491 (tp30) REVERT: X 440 GLN cc_start: 0.8750 (mt0) cc_final: 0.8544 (mt0) REVERT: X 531 VAL cc_start: 0.7373 (t) cc_final: 0.6841 (p) REVERT: Y 123 ASN cc_start: 0.8495 (m-40) cc_final: 0.8290 (m110) REVERT: Y 409 ASP cc_start: 0.8171 (m-30) cc_final: 0.7694 (m-30) REVERT: Y 411 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8354 (ttpt) REVERT: Y 424 GLU cc_start: 0.6592 (mp0) cc_final: 0.6303 (pm20) REVERT: Y 441 ARG cc_start: 0.8216 (mmt-90) cc_final: 0.7932 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7104 (m-30) cc_final: 0.6757 (m-30) outliers start: 133 outliers final: 73 residues processed: 558 average time/residue: 0.5888 time to fit residues: 408.1866 Evaluate side-chains 523 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 439 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 185 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 471 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 80 MET Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 411 LYS Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 41 optimal weight: 7.9990 chunk 371 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 379 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 233 optimal weight: 0.5980 chunk 238 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 43 GLN S 293 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 GLN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102986 restraints weight = 48949.505| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.71 r_work: 0.3053 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34412 Z= 0.166 Angle : 0.612 11.148 46638 Z= 0.310 Chirality : 0.046 0.344 5519 Planarity : 0.004 0.055 5997 Dihedral : 5.733 109.045 4828 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.97 % Favored : 95.81 % Rotamer: Outliers : 3.51 % Allowed : 21.16 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.12 (0.13), residues: 4461 helix: 0.67 (0.11), residues: 2219 sheet: -0.81 (0.22), residues: 567 loop : -0.69 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 199 TYR 0.015 0.002 TYR H 102 PHE 0.033 0.002 PHE E 107 TRP 0.006 0.001 TRP R 37 HIS 0.008 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (34412) covalent geometry : angle 0.61173 / 0.31 (46638) hydrogen bonds : bond 0.03587 / 2.41 ( 1721) hydrogen bonds : angle 4.52573 / 3.23 ( 5055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 449 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8422 (t0) cc_final: 0.8206 (t0) REVERT: B 104 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6987 (mm) REVERT: B 107 PHE cc_start: 0.8097 (t80) cc_final: 0.7794 (t80) REVERT: E 87 ASN cc_start: 0.7890 (m-40) cc_final: 0.7214 (t0) REVERT: G 111 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8162 (mt-10) REVERT: H 60 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7237 (mtpt) REVERT: H 61 MET cc_start: 0.7723 (mmm) cc_final: 0.6907 (tpp) REVERT: H 107 PHE cc_start: 0.8203 (t80) cc_final: 0.7960 (t80) REVERT: I 61 MET cc_start: 0.7868 (mmt) cc_final: 0.7553 (mmm) REVERT: I 81 MET cc_start: 0.8561 (ttp) cc_final: 0.8339 (ttm) REVERT: J 56 LEU cc_start: 0.6477 (tt) cc_final: 0.6036 (mt) REVERT: P 66 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: P 142 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7853 (mt-10) REVERT: P 150 LYS cc_start: 0.4792 (tptt) cc_final: 0.3846 (mmmt) REVERT: R 178 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: S 68 MET cc_start: 0.8508 (ttp) cc_final: 0.8082 (tmm) REVERT: S 220 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7601 (mm) REVERT: T 149 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: T 169 GLN cc_start: 0.8567 (mp10) cc_final: 0.8244 (mp10) REVERT: T 411 GLU cc_start: 0.8528 (pm20) cc_final: 0.8311 (mp0) REVERT: T 440 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8188 (ttmt) REVERT: T 471 GLN cc_start: 0.8284 (tp40) cc_final: 0.7761 (tp40) REVERT: T 549 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6486 (t70) REVERT: T 555 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7400 (mmt90) REVERT: U 472 TYR cc_start: 0.7292 (t80) cc_final: 0.7057 (t80) REVERT: U 553 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7833 (mm-30) REVERT: V 50 LYS cc_start: 0.8041 (tppt) cc_final: 0.7604 (tptt) REVERT: V 471 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6833 (mt0) REVERT: V 518 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8327 (t) REVERT: X 158 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: X 276 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: X 531 VAL cc_start: 0.7477 (t) cc_final: 0.6925 (p) REVERT: Y 409 ASP cc_start: 0.8237 (m-30) cc_final: 0.7796 (m-30) REVERT: Y 411 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8384 (ttpt) REVERT: Y 424 GLU cc_start: 0.6639 (mp0) cc_final: 0.6330 (pm20) REVERT: Y 441 ARG cc_start: 0.8339 (mmt-90) cc_final: 0.8077 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7129 (m-30) cc_final: 0.6787 (m-30) outliers start: 125 outliers final: 76 residues processed: 538 average time/residue: 0.5917 time to fit residues: 396.7061 Evaluate side-chains 518 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 431 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 422 ASN Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 185 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 471 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 411 LYS Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 307 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 438 optimal weight: 0.9990 chunk 397 optimal weight: 0.9980 chunk 254 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 433 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN C 98 GLN H 98 GLN I 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN T 134 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100323 restraints weight = 49336.702| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.88 r_work: 0.3086 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34412 Z= 0.141 Angle : 0.599 11.235 46638 Z= 0.302 Chirality : 0.045 0.338 5519 Planarity : 0.004 0.055 5997 Dihedral : 5.636 107.120 4828 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.77 % Favored : 96.01 % Rotamer: Outliers : 3.14 % Allowed : 21.32 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.02 (0.13), residues: 4461 helix: 0.77 (0.12), residues: 2212 sheet: -0.79 (0.22), residues: 567 loop : -0.66 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 199 TYR 0.015 0.001 TYR X 487 PHE 0.030 0.001 PHE E 107 TRP 0.004 0.001 TRP R 37 HIS 0.007 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (34412) covalent geometry : angle 0.59920 / 0.30 (46638) hydrogen bonds : bond 0.03415 / 2.29 ( 1721) hydrogen bonds : angle 4.46524 / 3.19 ( 5055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 450 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8394 (t0) cc_final: 0.8172 (t0) REVERT: B 104 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6991 (mm) REVERT: B 107 PHE cc_start: 0.8051 (t80) cc_final: 0.7657 (t80) REVERT: C 109 LEU cc_start: 0.8604 (mt) cc_final: 0.8394 (mt) REVERT: D 100 VAL cc_start: 0.8106 (t) cc_final: 0.7802 (m) REVERT: E 87 ASN cc_start: 0.7810 (m-40) cc_final: 0.7133 (t0) REVERT: G 92 ASN cc_start: 0.6975 (p0) cc_final: 0.5722 (p0) REVERT: G 111 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8035 (mt-10) REVERT: H 60 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7172 (mttm) REVERT: H 61 MET cc_start: 0.7702 (mmm) cc_final: 0.6836 (tpp) REVERT: H 107 PHE cc_start: 0.8145 (t80) cc_final: 0.7902 (t80) REVERT: I 61 MET cc_start: 0.7876 (mmt) cc_final: 0.7557 (mmm) REVERT: J 56 LEU cc_start: 0.6398 (tt) cc_final: 0.5967 (mt) REVERT: J 109 LEU cc_start: 0.8638 (tp) cc_final: 0.8429 (tp) REVERT: P 66 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: P 142 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7817 (mt-10) REVERT: P 150 LYS cc_start: 0.4443 (tptt) cc_final: 0.3564 (mmmt) REVERT: R 178 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: S 68 MET cc_start: 0.8445 (ttp) cc_final: 0.7997 (tmm) REVERT: S 220 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7524 (mm) REVERT: T 149 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: T 169 GLN cc_start: 0.8528 (mp10) cc_final: 0.8150 (mp10) REVERT: T 389 ASP cc_start: 0.8420 (t0) cc_final: 0.8078 (t0) REVERT: T 411 GLU cc_start: 0.8512 (pm20) cc_final: 0.8252 (mp0) REVERT: T 440 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8203 (ttmt) REVERT: T 471 GLN cc_start: 0.8191 (tp40) cc_final: 0.7701 (tp40) REVERT: T 549 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6390 (t70) REVERT: T 555 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7322 (mmt90) REVERT: U 116 LYS cc_start: 0.8819 (mttt) cc_final: 0.8613 (mtpt) REVERT: U 391 SER cc_start: 0.9071 (p) cc_final: 0.8759 (m) REVERT: U 447 LYS cc_start: 0.7674 (mtpm) cc_final: 0.7448 (mtpt) REVERT: U 472 TYR cc_start: 0.7269 (t80) cc_final: 0.7037 (t80) REVERT: U 553 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7767 (mm-30) REVERT: V 50 LYS cc_start: 0.7977 (tppt) cc_final: 0.7558 (tptt) REVERT: V 471 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6744 (mt0) REVERT: V 518 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8277 (t) REVERT: X 158 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7998 (mm-30) REVERT: X 276 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: X 531 VAL cc_start: 0.7333 (t) cc_final: 0.6797 (p) REVERT: Y 123 ASN cc_start: 0.8504 (m-40) cc_final: 0.8299 (m110) REVERT: Y 409 ASP cc_start: 0.8128 (m-30) cc_final: 0.7830 (m-30) REVERT: Y 424 GLU cc_start: 0.6595 (mp0) cc_final: 0.6290 (pm20) REVERT: Y 441 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7899 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7048 (m-30) cc_final: 0.6711 (m-30) outliers start: 112 outliers final: 77 residues processed: 533 average time/residue: 0.5848 time to fit residues: 388.1547 Evaluate side-chains 513 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 427 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 475 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 185 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 471 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 80 MET Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 109 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 325 optimal weight: 0.9980 chunk 404 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 313 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN I 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 GLN Q 40 GLN Q 43 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN Y 250 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102030 restraints weight = 49623.971| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.74 r_work: 0.3108 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34412 Z= 0.136 Angle : 0.604 11.164 46638 Z= 0.304 Chirality : 0.045 0.378 5519 Planarity : 0.004 0.062 5997 Dihedral : 5.553 103.070 4828 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.81 % Favored : 95.97 % Rotamer: Outliers : 2.92 % Allowed : 21.77 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.05 (0.13), residues: 4461 helix: 0.85 (0.12), residues: 2208 sheet: -0.77 (0.22), residues: 567 loop : -0.63 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 199 TYR 0.015 0.001 TYR U 98 PHE 0.029 0.002 PHE F 107 TRP 0.004 0.001 TRP R 37 HIS 0.006 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (34412) covalent geometry : angle 0.60364 / 0.30 (46638) hydrogen bonds : bond 0.03392 / 2.28 ( 1721) hydrogen bonds : angle 4.46717 / 3.20 ( 5055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 449 time to evaluate : 1.434 Fit side-chains REVERT: A 61 MET cc_start: 0.7624 (mtp) cc_final: 0.7321 (mtm) REVERT: A 87 ASN cc_start: 0.8430 (t0) cc_final: 0.8229 (t0) REVERT: A 116 PHE cc_start: 0.5742 (m-10) cc_final: 0.5507 (m-10) REVERT: B 104 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7021 (mm) REVERT: B 107 PHE cc_start: 0.8088 (t80) cc_final: 0.7741 (t80) REVERT: C 109 LEU cc_start: 0.8621 (mt) cc_final: 0.8388 (mt) REVERT: D 100 VAL cc_start: 0.8064 (t) cc_final: 0.7775 (m) REVERT: E 87 ASN cc_start: 0.7792 (m-40) cc_final: 0.7144 (t0) REVERT: G 92 ASN cc_start: 0.6737 (p0) cc_final: 0.5431 (p0) REVERT: G 102 TYR cc_start: 0.7784 (m-10) cc_final: 0.7249 (m-80) REVERT: G 111 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7992 (mt-10) REVERT: H 60 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7140 (mttm) REVERT: H 61 MET cc_start: 0.7688 (mmm) cc_final: 0.6860 (tpp) REVERT: H 107 PHE cc_start: 0.8178 (t80) cc_final: 0.7945 (t80) REVERT: I 61 MET cc_start: 0.7868 (mmt) cc_final: 0.7556 (mmm) REVERT: J 56 LEU cc_start: 0.6431 (tt) cc_final: 0.6010 (mt) REVERT: J 92 ASN cc_start: 0.7973 (p0) cc_final: 0.7665 (p0) REVERT: P 66 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: P 142 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7728 (mt-10) REVERT: P 150 LYS cc_start: 0.4226 (tptt) cc_final: 0.3438 (mmmt) REVERT: R 178 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: S 68 MET cc_start: 0.8432 (ttp) cc_final: 0.7971 (tmm) REVERT: S 220 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7445 (mm) REVERT: T 149 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: T 169 GLN cc_start: 0.8525 (mp10) cc_final: 0.8154 (mp10) REVERT: T 411 GLU cc_start: 0.8413 (pm20) cc_final: 0.8170 (mp0) REVERT: T 440 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8126 (ttmt) REVERT: T 471 GLN cc_start: 0.8224 (tp40) cc_final: 0.7765 (tp40) REVERT: T 549 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6385 (t70) REVERT: T 555 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7293 (mmt90) REVERT: U 134 ASN cc_start: 0.8592 (t0) cc_final: 0.8389 (t0) REVERT: U 391 SER cc_start: 0.9052 (p) cc_final: 0.8755 (m) REVERT: U 447 LYS cc_start: 0.7661 (mtpm) cc_final: 0.7443 (mtpt) REVERT: U 472 TYR cc_start: 0.7281 (t80) cc_final: 0.7074 (t80) REVERT: U 553 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7721 (mm-30) REVERT: V 50 LYS cc_start: 0.7969 (tppt) cc_final: 0.7566 (tptt) REVERT: V 471 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6777 (mt0) REVERT: X 158 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7985 (mm-30) REVERT: X 276 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: X 531 VAL cc_start: 0.7363 (t) cc_final: 0.6840 (p) REVERT: Y 409 ASP cc_start: 0.8083 (m-30) cc_final: 0.7769 (m-30) REVERT: Y 424 GLU cc_start: 0.6538 (mp0) cc_final: 0.6244 (pm20) REVERT: Y 430 LYS cc_start: 0.7580 (mttt) cc_final: 0.7304 (mtmm) REVERT: Y 441 ARG cc_start: 0.8177 (mmt-90) cc_final: 0.7877 (mpt-90) REVERT: Z 429 ASP cc_start: 0.7121 (m-30) cc_final: 0.6800 (m-30) outliers start: 104 outliers final: 71 residues processed: 522 average time/residue: 0.6004 time to fit residues: 389.4509 Evaluate side-chains 509 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 430 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 117 SER Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 353 ASP Chi-restraints excluded: chain T residue 475 GLU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 185 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 532 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 411 GLU Chi-restraints excluded: chain V residue 471 GLN Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 417 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 32 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 159 optimal weight: 0.4980 chunk 404 optimal weight: 0.9980 chunk 357 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 396 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 354 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 98 GLN J 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 549 HIS ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 414 GLN Y 198 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103894 restraints weight = 49457.263| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.73 r_work: 0.3149 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34412 Z= 0.119 Angle : 0.599 12.461 46638 Z= 0.300 Chirality : 0.044 0.351 5519 Planarity : 0.004 0.066 5997 Dihedral : 5.380 93.916 4828 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.19 % Rotamer: Outliers : 2.22 % Allowed : 22.64 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.14 (0.13), residues: 4461 helix: 0.93 (0.12), residues: 2212 sheet: -0.74 (0.22), residues: 567 loop : -0.60 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 199 TYR 0.015 0.001 TYR C 102 PHE 0.037 0.001 PHE D 107 TRP 0.004 0.001 TRP R 37 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (34412) covalent geometry : angle 0.59909 / 0.30 (46638) hydrogen bonds : bond 0.03231 / 2.17 ( 1721) hydrogen bonds : angle 4.41518 / 3.16 ( 5055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13313.33 seconds wall clock time: 227 minutes 27.74 seconds (13647.74 seconds total)