Starting phenix.real_space_refine on Fri Mar 6 19:09:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6re7_4844/03_2026/6re7_4844.cif Found real_map, /net/cci-nas-00/data/ceres_data/6re7_4844/03_2026/6re7_4844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6re7_4844/03_2026/6re7_4844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6re7_4844/03_2026/6re7_4844.map" model { file = "/net/cci-nas-00/data/ceres_data/6re7_4844/03_2026/6re7_4844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6re7_4844/03_2026/6re7_4844.cif" } resolution = 3.1 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= 0.006 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 21526 2.51 5 N 5790 2.21 5 O 6413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33863 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: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" 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: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "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: "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} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.46, per 1000 atoms: 0.22 Number of scatterers: 33863 At special positions: 0 Unit cell: (163.215, 130.572, 208.494, 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 6413 8.00 N 5790 7.00 C 21526 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: 2.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8150 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 28 sheets defined 53.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.521A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.029A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.732A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.641A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.944A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.870A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.542A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.555A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.044A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 3.988A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.572A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 4.148A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.222A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 124 removed outlier: 4.251A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.783A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 92 removed outlier: 3.891A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 127 removed outlier: 3.746A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.018A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.199A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 4.078A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.800A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 90 removed outlier: 4.100A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 95 through 126 removed outlier: 4.572A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.801A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 90 removed outlier: 4.209A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 94 No H-bonds generated for 'chain 'I' and resid 92 through 94' Processing helix chain 'I' and resid 95 through 126 removed outlier: 4.004A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.409A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 92 removed outlier: 3.801A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.554A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.661A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.532A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.910A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.773A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 149 removed outlier: 4.141A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 3.701A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.847A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 29 through 39 removed outlier: 3.533A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.611A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR R 55 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 158 through 169 removed outlier: 3.942A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 3.942A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 79 removed outlier: 3.745A pdb=" N ARG S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.472A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 131 removed outlier: 3.503A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU S 131 " --> pdb=" O LEU S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 Processing helix chain 'S' and resid 149 through 154 removed outlier: 4.084A pdb=" N ILE S 153 " --> pdb=" O GLN S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 Processing helix chain 'S' and resid 212 through 222 removed outlier: 5.375A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 274 removed outlier: 3.650A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 313 Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.919A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 156 through 160 removed outlier: 3.596A pdb=" N LEU T 160 " --> pdb=" O PRO T 157 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 213 Processing helix chain 'T' and resid 230 through 246 Processing helix chain 'T' and resid 265 through 279 Processing helix chain 'T' and resid 280 through 284 removed outlier: 3.707A pdb=" N ARG T 283 " --> pdb=" O GLY T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.264A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.715A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.734A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 removed outlier: 3.563A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 431 through 435 Processing helix chain 'T' and resid 436 through 443 removed outlier: 3.530A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 443 through 458 Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.652A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.562A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 528 removed outlier: 4.361A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 4.379A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 545 through 556 removed outlier: 3.686A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 49 removed outlier: 3.835A pdb=" N ARG U 49 " --> pdb=" O ASP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 72 removed outlier: 4.275A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 134 through 138 removed outlier: 4.110A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.687A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.524A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 280 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.880A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.536A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.017A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 467 through 485 removed outlier: 3.607A pdb=" N GLN U 471 " --> pdb=" O ASP U 467 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.622A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.890A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 43 through 49 removed outlier: 3.741A pdb=" N ASP V 46 " --> pdb=" O LYS V 43 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.810A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.937A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.508A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 212 removed outlier: 3.525A pdb=" N LEU V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.697A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 285 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.818A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.628A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.588A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.884A 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 438 through 457 removed outlier: 3.572A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA V 457 " --> pdb=" O TYR V 453 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 484 removed outlier: 3.616A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.644A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.747A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 540 removed outlier: 3.872A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 554 removed outlier: 3.518A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.529A 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 203 Processing helix chain 'X' and resid 216 through 231 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.961A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.648A 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: 3.608A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 301 Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.557A pdb=" N ASP X 344 " --> pdb=" O VAL X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 413 Processing helix chain 'X' and resid 414 through 420 Processing helix chain 'X' and resid 421 through 425 removed outlier: 3.733A pdb=" N GLU X 424 " --> pdb=" O GLY X 421 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU X 425 " --> pdb=" O MET X 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 421 through 425' Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.564A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 449 through 453 removed outlier: 4.299A pdb=" N VAL X 452 " --> pdb=" O VAL X 449 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 482 through 487 removed outlier: 3.934A pdb=" N PHE X 486 " --> pdb=" O PRO X 482 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR X 487 " --> pdb=" O GLU X 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 482 through 487' Processing helix chain 'X' and resid 491 through 504 removed outlier: 3.537A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 505 through 507 No H-bonds generated for 'chain 'X' and resid 505 through 507' Processing helix chain 'X' and resid 526 through 532 Processing helix chain 'Y' and resid 114 through 118 removed outlier: 3.738A pdb=" N THR Y 117 " --> pdb=" O GLY Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 190 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 237 through 242 removed outlier: 4.607A 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 removed outlier: 3.600A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 299 removed outlier: 3.759A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.592A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) 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 Processing helix chain 'Y' and resid 388 through 393 removed outlier: 3.566A pdb=" N GLY Y 393 " --> pdb=" O PRO Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 393 through 412 Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 421 through 425 removed outlier: 3.705A pdb=" N GLU Y 424 " --> pdb=" O GLY Y 421 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU Y 425 " --> pdb=" O MET Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 421 through 425' Processing helix chain 'Y' and resid 426 through 443 removed outlier: 3.901A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.517A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 491 through 505 removed outlier: 4.027A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 506 through 508 No H-bonds generated for 'chain 'Y' and resid 506 through 508' Processing helix chain 'Y' and resid 511 through 515 removed outlier: 4.155A pdb=" N ASN Y 514 " --> pdb=" O GLU Y 511 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS Y 515 " --> pdb=" O ALA Y 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 511 through 515' Processing helix chain 'Y' and resid 526 through 532 removed outlier: 3.554A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 550 removed outlier: 4.177A pdb=" N ASP Y 548 " --> pdb=" O GLY Y 544 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE Y 549 " --> pdb=" O LEU Y 545 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 544 through 550' Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 201 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.571A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 4.874A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.965A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 342 through 345 Processing helix chain 'Z' and resid 348 through 354 removed outlier: 4.033A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.561A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 418 removed outlier: 7.600A pdb=" N ALA Z 394 " --> pdb=" O ASN Z 390 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N GLU Z 395 " --> pdb=" O VAL Z 391 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR Z 397 " --> pdb=" O GLY Z 393 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.601A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 491 through 506 removed outlier: 4.012A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 507 through 509 No H-bonds generated for 'chain 'Z' and resid 507 through 509' Processing helix chain 'Z' and resid 526 through 534 removed outlier: 3.918A pdb=" N LEU Z 530 " --> pdb=" O SER Z 526 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE Z 534 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 61 through 65 removed outlier: 9.915A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.549A 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 Processing sheet with id=AA4, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.538A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 87 through 89 removed outlier: 5.433A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.904A 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 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA6, first strand: chain 'T' and resid 87 through 89 removed outlier: 5.433A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.904A 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 61 through 65 removed outlier: 4.473A pdb=" N SER Y 61 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.502A 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 37 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 Processing sheet with id=AA9, first strand: chain 'T' and resid 382 through 384 removed outlier: 6.515A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 116 through 122 removed outlier: 4.068A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB3, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.269A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.526A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.405A 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=AB5, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.526A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.405A 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: 4.836A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.575A 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=AB6, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB7, first strand: chain 'V' and resid 163 through 164 Processing sheet with id=AB8, first strand: chain 'V' and resid 382 through 384 removed outlier: 6.715A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.620A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.213A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLN X 250 " --> pdb=" O MET X 122 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL X 284 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.446A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC4, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id=AC5, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.316A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE Y 207 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.089A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AC8, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.944A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.369A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 559 through 561 1728 hydrogen bonds defined for protein. 5004 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: 7.52 Time building geometry restraints manager: 3.95 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: 8797 1.33 - 1.45: 5813 1.45 - 1.57: 19553 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.04e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.74e+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 3.45e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 46266 3.93 - 7.87: 303 7.87 - 11.80: 20 11.80 - 15.74: 6 15.74 - 19.67: 3 Bond angle restraints: 46598 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.20 19.67 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 123.94 15.93 1.00e+00 1.00e+00 2.54e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 121.89 14.94 1.00e+00 1.00e+00 2.23e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 20347 35.83 - 71.67: 428 71.67 - 107.50: 27 107.50 - 143.33: 0 143.33 - 179.17: 1 Dihedral angle restraints: 20803 sinusoidal: 8060 harmonic: 12743 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -130.24 -49.76 0 5.00e+00 4.00e-02 9.90e+01 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 -135.40 -44.60 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" C5' ADP Z 601 " pdb=" O5' ADP Z 601 " pdb=" PA ADP Z 601 " pdb=" O2A ADP Z 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.17 -179.17 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4245 0.070 - 0.139: 1139 0.139 - 0.209: 114 0.209 - 0.279: 13 0.279 - 0.349: 2 Chirality restraints: 5513 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB THR U 378 " pdb=" CA THR U 378 " pdb=" OG1 THR U 378 " pdb=" CG2 THR U 378 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 5510 not shown) Planarity restraints: 5991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.032 2.00e-02 2.50e+03 6.27e-02 3.93e+01 pdb=" C ALA Y 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.79e-02 3.36e+01 pdb=" C ALA Z 503 " -0.100 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.037 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU T 509 " 0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU T 509 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU T 509 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP T 510 " 0.019 2.00e-02 2.50e+03 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1681 2.71 - 3.26: 32762 3.26 - 3.81: 57653 3.81 - 4.35: 74471 4.35 - 4.90: 125735 Nonbonded interactions: 292302 Sorted by model distance: nonbonded pdb=" O3B ADP Z 601 " pdb="MG MG Z 602 " model vdw 2.164 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.225 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.226 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.228 2.170 nonbonded pdb=" O LYS Z 515 " pdb=" N VAL Z 517 " model vdw 2.234 3.120 ... (remaining 292297 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 1002) selection = (chain 'V' and resid 85 through 1002) } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } 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: 11.950 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: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.540 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 0.106 34384 Z= 0.457 Angle : 0.975 19.670 46598 Z= 0.569 Chirality : 0.060 0.349 5513 Planarity : 0.007 0.072 5991 Dihedral : 14.722 179.168 12653 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.53 % Favored : 95.24 % Rotamer: Outliers : 0.34 % Allowed : 10.19 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.86 (0.10), residues: 4457 helix: -2.86 (0.08), residues: 2136 sheet: -1.51 (0.21), residues: 548 loop : -2.27 (0.12), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 454 TYR 0.024 0.003 TYR T 324 PHE 0.034 0.003 PHE S 249 TRP 0.032 0.004 TRP Y 141 HIS 0.011 0.002 HIS S 250 Details of bonding type rmsd covalent geometry : bond 0.01053 (34384) covalent geometry : angle 0.97473 (46598) hydrogen bonds : bond 0.17191 ( 1709) hydrogen bonds : angle 7.66002 ( 5004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 661 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ILE cc_start: 0.8502 (tt) cc_final: 0.7959 (tt) REVERT: F 56 LEU cc_start: 0.5977 (tp) cc_final: 0.5442 (mt) REVERT: H 97 LYS cc_start: 0.6939 (mmtt) cc_final: 0.5827 (mtpt) REVERT: J 105 LEU cc_start: 0.7848 (tt) cc_final: 0.7283 (mt) REVERT: P 50 SER cc_start: 0.8787 (t) cc_final: 0.8330 (m) REVERT: P 79 GLU cc_start: 0.7849 (tp30) cc_final: 0.7383 (tp30) REVERT: S 241 ASP cc_start: 0.7558 (m-30) cc_final: 0.6830 (m-30) REVERT: T 101 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7805 (mtpp) REVERT: T 492 ILE cc_start: 0.8795 (mt) cc_final: 0.8573 (mm) REVERT: T 537 LYS cc_start: 0.8522 (tmmt) cc_final: 0.8116 (ttpt) REVERT: U 483 MET cc_start: 0.6709 (tmm) cc_final: 0.6213 (tmm) REVERT: U 550 LEU cc_start: 0.8907 (tp) cc_final: 0.8679 (mt) REVERT: X 90 MET cc_start: 0.9006 (mmt) cc_final: 0.8511 (mmt) REVERT: X 386 MET cc_start: 0.8471 (mmm) cc_final: 0.7869 (mmm) REVERT: Z 195 GLU cc_start: 0.7581 (tp30) cc_final: 0.7337 (tp30) REVERT: Z 248 TYR cc_start: 0.8567 (m-80) cc_final: 0.8070 (m-80) REVERT: Z 448 GLN cc_start: 0.7399 (tm-30) cc_final: 0.6958 (mm-40) REVERT: Z 484 MET cc_start: 0.7384 (mmt) cc_final: 0.6974 (mmt) REVERT: Z 504 LYS cc_start: 0.7049 (mttt) cc_final: 0.6702 (mttt) outliers start: 12 outliers final: 6 residues processed: 670 average time/residue: 0.2236 time to fit residues: 235.6361 Evaluate side-chains 474 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 468 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN C 87 ASN G 98 GLN I 87 ASN I 94 ASN Q 43 GLN Q 49 GLN R 53 ASN R 83 GLN R 137 HIS S 98 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN S 262 ASN S 267 HIS T 134 ASN T 196 GLN T 241 HIS T 358 HIS T 386 GLN T 441 GLN U 104 GLN U 149 GLN U 152 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 248 GLN U 264 GLN U 319 HIS U 358 HIS U 386 GLN U 515 GLN U 539 ASN V 61 HIS V 121 ASN V 126 HIS V 134 ASN V 139 HIS V 149 GLN V 152 ASN V 179 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 244 ASN V 278 GLN V 358 HIS V 486 GLN V 497 GLN X 78 GLN X 278 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 404 GLN X 574 ASN Y 174 GLN Y 199 ASN Y 278 GLN Y 414 GLN Z 83 ASN Z 174 GLN Z 204 HIS Z 337 GLN Z 408 GLN Z 414 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108388 restraints weight = 51528.377| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.74 r_work: 0.3117 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34384 Z= 0.132 Angle : 0.564 9.452 46598 Z= 0.295 Chirality : 0.043 0.166 5513 Planarity : 0.005 0.056 5991 Dihedral : 6.711 168.583 4918 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.93 % Rotamer: Outliers : 1.83 % Allowed : 13.06 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.12), residues: 4457 helix: -1.02 (0.10), residues: 2175 sheet: -1.15 (0.22), residues: 553 loop : -1.66 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 89 TYR 0.015 0.001 TYR X 310 PHE 0.017 0.001 PHE P 77 TRP 0.014 0.002 TRP Y 141 HIS 0.006 0.001 HIS T 549 Details of bonding type rmsd covalent geometry : bond 0.00290 (34384) covalent geometry : angle 0.56443 (46598) hydrogen bonds : bond 0.04022 ( 1709) hydrogen bonds : angle 4.99548 ( 5004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 556 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8507 (t0) cc_final: 0.7939 (t0) REVERT: B 92 ASN cc_start: 0.8104 (t0) cc_final: 0.7669 (t0) REVERT: B 95 ILE cc_start: 0.8491 (tt) cc_final: 0.8256 (tt) REVERT: C 109 LEU cc_start: 0.8195 (mp) cc_final: 0.7859 (tp) REVERT: C 124 ILE cc_start: 0.7391 (mm) cc_final: 0.7014 (mt) REVERT: D 92 ASN cc_start: 0.8613 (t0) cc_final: 0.8396 (t0) REVERT: E 91 ARG cc_start: 0.7742 (mmt-90) cc_final: 0.7482 (mpt180) REVERT: E 107 PHE cc_start: 0.7766 (t80) cc_final: 0.7463 (t80) REVERT: F 56 LEU cc_start: 0.6726 (tp) cc_final: 0.6148 (pp) REVERT: H 97 LYS cc_start: 0.6830 (mmtt) cc_final: 0.5545 (mtpt) REVERT: I 68 THR cc_start: 0.7954 (t) cc_final: 0.7678 (p) REVERT: I 118 LEU cc_start: 0.8605 (mt) cc_final: 0.8208 (mt) REVERT: J 84 SER cc_start: 0.8216 (m) cc_final: 0.7767 (p) REVERT: J 123 LEU cc_start: 0.7334 (tp) cc_final: 0.7066 (mt) REVERT: P 49 THR cc_start: 0.8844 (t) cc_final: 0.8592 (t) REVERT: P 72 ASP cc_start: 0.7690 (t0) cc_final: 0.7463 (t0) REVERT: P 75 TYR cc_start: 0.8223 (m-10) cc_final: 0.8009 (m-10) REVERT: P 79 GLU cc_start: 0.8414 (tp30) cc_final: 0.8144 (tp30) REVERT: P 120 LYS cc_start: 0.8440 (mmpt) cc_final: 0.7829 (mttt) REVERT: R 86 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7784 (mmtp) REVERT: R 171 GLN cc_start: 0.8120 (mm110) cc_final: 0.7647 (mp10) REVERT: R 188 TYR cc_start: 0.6571 (m-10) cc_final: 0.6298 (m-10) REVERT: S 217 GLU cc_start: 0.7707 (tp30) cc_final: 0.7299 (tp30) REVERT: S 241 ASP cc_start: 0.8362 (m-30) cc_final: 0.8079 (m-30) REVERT: S 245 ASP cc_start: 0.8431 (m-30) cc_final: 0.8228 (m-30) REVERT: T 101 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8498 (mtpp) REVERT: T 537 LYS cc_start: 0.8748 (tmmt) cc_final: 0.8327 (ttpt) REVERT: U 121 ASN cc_start: 0.8472 (p0) cc_final: 0.8187 (p0) REVERT: U 489 PHE cc_start: 0.8078 (m-10) cc_final: 0.7803 (m-10) REVERT: U 515 GLN cc_start: 0.8220 (mp-120) cc_final: 0.8010 (mm-40) REVERT: V 49 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.7166 (mmm-85) REVERT: V 407 PHE cc_start: 0.8120 (t80) cc_final: 0.7901 (t80) REVERT: V 547 ASP cc_start: 0.7186 (p0) cc_final: 0.6430 (t0) REVERT: V 551 LYS cc_start: 0.7443 (tppp) cc_final: 0.7072 (mtpt) REVERT: X 90 MET cc_start: 0.9353 (mmt) cc_final: 0.8758 (mmt) REVERT: X 289 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8493 (mtm-85) REVERT: X 374 TYR cc_start: 0.8665 (m-80) cc_final: 0.8259 (m-80) REVERT: X 386 MET cc_start: 0.8854 (mmm) cc_final: 0.8589 (mmm) REVERT: Y 385 ARG cc_start: 0.8260 (mtt90) cc_final: 0.7941 (mtp-110) REVERT: Y 502 MET cc_start: 0.7956 (ptp) cc_final: 0.7411 (ptp) REVERT: Z 193 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8439 (tt) REVERT: Z 195 GLU cc_start: 0.8065 (tp30) cc_final: 0.7645 (tp30) REVERT: Z 248 TYR cc_start: 0.8933 (m-80) cc_final: 0.8568 (m-80) REVERT: Z 386 MET cc_start: 0.9076 (mmm) cc_final: 0.8604 (mmm) REVERT: Z 448 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7150 (mm-40) REVERT: Z 516 LYS cc_start: 0.3040 (OUTLIER) cc_final: 0.2541 (mmmm) outliers start: 65 outliers final: 44 residues processed: 592 average time/residue: 0.2238 time to fit residues: 210.6686 Evaluate side-chains 531 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 485 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 169 GLN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 278 GLN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 328 optimal weight: 0.4980 chunk 388 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 435 optimal weight: 0.0570 chunk 294 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN E 98 GLN G 98 GLN Q 43 GLN R 53 ASN R 83 GLN S 174 GLN S 262 ASN T 435 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN U 549 HIS V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 414 GLN Z 337 GLN Z 414 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108453 restraints weight = 51411.132| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.65 r_work: 0.3180 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34384 Z= 0.125 Angle : 0.532 9.560 46598 Z= 0.277 Chirality : 0.043 0.162 5513 Planarity : 0.004 0.052 5991 Dihedral : 6.266 146.915 4917 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 1.83 % Allowed : 14.94 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.22 (0.12), residues: 4457 helix: -0.25 (0.11), residues: 2186 sheet: -0.97 (0.22), residues: 560 loop : -1.33 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 49 TYR 0.012 0.001 TYR U 77 PHE 0.017 0.001 PHE P 77 TRP 0.008 0.001 TRP Y 141 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00276 (34384) covalent geometry : angle 0.53240 (46598) hydrogen bonds : bond 0.03692 ( 1709) hydrogen bonds : angle 4.61072 ( 5004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 514 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8478 (t0) cc_final: 0.7974 (t0) REVERT: B 81 MET cc_start: 0.8312 (ttp) cc_final: 0.7966 (ttm) REVERT: B 92 ASN cc_start: 0.8159 (t0) cc_final: 0.7679 (t0) REVERT: B 95 ILE cc_start: 0.8551 (tt) cc_final: 0.8230 (tt) REVERT: B 105 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7231 (tp) REVERT: C 81 MET cc_start: 0.7326 (ttp) cc_final: 0.7083 (ttm) REVERT: C 111 GLU cc_start: 0.7082 (tp30) cc_final: 0.6852 (pp20) REVERT: C 124 ILE cc_start: 0.7542 (mm) cc_final: 0.6756 (mm) REVERT: F 56 LEU cc_start: 0.6723 (tp) cc_final: 0.6209 (pp) REVERT: G 109 LEU cc_start: 0.7481 (mt) cc_final: 0.7207 (mt) REVERT: H 97 LYS cc_start: 0.6819 (mmtt) cc_final: 0.5594 (mtpt) REVERT: I 68 THR cc_start: 0.7899 (t) cc_final: 0.7695 (p) REVERT: I 98 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7183 (pt0) REVERT: I 118 LEU cc_start: 0.8586 (mt) cc_final: 0.8185 (mt) REVERT: J 56 LEU cc_start: 0.7602 (pt) cc_final: 0.6625 (tp) REVERT: J 78 LEU cc_start: 0.7095 (mm) cc_final: 0.6809 (mt) REVERT: J 84 SER cc_start: 0.8136 (m) cc_final: 0.7777 (p) REVERT: J 105 LEU cc_start: 0.8242 (tp) cc_final: 0.7570 (mt) REVERT: J 123 LEU cc_start: 0.7546 (tp) cc_final: 0.7225 (mt) REVERT: P 49 THR cc_start: 0.8790 (t) cc_final: 0.8503 (t) REVERT: P 72 ASP cc_start: 0.7690 (t0) cc_final: 0.7465 (t0) REVERT: P 75 TYR cc_start: 0.8236 (m-10) cc_final: 0.8033 (m-10) REVERT: P 79 GLU cc_start: 0.8435 (tp30) cc_final: 0.8216 (tp30) REVERT: P 111 ASP cc_start: 0.6255 (p0) cc_final: 0.6004 (p0) REVERT: P 120 LYS cc_start: 0.8425 (mmpt) cc_final: 0.8174 (mmmt) REVERT: R 171 GLN cc_start: 0.8114 (mm110) cc_final: 0.7618 (mp10) REVERT: R 188 TYR cc_start: 0.6523 (m-10) cc_final: 0.6158 (m-10) REVERT: S 217 GLU cc_start: 0.7733 (tp30) cc_final: 0.7193 (tp30) REVERT: S 241 ASP cc_start: 0.8404 (m-30) cc_final: 0.7975 (m-30) REVERT: S 245 ASP cc_start: 0.8388 (m-30) cc_final: 0.8149 (m-30) REVERT: T 86 ARG cc_start: 0.8920 (mtm110) cc_final: 0.8265 (mmt-90) REVERT: T 511 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7721 (ptpt) REVERT: T 537 LYS cc_start: 0.8743 (tmmt) cc_final: 0.8328 (ttpt) REVERT: U 489 PHE cc_start: 0.8017 (m-10) cc_final: 0.7773 (m-10) REVERT: V 547 ASP cc_start: 0.7141 (p0) cc_final: 0.6479 (t0) REVERT: V 551 LYS cc_start: 0.7430 (tppp) cc_final: 0.7090 (mtpt) REVERT: X 90 MET cc_start: 0.9341 (mmt) cc_final: 0.8701 (mmt) REVERT: X 289 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8417 (mtm-85) REVERT: X 374 TYR cc_start: 0.8678 (m-80) cc_final: 0.8230 (m-80) REVERT: X 386 MET cc_start: 0.8792 (mmm) cc_final: 0.8539 (mmm) REVERT: Y 310 TYR cc_start: 0.9027 (m-80) cc_final: 0.8605 (m-80) REVERT: Y 385 ARG cc_start: 0.8292 (mtt90) cc_final: 0.8039 (mtp-110) REVERT: Y 502 MET cc_start: 0.7897 (ptp) cc_final: 0.7364 (ptm) REVERT: Z 193 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8459 (tt) REVERT: Z 195 GLU cc_start: 0.8111 (tp30) cc_final: 0.7742 (tp30) REVERT: Z 248 TYR cc_start: 0.8871 (m-80) cc_final: 0.8552 (m-80) REVERT: Z 310 TYR cc_start: 0.8300 (m-80) cc_final: 0.7792 (m-80) REVERT: Z 386 MET cc_start: 0.9054 (mmm) cc_final: 0.8528 (mmm) REVERT: Z 448 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7348 (mm-40) outliers start: 65 outliers final: 39 residues processed: 558 average time/residue: 0.2120 time to fit residues: 190.9307 Evaluate side-chains 501 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 458 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 96 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 414 optimal weight: 0.0970 chunk 255 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 312 optimal weight: 0.5980 chunk 310 optimal weight: 1.9990 chunk 387 optimal weight: 0.0770 chunk 273 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 98 GLN E 98 GLN G 98 GLN R 53 ASN R 83 GLN R 85 GLN T 134 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 412 ASN Y 414 GLN Z 337 GLN Z 414 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108588 restraints weight = 50945.812| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.61 r_work: 0.3179 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34384 Z= 0.128 Angle : 0.523 9.530 46598 Z= 0.271 Chirality : 0.043 0.160 5513 Planarity : 0.004 0.050 5991 Dihedral : 5.989 122.659 4916 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.19 % Favored : 96.66 % Rotamer: Outliers : 2.16 % Allowed : 15.92 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.73 (0.13), residues: 4457 helix: 0.19 (0.11), residues: 2194 sheet: -0.84 (0.22), residues: 562 loop : -1.11 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 96 TYR 0.013 0.001 TYR U 77 PHE 0.017 0.001 PHE E 107 TRP 0.006 0.001 TRP Y 141 HIS 0.003 0.001 HIS S 250 Details of bonding type rmsd covalent geometry : bond 0.00287 (34384) covalent geometry : angle 0.52264 (46598) hydrogen bonds : bond 0.03567 ( 1709) hydrogen bonds : angle 4.41549 ( 5004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 510 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8494 (t0) cc_final: 0.7985 (t0) REVERT: B 92 ASN cc_start: 0.8191 (t0) cc_final: 0.7675 (t0) REVERT: B 95 ILE cc_start: 0.8613 (tt) cc_final: 0.8231 (tt) REVERT: C 81 MET cc_start: 0.7250 (ttp) cc_final: 0.6992 (ttm) REVERT: C 118 LEU cc_start: 0.7357 (mt) cc_final: 0.6945 (pp) REVERT: C 124 ILE cc_start: 0.7349 (mm) cc_final: 0.6885 (mt) REVERT: E 61 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5916 (tmm) REVERT: F 56 LEU cc_start: 0.6693 (tp) cc_final: 0.6168 (pp) REVERT: F 116 PHE cc_start: 0.6859 (m-10) cc_final: 0.6558 (m-80) REVERT: G 109 LEU cc_start: 0.7489 (mt) cc_final: 0.7196 (mt) REVERT: H 97 LYS cc_start: 0.6573 (mmtt) cc_final: 0.5506 (mtpt) REVERT: I 118 LEU cc_start: 0.8538 (mt) cc_final: 0.8134 (mt) REVERT: J 56 LEU cc_start: 0.7627 (pt) cc_final: 0.6530 (tp) REVERT: J 78 LEU cc_start: 0.7189 (mm) cc_final: 0.6930 (mt) REVERT: J 105 LEU cc_start: 0.8206 (tp) cc_final: 0.7586 (mt) REVERT: J 123 LEU cc_start: 0.7520 (tp) cc_final: 0.7282 (mt) REVERT: P 49 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8286 (t) REVERT: P 72 ASP cc_start: 0.7638 (t0) cc_final: 0.7369 (t0) REVERT: P 73 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7927 (mt-10) REVERT: P 79 GLU cc_start: 0.8487 (tp30) cc_final: 0.8107 (tp30) REVERT: P 111 ASP cc_start: 0.6347 (p0) cc_final: 0.6073 (p0) REVERT: P 120 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8183 (mmmt) REVERT: Q 32 LYS cc_start: 0.6737 (mmmt) cc_final: 0.6524 (mmtm) REVERT: R 188 TYR cc_start: 0.6661 (m-10) cc_final: 0.6061 (m-10) REVERT: S 217 GLU cc_start: 0.7717 (tp30) cc_final: 0.7456 (tp30) REVERT: S 241 ASP cc_start: 0.8459 (m-30) cc_final: 0.8038 (m-30) REVERT: T 86 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8282 (mmt-90) REVERT: T 511 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7637 (ptpt) REVERT: T 537 LYS cc_start: 0.8736 (tmmt) cc_final: 0.8331 (ttpt) REVERT: U 348 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8654 (mt-10) REVERT: U 483 MET cc_start: 0.7691 (ttp) cc_final: 0.7475 (ptm) REVERT: V 283 ARG cc_start: 0.8393 (ptm-80) cc_final: 0.7990 (ttp-170) REVERT: V 547 ASP cc_start: 0.7085 (p0) cc_final: 0.6491 (t0) REVERT: V 551 LYS cc_start: 0.7466 (tppp) cc_final: 0.7157 (mtpt) REVERT: X 90 MET cc_start: 0.9356 (mmt) cc_final: 0.8707 (mmt) REVERT: X 289 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8544 (mtm-85) REVERT: X 374 TYR cc_start: 0.8677 (m-80) cc_final: 0.8190 (m-80) REVERT: X 386 MET cc_start: 0.8732 (mmm) cc_final: 0.8467 (mmm) REVERT: Y 310 TYR cc_start: 0.9044 (m-80) cc_final: 0.8825 (m-80) REVERT: Y 385 ARG cc_start: 0.8285 (mtt90) cc_final: 0.8064 (mtp-110) REVERT: Y 386 MET cc_start: 0.8466 (mmm) cc_final: 0.8251 (mmm) REVERT: Y 502 MET cc_start: 0.7847 (ptp) cc_final: 0.7313 (ptm) REVERT: Y 535 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7084 (mppt) REVERT: Z 139 ASP cc_start: 0.7921 (t70) cc_final: 0.7712 (t0) REVERT: Z 193 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8458 (tt) REVERT: Z 195 GLU cc_start: 0.8139 (tp30) cc_final: 0.7801 (tp30) REVERT: Z 248 TYR cc_start: 0.8863 (m-80) cc_final: 0.8587 (m-80) REVERT: Z 310 TYR cc_start: 0.8195 (m-80) cc_final: 0.7702 (m-80) REVERT: Z 386 MET cc_start: 0.9031 (mmm) cc_final: 0.8463 (mmm) REVERT: Z 448 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7274 (mm-40) REVERT: Z 536 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6287 (mm-30) outliers start: 77 outliers final: 59 residues processed: 560 average time/residue: 0.2137 time to fit residues: 193.1555 Evaluate side-chains 524 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 461 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 3 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 221 optimal weight: 0.0040 chunk 428 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN E 98 GLN G 98 GLN R 53 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 154 GLN T 134 ASN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 250 GLN Y 278 GLN Z 337 GLN Z 414 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106450 restraints weight = 51465.941| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.67 r_work: 0.3139 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34384 Z= 0.173 Angle : 0.555 9.540 46598 Z= 0.288 Chirality : 0.044 0.264 5513 Planarity : 0.004 0.046 5991 Dihedral : 6.065 109.625 4916 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.19 % Rotamer: Outliers : 2.67 % Allowed : 17.44 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.55 (0.13), residues: 4457 helix: 0.33 (0.11), residues: 2188 sheet: -0.85 (0.22), residues: 566 loop : -0.97 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 435 TYR 0.015 0.001 TYR T 324 PHE 0.025 0.001 PHE B 107 TRP 0.006 0.001 TRP U 73 HIS 0.004 0.001 HIS Z 144 Details of bonding type rmsd covalent geometry : bond 0.00400 (34384) covalent geometry : angle 0.55458 (46598) hydrogen bonds : bond 0.03785 ( 1709) hydrogen bonds : angle 4.44936 ( 5004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 491 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8552 (t0) cc_final: 0.8073 (t0) REVERT: B 92 ASN cc_start: 0.8190 (t0) cc_final: 0.7609 (t0) REVERT: B 95 ILE cc_start: 0.8594 (tt) cc_final: 0.8193 (tt) REVERT: C 81 MET cc_start: 0.7336 (ttp) cc_final: 0.7047 (ttm) REVERT: C 118 LEU cc_start: 0.7178 (mt) cc_final: 0.6750 (pp) REVERT: C 124 ILE cc_start: 0.7424 (mm) cc_final: 0.6831 (mt) REVERT: E 61 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.5967 (tmm) REVERT: F 116 PHE cc_start: 0.6923 (m-10) cc_final: 0.6651 (m-80) REVERT: G 109 LEU cc_start: 0.7435 (mt) cc_final: 0.7148 (mt) REVERT: H 97 LYS cc_start: 0.6614 (mmtt) cc_final: 0.5406 (mtpt) REVERT: I 118 LEU cc_start: 0.8564 (mt) cc_final: 0.8170 (mt) REVERT: J 56 LEU cc_start: 0.7920 (pt) cc_final: 0.6858 (tp) REVERT: J 105 LEU cc_start: 0.8252 (tp) cc_final: 0.7671 (mt) REVERT: J 123 LEU cc_start: 0.7757 (tp) cc_final: 0.7401 (mt) REVERT: P 49 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8386 (t) REVERT: P 72 ASP cc_start: 0.7867 (t0) cc_final: 0.7595 (t0) REVERT: P 73 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7922 (mt-10) REVERT: P 79 GLU cc_start: 0.8614 (tp30) cc_final: 0.8235 (tp30) REVERT: P 111 ASP cc_start: 0.6339 (p0) cc_final: 0.6068 (p0) REVERT: P 115 SER cc_start: 0.8350 (t) cc_final: 0.8099 (p) REVERT: P 120 LYS cc_start: 0.8454 (mmpt) cc_final: 0.8208 (mmmt) REVERT: R 188 TYR cc_start: 0.6752 (m-10) cc_final: 0.6244 (m-10) REVERT: S 217 GLU cc_start: 0.7790 (tp30) cc_final: 0.7437 (tp30) REVERT: T 86 ARG cc_start: 0.9050 (mtm110) cc_final: 0.8307 (mmt-90) REVERT: T 511 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7674 (ptpt) REVERT: T 537 LYS cc_start: 0.8792 (tmmt) cc_final: 0.8386 (ttpt) REVERT: V 479 ARG cc_start: 0.7642 (mmt-90) cc_final: 0.7173 (mmt90) REVERT: V 547 ASP cc_start: 0.7161 (p0) cc_final: 0.6596 (t0) REVERT: V 551 LYS cc_start: 0.7430 (tppp) cc_final: 0.7033 (tttt) REVERT: X 90 MET cc_start: 0.9396 (mmt) cc_final: 0.8714 (mmt) REVERT: X 289 ARG cc_start: 0.8848 (mtm-85) cc_final: 0.8569 (mtm-85) REVERT: X 386 MET cc_start: 0.8772 (mmm) cc_final: 0.8527 (mmm) REVERT: Y 386 MET cc_start: 0.8587 (mmm) cc_final: 0.8320 (mmm) REVERT: Y 502 MET cc_start: 0.7847 (ptp) cc_final: 0.7443 (ptm) REVERT: Y 535 LYS cc_start: 0.7628 (mtpt) cc_final: 0.7124 (mppt) REVERT: Z 195 GLU cc_start: 0.8176 (tp30) cc_final: 0.7813 (tp30) REVERT: Z 248 TYR cc_start: 0.8877 (m-80) cc_final: 0.8592 (m-80) REVERT: Z 310 TYR cc_start: 0.8384 (m-80) cc_final: 0.7874 (m-80) REVERT: Z 448 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7415 (mm-40) REVERT: Z 516 LYS cc_start: 0.3123 (OUTLIER) cc_final: 0.2417 (mmmm) REVERT: Z 536 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6313 (mm-30) outliers start: 95 outliers final: 65 residues processed: 553 average time/residue: 0.2095 time to fit residues: 188.0921 Evaluate side-chains 526 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 457 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 72 GLU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 154 SER Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 158 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 371 optimal weight: 2.9990 chunk 337 optimal weight: 2.9990 chunk 239 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 429 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 252 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN E 98 GLN P 65 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 85 GLN T 134 ASN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN Z 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107168 restraints weight = 51115.016| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.62 r_work: 0.3097 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34384 Z= 0.153 Angle : 0.542 9.444 46598 Z= 0.281 Chirality : 0.044 0.204 5513 Planarity : 0.004 0.047 5991 Dihedral : 5.996 97.667 4916 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 2.78 % Allowed : 18.31 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.35 (0.13), residues: 4457 helix: 0.51 (0.12), residues: 2181 sheet: -0.84 (0.22), residues: 566 loop : -0.86 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 479 TYR 0.013 0.001 TYR T 324 PHE 0.021 0.001 PHE B 107 TRP 0.006 0.001 TRP U 73 HIS 0.003 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00352 (34384) covalent geometry : angle 0.54180 (46598) hydrogen bonds : bond 0.03634 ( 1709) hydrogen bonds : angle 4.38987 ( 5004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 491 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8448 (t0) cc_final: 0.7853 (t0) REVERT: B 92 ASN cc_start: 0.8204 (t0) cc_final: 0.7594 (t0) REVERT: B 95 ILE cc_start: 0.8620 (tt) cc_final: 0.8208 (tt) REVERT: C 81 MET cc_start: 0.7314 (ttp) cc_final: 0.7025 (ttm) REVERT: C 118 LEU cc_start: 0.7000 (mt) cc_final: 0.6599 (pp) REVERT: D 122 PHE cc_start: 0.6039 (t80) cc_final: 0.5604 (t80) REVERT: E 61 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6063 (tmm) REVERT: F 116 PHE cc_start: 0.6989 (m-10) cc_final: 0.6749 (m-80) REVERT: G 109 LEU cc_start: 0.7435 (mt) cc_final: 0.7125 (mt) REVERT: H 97 LYS cc_start: 0.6598 (mmtt) cc_final: 0.5389 (mtpt) REVERT: I 118 LEU cc_start: 0.8565 (mt) cc_final: 0.8178 (mt) REVERT: J 56 LEU cc_start: 0.7960 (pt) cc_final: 0.6924 (tp) REVERT: J 78 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6841 (mt) REVERT: J 105 LEU cc_start: 0.8257 (tp) cc_final: 0.7710 (mt) REVERT: J 123 LEU cc_start: 0.7779 (tp) cc_final: 0.7412 (mt) REVERT: P 49 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8412 (t) REVERT: P 72 ASP cc_start: 0.7872 (t0) cc_final: 0.7629 (t0) REVERT: P 79 GLU cc_start: 0.8616 (tp30) cc_final: 0.8247 (tp30) REVERT: P 120 LYS cc_start: 0.8447 (mmpt) cc_final: 0.8210 (mmmt) REVERT: Q 32 LYS cc_start: 0.6608 (mmmt) cc_final: 0.6255 (mmtm) REVERT: Q 71 LYS cc_start: 0.7741 (mtpt) cc_final: 0.7531 (mttt) REVERT: R 188 TYR cc_start: 0.6802 (m-10) cc_final: 0.6216 (m-10) REVERT: S 217 GLU cc_start: 0.7782 (tp30) cc_final: 0.7460 (tp30) REVERT: T 86 ARG cc_start: 0.9071 (mtm110) cc_final: 0.8318 (mmt-90) REVERT: T 96 ARG cc_start: 0.8826 (mtt-85) cc_final: 0.8564 (mmt90) REVERT: T 511 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7621 (ptpt) REVERT: T 537 LYS cc_start: 0.8774 (tmmt) cc_final: 0.8377 (ttpt) REVERT: U 282 MET cc_start: 0.9240 (mmt) cc_final: 0.8968 (mmt) REVERT: V 283 ARG cc_start: 0.8432 (ptm-80) cc_final: 0.8035 (ttp-170) REVERT: V 479 ARG cc_start: 0.7638 (mmt-90) cc_final: 0.7183 (mmt90) REVERT: V 547 ASP cc_start: 0.7162 (p0) cc_final: 0.6557 (t0) REVERT: V 551 LYS cc_start: 0.7499 (tppp) cc_final: 0.7110 (tttt) REVERT: X 90 MET cc_start: 0.9400 (mmt) cc_final: 0.8727 (mmt) REVERT: X 289 ARG cc_start: 0.8856 (mtm-85) cc_final: 0.8630 (mtm-85) REVERT: X 386 MET cc_start: 0.8740 (mmm) cc_final: 0.8478 (mmm) REVERT: Y 66 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: Y 310 TYR cc_start: 0.9175 (m-80) cc_final: 0.8830 (m-80) REVERT: Y 502 MET cc_start: 0.7743 (ptp) cc_final: 0.7353 (ptm) REVERT: Y 535 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7140 (mppt) REVERT: Z 193 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8449 (tt) REVERT: Z 195 GLU cc_start: 0.8193 (tp30) cc_final: 0.7822 (tp30) REVERT: Z 248 TYR cc_start: 0.8891 (m-80) cc_final: 0.8620 (m-80) REVERT: Z 310 TYR cc_start: 0.8284 (m-80) cc_final: 0.7795 (m-80) REVERT: Z 448 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7301 (mm-40) REVERT: Z 516 LYS cc_start: 0.3196 (OUTLIER) cc_final: 0.2449 (mmmm) outliers start: 99 outliers final: 74 residues processed: 555 average time/residue: 0.2053 time to fit residues: 184.5484 Evaluate side-chains 539 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 458 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 66 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 72 GLU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 121 ASN Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 154 SER Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 440 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 364 optimal weight: 1.9990 chunk 300 optimal weight: 0.0040 chunk 102 optimal weight: 5.9990 chunk 344 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN E 98 GLN P 65 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN T 134 ASN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 169 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN Y 278 GLN Z 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106700 restraints weight = 51210.493| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.64 r_work: 0.3136 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34384 Z= 0.158 Angle : 0.548 9.436 46598 Z= 0.284 Chirality : 0.044 0.292 5513 Planarity : 0.004 0.049 5991 Dihedral : 5.983 91.544 4916 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.25 % Rotamer: Outliers : 2.86 % Allowed : 18.87 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.29 (0.13), residues: 4457 helix: 0.56 (0.12), residues: 2187 sheet: -0.82 (0.22), residues: 561 loop : -0.83 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 479 TYR 0.013 0.001 TYR T 324 PHE 0.020 0.001 PHE P 77 TRP 0.005 0.001 TRP U 73 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00363 (34384) covalent geometry : angle 0.54843 (46598) hydrogen bonds : bond 0.03652 ( 1709) hydrogen bonds : angle 4.37664 ( 5004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 482 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8450 (t0) cc_final: 0.8147 (t0) REVERT: B 92 ASN cc_start: 0.8243 (t0) cc_final: 0.7631 (t0) REVERT: B 95 ILE cc_start: 0.8683 (tt) cc_final: 0.8274 (tt) REVERT: C 81 MET cc_start: 0.7314 (ttp) cc_final: 0.7016 (ttm) REVERT: C 118 LEU cc_start: 0.6912 (mt) cc_final: 0.6536 (pp) REVERT: D 81 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8239 (ttp) REVERT: D 122 PHE cc_start: 0.6013 (t80) cc_final: 0.5605 (t80) REVERT: F 116 PHE cc_start: 0.7006 (m-10) cc_final: 0.6761 (m-80) REVERT: G 109 LEU cc_start: 0.7425 (mt) cc_final: 0.7105 (mt) REVERT: G 113 ILE cc_start: 0.8103 (mp) cc_final: 0.7811 (mp) REVERT: H 97 LYS cc_start: 0.6469 (mmtt) cc_final: 0.5297 (mtpt) REVERT: I 118 LEU cc_start: 0.8558 (mt) cc_final: 0.8172 (mt) REVERT: J 78 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6929 (mt) REVERT: J 123 LEU cc_start: 0.7881 (tp) cc_final: 0.7433 (mt) REVERT: P 49 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8410 (t) REVERT: P 64 GLU cc_start: 0.8202 (mp0) cc_final: 0.7720 (mp0) REVERT: P 72 ASP cc_start: 0.7885 (t0) cc_final: 0.7642 (t0) REVERT: P 75 TYR cc_start: 0.8376 (m-10) cc_final: 0.8134 (m-10) REVERT: P 79 GLU cc_start: 0.8567 (tp30) cc_final: 0.8224 (tp30) REVERT: P 120 LYS cc_start: 0.8477 (mmpt) cc_final: 0.8247 (mmmt) REVERT: P 142 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8100 (mt-10) REVERT: Q 32 LYS cc_start: 0.6540 (mmmt) cc_final: 0.5987 (mmtm) REVERT: R 188 TYR cc_start: 0.6821 (m-10) cc_final: 0.6210 (m-10) REVERT: S 217 GLU cc_start: 0.7759 (tp30) cc_final: 0.7434 (tp30) REVERT: T 86 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8325 (mmt-90) REVERT: T 511 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7592 (ptpt) REVERT: T 537 LYS cc_start: 0.8787 (tmmt) cc_final: 0.8389 (ttpt) REVERT: U 282 MET cc_start: 0.9228 (mmt) cc_final: 0.8951 (mmt) REVERT: V 479 ARG cc_start: 0.7649 (mmt-90) cc_final: 0.7188 (mmt90) REVERT: V 547 ASP cc_start: 0.7162 (p0) cc_final: 0.6626 (t0) REVERT: V 551 LYS cc_start: 0.7469 (tppp) cc_final: 0.7098 (tttt) REVERT: X 90 MET cc_start: 0.9391 (mmt) cc_final: 0.8715 (mmt) REVERT: X 289 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8623 (mtm-85) REVERT: X 386 MET cc_start: 0.8728 (mmm) cc_final: 0.8470 (mmm) REVERT: Y 66 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: Y 428 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: Y 502 MET cc_start: 0.7667 (ptp) cc_final: 0.7318 (ptm) REVERT: Y 535 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7150 (mppt) REVERT: Z 193 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8458 (tt) REVERT: Z 195 GLU cc_start: 0.8183 (tp30) cc_final: 0.7828 (tp30) REVERT: Z 248 TYR cc_start: 0.8894 (m-80) cc_final: 0.8618 (m-80) REVERT: Z 310 TYR cc_start: 0.8295 (m-80) cc_final: 0.7807 (m-80) REVERT: Z 448 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7287 (mm-40) REVERT: Z 516 LYS cc_start: 0.3072 (OUTLIER) cc_final: 0.2336 (mmmm) REVERT: Z 536 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6330 (mm-30) outliers start: 102 outliers final: 76 residues processed: 549 average time/residue: 0.2048 time to fit residues: 182.6337 Evaluate side-chains 554 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 470 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 72 GLU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 154 SER Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 428 GLU Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 241 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 415 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 376 optimal weight: 0.8980 chunk 386 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 346 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN E 98 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN T 134 ASN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 169 GLN U 241 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN X 408 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107863 restraints weight = 51111.106| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.56 r_work: 0.3153 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34384 Z= 0.138 Angle : 0.538 10.240 46598 Z= 0.277 Chirality : 0.044 0.260 5513 Planarity : 0.004 0.050 5991 Dihedral : 5.887 88.506 4915 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.52 % Rotamer: Outliers : 2.70 % Allowed : 19.24 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.18 (0.13), residues: 4457 helix: 0.67 (0.12), residues: 2183 sheet: -0.76 (0.22), residues: 571 loop : -0.81 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 479 TYR 0.014 0.001 TYR T 414 PHE 0.027 0.001 PHE V 300 TRP 0.004 0.001 TRP U 73 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00315 (34384) covalent geometry : angle 0.53760 (46598) hydrogen bonds : bond 0.03539 ( 1709) hydrogen bonds : angle 4.32011 ( 5004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 484 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8425 (t0) cc_final: 0.8113 (t0) REVERT: B 60 LYS cc_start: 0.6847 (tptp) cc_final: 0.6637 (tppt) REVERT: B 92 ASN cc_start: 0.8216 (t0) cc_final: 0.7633 (t0) REVERT: B 95 ILE cc_start: 0.8695 (tt) cc_final: 0.8302 (tt) REVERT: C 66 CYS cc_start: 0.7822 (m) cc_final: 0.7466 (m) REVERT: C 118 LEU cc_start: 0.6922 (mt) cc_final: 0.6535 (pp) REVERT: D 81 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8147 (ttp) REVERT: D 122 PHE cc_start: 0.6053 (t80) cc_final: 0.5652 (t80) REVERT: E 91 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7540 (mpt180) REVERT: E 95 ILE cc_start: 0.7788 (pt) cc_final: 0.7310 (tp) REVERT: F 102 TYR cc_start: 0.8512 (m-10) cc_final: 0.8229 (m-10) REVERT: G 109 LEU cc_start: 0.7322 (mt) cc_final: 0.6999 (mt) REVERT: G 113 ILE cc_start: 0.8050 (mp) cc_final: 0.7784 (mp) REVERT: H 97 LYS cc_start: 0.6440 (mmtt) cc_final: 0.5274 (mtpt) REVERT: I 118 LEU cc_start: 0.8508 (mt) cc_final: 0.8123 (mt) REVERT: J 78 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7035 (mt) REVERT: J 105 LEU cc_start: 0.8220 (tp) cc_final: 0.7554 (mt) REVERT: J 123 LEU cc_start: 0.7896 (tp) cc_final: 0.7389 (mt) REVERT: P 49 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8387 (t) REVERT: P 64 GLU cc_start: 0.8180 (mp0) cc_final: 0.7767 (mp0) REVERT: P 72 ASP cc_start: 0.7884 (t0) cc_final: 0.7642 (t0) REVERT: P 75 TYR cc_start: 0.8375 (m-10) cc_final: 0.8024 (m-10) REVERT: P 79 GLU cc_start: 0.8527 (tp30) cc_final: 0.8200 (tp30) REVERT: P 120 LYS cc_start: 0.8450 (mmpt) cc_final: 0.8233 (mmmt) REVERT: P 142 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7991 (mm-30) REVERT: R 188 TYR cc_start: 0.6769 (m-10) cc_final: 0.6157 (m-10) REVERT: S 217 GLU cc_start: 0.7692 (tp30) cc_final: 0.7371 (tp30) REVERT: T 86 ARG cc_start: 0.9047 (mtm110) cc_final: 0.8315 (mmt-90) REVERT: T 96 ARG cc_start: 0.8738 (mtt-85) cc_final: 0.8465 (mmt90) REVERT: T 483 MET cc_start: 0.7625 (tpp) cc_final: 0.7400 (tpt) REVERT: T 511 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7592 (ptpt) REVERT: T 537 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8375 (ttpt) REVERT: U 282 MET cc_start: 0.9217 (mmt) cc_final: 0.8979 (mmt) REVERT: V 283 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8146 (ttp-170) REVERT: V 300 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8892 (t80) REVERT: V 479 ARG cc_start: 0.7608 (mmt-90) cc_final: 0.7175 (mmt90) REVERT: V 547 ASP cc_start: 0.7159 (p0) cc_final: 0.6626 (t0) REVERT: V 551 LYS cc_start: 0.7450 (tppp) cc_final: 0.7089 (tttt) REVERT: X 289 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8582 (mtm-85) REVERT: X 386 MET cc_start: 0.8677 (mmm) cc_final: 0.8445 (mmm) REVERT: Y 310 TYR cc_start: 0.9129 (m-80) cc_final: 0.8841 (m-80) REVERT: Y 502 MET cc_start: 0.7556 (ptp) cc_final: 0.7230 (ptm) REVERT: Y 535 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7157 (mppt) REVERT: Z 193 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8455 (tt) REVERT: Z 195 GLU cc_start: 0.8162 (tp30) cc_final: 0.7822 (tp30) REVERT: Z 248 TYR cc_start: 0.8872 (m-80) cc_final: 0.8610 (m-80) REVERT: Z 310 TYR cc_start: 0.8197 (m-80) cc_final: 0.7777 (m-80) REVERT: Z 448 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7318 (mm-40) REVERT: Z 516 LYS cc_start: 0.3124 (OUTLIER) cc_final: 0.2378 (mmmm) outliers start: 96 outliers final: 74 residues processed: 547 average time/residue: 0.2111 time to fit residues: 187.5286 Evaluate side-chains 541 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 460 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 72 GLU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 154 SER Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 332 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 249 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 384 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 418 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN E 94 ASN P 52 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN T 405 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN Y 278 GLN Z 414 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109622 restraints weight = 50913.445| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.62 r_work: 0.3168 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34384 Z= 0.111 Angle : 0.523 9.510 46598 Z= 0.268 Chirality : 0.043 0.232 5513 Planarity : 0.004 0.052 5991 Dihedral : 5.716 88.308 4915 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.23 % Favored : 96.63 % Rotamer: Outliers : 2.53 % Allowed : 19.60 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 4457 helix: 0.79 (0.12), residues: 2197 sheet: -0.66 (0.22), residues: 571 loop : -0.72 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 479 TYR 0.011 0.001 TYR T 414 PHE 0.025 0.001 PHE V 300 TRP 0.003 0.001 TRP U 73 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00247 (34384) covalent geometry : angle 0.52347 (46598) hydrogen bonds : bond 0.03328 ( 1709) hydrogen bonds : angle 4.21856 ( 5004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 498 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8412 (t0) cc_final: 0.8092 (t0) REVERT: B 92 ASN cc_start: 0.8184 (t0) cc_final: 0.7857 (t0) REVERT: C 66 CYS cc_start: 0.7688 (m) cc_final: 0.7366 (m) REVERT: C 118 LEU cc_start: 0.6856 (mt) cc_final: 0.6467 (pp) REVERT: D 61 MET cc_start: 0.7231 (mmm) cc_final: 0.6987 (mmm) REVERT: D 81 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8120 (ttp) REVERT: D 122 PHE cc_start: 0.6113 (t80) cc_final: 0.5694 (t80) REVERT: F 102 TYR cc_start: 0.8483 (m-10) cc_final: 0.8217 (m-10) REVERT: G 109 LEU cc_start: 0.7348 (mt) cc_final: 0.7116 (mt) REVERT: G 113 ILE cc_start: 0.7921 (mp) cc_final: 0.7670 (mp) REVERT: H 97 LYS cc_start: 0.6119 (mmtt) cc_final: 0.5083 (mtpt) REVERT: I 118 LEU cc_start: 0.8501 (mt) cc_final: 0.8115 (mt) REVERT: J 105 LEU cc_start: 0.8233 (tp) cc_final: 0.7609 (mt) REVERT: J 123 LEU cc_start: 0.7793 (tp) cc_final: 0.7404 (mt) REVERT: P 49 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8132 (t) REVERT: P 72 ASP cc_start: 0.7881 (t0) cc_final: 0.7613 (t0) REVERT: P 75 TYR cc_start: 0.8359 (m-10) cc_final: 0.8127 (m-10) REVERT: P 79 GLU cc_start: 0.8563 (tp30) cc_final: 0.8216 (tp30) REVERT: P 142 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8057 (mt-10) REVERT: R 188 TYR cc_start: 0.6752 (m-10) cc_final: 0.5926 (m-10) REVERT: T 86 ARG cc_start: 0.9022 (mtm110) cc_final: 0.8310 (mmt-90) REVERT: T 96 ARG cc_start: 0.8736 (mtt-85) cc_final: 0.8473 (mmt90) REVERT: T 483 MET cc_start: 0.7632 (tpp) cc_final: 0.7423 (tpt) REVERT: T 511 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7506 (ptpt) REVERT: T 537 LYS cc_start: 0.8739 (tmmt) cc_final: 0.8363 (ttpt) REVERT: V 283 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8134 (ttp-170) REVERT: V 300 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8827 (t80) REVERT: V 479 ARG cc_start: 0.7570 (mmt-90) cc_final: 0.7170 (mmt90) REVERT: V 547 ASP cc_start: 0.7104 (p0) cc_final: 0.6587 (t0) REVERT: V 551 LYS cc_start: 0.7473 (tppp) cc_final: 0.7055 (tttt) REVERT: X 289 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8543 (mtm-85) REVERT: X 386 MET cc_start: 0.8652 (mmm) cc_final: 0.8413 (mmm) REVERT: X 484 MET cc_start: 0.8233 (mmt) cc_final: 0.7787 (mmt) REVERT: Y 502 MET cc_start: 0.7462 (ptp) cc_final: 0.7152 (ptm) REVERT: Y 535 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7160 (mppt) REVERT: Z 193 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8454 (tt) REVERT: Z 195 GLU cc_start: 0.8085 (tp30) cc_final: 0.7788 (tp30) REVERT: Z 248 TYR cc_start: 0.8864 (m-80) cc_final: 0.8629 (m-10) REVERT: Z 310 TYR cc_start: 0.7923 (m-80) cc_final: 0.7536 (m-80) REVERT: Z 386 MET cc_start: 0.9026 (mmm) cc_final: 0.8699 (mmm) REVERT: Z 397 TYR cc_start: 0.8540 (t80) cc_final: 0.8258 (t80) REVERT: Z 422 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5981 (tpp) REVERT: Z 448 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7307 (mm-40) REVERT: Z 516 LYS cc_start: 0.2942 (OUTLIER) cc_final: 0.2611 (mmmm) REVERT: Z 536 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6242 (mm-30) outliers start: 90 outliers final: 68 residues processed: 553 average time/residue: 0.2092 time to fit residues: 188.3790 Evaluate side-chains 545 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 470 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 154 SER Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 146 optimal weight: 0.9980 chunk 399 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 144 optimal weight: 0.0270 chunk 151 optimal weight: 5.9990 chunk 413 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 434 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN E 98 GLN G 98 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN T 134 ASN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN Y 278 GLN Z 414 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108085 restraints weight = 51256.529| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.59 r_work: 0.3169 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34384 Z= 0.140 Angle : 0.549 12.263 46598 Z= 0.281 Chirality : 0.044 0.240 5513 Planarity : 0.004 0.061 5991 Dihedral : 5.696 88.114 4915 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 2.47 % Allowed : 20.02 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.01 (0.13), residues: 4457 helix: 0.81 (0.12), residues: 2190 sheet: -0.62 (0.22), residues: 571 loop : -0.70 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 513 TYR 0.018 0.001 TYR X 487 PHE 0.027 0.001 PHE V 300 TRP 0.004 0.001 TRP U 73 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00321 (34384) covalent geometry : angle 0.54852 (46598) hydrogen bonds : bond 0.03515 ( 1709) hydrogen bonds : angle 4.27090 ( 5004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 478 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7602 (tpp) cc_final: 0.7384 (ttm) REVERT: A 92 ASN cc_start: 0.8427 (t0) cc_final: 0.8091 (t0) REVERT: B 92 ASN cc_start: 0.8203 (t0) cc_final: 0.7655 (t0) REVERT: B 95 ILE cc_start: 0.8744 (tt) cc_final: 0.8378 (tt) REVERT: C 66 CYS cc_start: 0.7829 (m) cc_final: 0.7466 (m) REVERT: C 81 MET cc_start: 0.7285 (ttp) cc_final: 0.6918 (ttm) REVERT: C 118 LEU cc_start: 0.6855 (mt) cc_final: 0.6473 (pp) REVERT: D 61 MET cc_start: 0.6804 (mmm) cc_final: 0.6541 (mmm) REVERT: D 81 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8116 (ttp) REVERT: D 92 ASN cc_start: 0.8450 (t0) cc_final: 0.8233 (t0) REVERT: D 122 PHE cc_start: 0.6107 (t80) cc_final: 0.5673 (t80) REVERT: E 91 ARG cc_start: 0.7799 (mmt-90) cc_final: 0.7556 (mpt180) REVERT: E 95 ILE cc_start: 0.7805 (pt) cc_final: 0.7209 (tp) REVERT: E 116 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6437 (m-10) REVERT: F 102 TYR cc_start: 0.8450 (m-10) cc_final: 0.8196 (m-10) REVERT: G 109 LEU cc_start: 0.7335 (mt) cc_final: 0.7134 (mt) REVERT: H 97 LYS cc_start: 0.6240 (mmtt) cc_final: 0.5075 (mtpt) REVERT: I 118 LEU cc_start: 0.8503 (mt) cc_final: 0.8121 (mt) REVERT: J 78 LEU cc_start: 0.7651 (mt) cc_final: 0.7448 (mt) REVERT: J 105 LEU cc_start: 0.8226 (tp) cc_final: 0.7541 (mt) REVERT: J 123 LEU cc_start: 0.7759 (tp) cc_final: 0.7342 (mt) REVERT: P 64 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7902 (mp0) REVERT: P 72 ASP cc_start: 0.7875 (t0) cc_final: 0.7633 (t0) REVERT: P 75 TYR cc_start: 0.8343 (m-10) cc_final: 0.7940 (m-10) REVERT: P 79 GLU cc_start: 0.8533 (tp30) cc_final: 0.8213 (tp30) REVERT: P 142 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7992 (mm-30) REVERT: R 188 TYR cc_start: 0.6727 (m-10) cc_final: 0.5930 (m-10) REVERT: T 86 ARG cc_start: 0.9050 (mtm110) cc_final: 0.8343 (mmt-90) REVERT: T 96 ARG cc_start: 0.8742 (mtt-85) cc_final: 0.8484 (mmt90) REVERT: T 483 MET cc_start: 0.7517 (tpp) cc_final: 0.7288 (tpt) REVERT: T 511 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7516 (ptpt) REVERT: T 537 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8379 (ttpt) REVERT: V 300 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8856 (t80) REVERT: V 479 ARG cc_start: 0.7619 (mmt-90) cc_final: 0.7218 (mmt90) REVERT: V 547 ASP cc_start: 0.7189 (p0) cc_final: 0.6515 (t0) REVERT: V 551 LYS cc_start: 0.7578 (tppp) cc_final: 0.7230 (tppt) REVERT: X 289 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8495 (mtm-85) REVERT: X 386 MET cc_start: 0.8647 (mmm) cc_final: 0.8431 (mmm) REVERT: Y 502 MET cc_start: 0.7450 (ptp) cc_final: 0.7176 (ptm) REVERT: Y 535 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7178 (mppt) REVERT: Z 193 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8476 (tt) REVERT: Z 195 GLU cc_start: 0.8109 (tp30) cc_final: 0.7779 (tp30) REVERT: Z 248 TYR cc_start: 0.8852 (m-80) cc_final: 0.8608 (m-10) REVERT: Z 310 TYR cc_start: 0.8012 (m-80) cc_final: 0.7614 (m-80) REVERT: Z 422 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5944 (tpp) REVERT: Z 448 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7307 (mm-40) REVERT: Z 516 LYS cc_start: 0.2989 (OUTLIER) cc_final: 0.2652 (mmmm) REVERT: Z 536 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6245 (mm-30) outliers start: 88 outliers final: 70 residues processed: 529 average time/residue: 0.2085 time to fit residues: 179.0997 Evaluate side-chains 543 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 466 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 154 SER Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 467 ILE Chi-restraints excluded: chain Z residue 516 LYS Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.7980 chunk 323 optimal weight: 0.7980 chunk 384 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 410 optimal weight: 0.2980 chunk 114 optimal weight: 8.9990 chunk 330 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 396 optimal weight: 0.0670 chunk 407 optimal weight: 1.9990 chunk 387 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN P 65 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110591 restraints weight = 51088.036| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.60 r_work: 0.3202 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34384 Z= 0.108 Angle : 0.532 13.956 46598 Z= 0.271 Chirality : 0.043 0.215 5513 Planarity : 0.004 0.065 5991 Dihedral : 5.528 88.205 4915 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 2.30 % Allowed : 20.25 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.17 (0.13), residues: 4457 helix: 0.92 (0.12), residues: 2203 sheet: -0.49 (0.22), residues: 558 loop : -0.62 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 513 TYR 0.010 0.001 TYR I 102 PHE 0.026 0.001 PHE V 300 TRP 0.002 0.001 TRP U 73 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd covalent geometry : bond 0.00237 (34384) covalent geometry : angle 0.53157 (46598) hydrogen bonds : bond 0.03249 ( 1709) hydrogen bonds : angle 4.18014 ( 5004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9456.24 seconds wall clock time: 162 minutes 9.16 seconds (9729.16 seconds total)