Starting phenix.real_space_refine on Thu Oct 29 18:45:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.cif Found real_map, /net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.map" model { file = "/net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6re1_4838/10_2026/6re1_4838.cif" } resolution = 3.2 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 278 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/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: 7.65, per 1000 atoms: 0.23 Number of scatterers: 33863 At special positions: 0 Unit cell: (165.321, 127.413, 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: 3.35 Conformation dependent library (CDL) restraints added in 1.9 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: 178 helices and 31 sheets defined 51.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.513A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.798A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.995A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.916A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 4.138A 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 111 through 126 Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.331A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.695A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.037A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.041A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.917A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.733A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 3.697A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 3.835A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 98 through 127 removed outlier: 4.286A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.998A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 91 removed outlier: 3.850A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.652A pdb=" N ILE F 95 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' Processing helix chain 'F' and resid 97 through 126 removed outlier: 3.769A pdb=" N LEU F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 removed outlier: 3.970A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 90 removed outlier: 4.386A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 3.528A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.918A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 90 removed outlier: 4.087A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.866A 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: 4.026A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 126 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 4.348A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.038A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.088A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.113A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 92 removed outlier: 4.053A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 127 removed outlier: 3.787A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 62 Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.564A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.980A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 127 removed outlier: 3.733A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 134 removed outlier: 4.472A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 149 removed outlier: 4.014A pdb=" N ALA P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS P 148 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 42 removed outlier: 3.622A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 39 removed outlier: 4.444A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 161 through 170 removed outlier: 3.958A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 3.508A pdb=" N LEU R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 79 removed outlier: 3.836A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 Processing helix chain 'S' and resid 117 through 130 removed outlier: 3.507A pdb=" N LEU S 127 " --> pdb=" O THR S 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 3.616A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 removed outlier: 3.561A pdb=" N ALA S 175 " --> pdb=" O THR S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 222 removed outlier: 3.980A pdb=" N ASP S 222 " --> pdb=" O GLN S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.759A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.641A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.525A pdb=" N VAL T 234 " --> pdb=" O GLY T 230 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.175A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR T 316 " --> pdb=" O TYR T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 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: 3.690A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 431 through 435 removed outlier: 4.107A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 460 removed outlier: 3.561A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU T 446 " --> pdb=" O VAL T 442 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.790A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.572A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 528 removed outlier: 4.519A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 4.175A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 545 through 556 removed outlier: 4.120A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 49 removed outlier: 3.538A pdb=" N LEU U 48 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 72 removed outlier: 4.427A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.771A 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: 3.905A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.937A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 284 removed outlier: 3.723A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.870A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 346 through 350 removed outlier: 3.579A pdb=" N PHE U 350 " --> pdb=" O ARG U 347 " (cutoff:3.500A) 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: 3.680A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 removed outlier: 3.542A pdb=" N GLY U 373 " --> pdb=" O LYS U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 415 removed outlier: 3.591A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 458 removed outlier: 4.288A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 467 through 484 removed outlier: 3.853A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 496 Processing helix chain 'U' and resid 497 through 506 Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.914A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.514A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.601A 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 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.926A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (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: 3.955A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.583A pdb=" N THR V 159 " --> pdb=" O GLY V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 211 Processing helix chain 'V' and resid 230 through 246 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 284 removed outlier: 3.847A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.616A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.173A 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: 3.680A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.617A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.615A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 439 through 457 removed outlier: 3.861A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 484 removed outlier: 3.574A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.805A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS V 506 " --> pdb=" O TYR V 502 " (cutoff:3.500A) Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.989A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 540 removed outlier: 3.784A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 548 removed outlier: 4.087A pdb=" N ALA V 548 " --> pdb=" O PRO V 544 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 553 removed outlier: 3.764A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.143A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.756A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 300 Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.605A 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 393 through 420 removed outlier: 3.620A pdb=" N LEU X 413 " --> pdb=" O ASP X 409 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU X 420 " --> pdb=" O ILE X 416 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.697A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 475 Processing helix chain 'X' and resid 482 through 486 Processing helix chain 'X' and resid 491 through 503 removed outlier: 4.033A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 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 235 through 242 removed outlier: 4.232A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.110A 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: 3.570A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 299 removed outlier: 3.815A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 342 through 345 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.668A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) 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 371 removed outlier: 3.613A pdb=" N ALA Y 369 " --> pdb=" O SER Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 393 through 412 removed outlier: 3.928A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 421 Processing helix chain 'Y' and resid 422 through 425 removed outlier: 3.709A pdb=" N LEU Y 425 " --> pdb=" O MET Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 422 through 425' Processing helix chain 'Y' and resid 426 through 443 removed outlier: 3.535A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU Y 443 " --> pdb=" O ILE Y 439 " (cutoff:3.500A) Processing helix chain 'Y' and resid 450 through 455 Processing helix chain 'Y' and resid 462 through 476 Processing helix chain 'Y' and resid 482 through 486 removed outlier: 3.606A pdb=" N ALA Y 485 " --> pdb=" O PRO Y 482 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 505 removed outlier: 3.786A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 511 through 515 removed outlier: 4.663A pdb=" N ASN Y 514 " --> pdb=" O GLU Y 511 " (cutoff:3.500A) removed outlier: 4.226A 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 Processing helix chain 'Y' and resid 541 through 543 No H-bonds generated for 'chain 'Y' and resid 541 through 543' Processing helix chain 'Y' and resid 544 through 550 removed outlier: 3.783A pdb=" N ASP Y 548 " --> pdb=" O GLY Y 544 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 170 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: 3.730A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.633A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.793A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 4.348A 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: 4.201A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.589A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 418 removed outlier: 4.654A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.581A pdb=" N VAL Z 433 " --> pdb=" O ASP Z 429 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.687A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 506 removed outlier: 3.672A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 534 removed outlier: 4.011A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.600A pdb=" N GLN Q 49 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN S 159 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA S 163 " --> pdb=" O SER S 141 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N PHE S 197 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'R' and resid 80 through 82 removed outlier: 7.801A pdb=" N ILE R 144 " --> pdb=" O PRO R 71 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN R 73 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 99 through 100 removed outlier: 4.176A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.572A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.863A 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 86 through 91 removed outlier: 6.572A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.863A 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: 4.455A pdb=" N SER Y 61 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (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 removed outlier: 6.600A pdb=" N GLY T 320 " --> pdb=" O THR T 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 201 through 202 removed outlier: 4.237A pdb=" N ILE T 215 " --> pdb=" O LEU T 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 382 through 384 removed outlier: 7.095A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 116 through 122 removed outlier: 3.909A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL U 87 " --> pdb=" O TYR U 98 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N TYR U 98 " --> pdb=" O VAL U 87 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB4, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.692A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR U 256 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE U 323 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL U 258 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP U 325 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL U 260 " --> pdb=" O ASP U 325 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR U 378 " --> pdb=" O GLY U 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 201 through 202 removed outlier: 4.441A pdb=" N ILE U 215 " --> pdb=" O LEU U 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 223 through 225 Processing sheet with id=AB7, first strand: chain 'V' and resid 84 through 91 removed outlier: 6.587A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR V 147 " --> pdb=" O LEU V 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB9, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.483A pdb=" N THR V 164 " --> pdb=" O SER V 289 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR V 256 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE V 323 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL V 258 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP V 325 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL V 260 " --> pdb=" O ASP V 325 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 201 through 202 removed outlier: 4.452A pdb=" N ILE V 215 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 382 through 384 removed outlier: 7.935A pdb=" N ILE V 383 " --> pdb=" O GLU V 221 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE V 223 " --> pdb=" O ILE V 383 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.552A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.080A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLN X 250 " --> pdb=" O MET X 122 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL X 280 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL X 336 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU X 282 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA X 338 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL X 284 " --> pdb=" O ALA X 338 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC6, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id=AC7, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.212A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE Y 207 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS Y 178 " --> pdb=" O ALA Y 360 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR Y 362 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY Y 180 " --> pdb=" O THR Y 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.326A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.536A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.593A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.357A pdb=" N MET Z 122 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR Z 340 " --> pdb=" O VAL Z 284 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL Z 339 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU Z 181 " --> pdb=" O VAL Z 339 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY Z 180 " --> pdb=" O THR Z 362 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 159 through 160 removed outlier: 3.956A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 559 through 561 1665 hydrogen bonds defined for protein. 4800 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: 7.47 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10562 1.34 - 1.46: 5559 1.46 - 1.57: 18042 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.46e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.44e+01 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 5.26e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.22e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.63e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 46264 4.09 - 8.18: 297 8.18 - 12.27: 31 12.27 - 16.36: 2 16.36 - 20.45: 4 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 139.87 119.42 20.45 1.00e+00 1.00e+00 4.18e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.65 19.22 1.00e+00 1.00e+00 3.69e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 121.46 18.41 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 120.06 16.77 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.63 13.20 1.00e+00 1.00e+00 1.74e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 20241 35.22 - 70.44: 428 70.44 - 105.66: 39 105.66 - 140.89: 1 140.89 - 176.11: 1 Dihedral angle restraints: 20710 sinusoidal: 7967 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 -127.71 -52.29 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -144.46 -35.54 0 5.00e+00 4.00e-02 5.05e+01 ... (remaining 20707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4484 0.076 - 0.151: 942 0.151 - 0.227: 72 0.227 - 0.303: 14 0.303 - 0.379: 1 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 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB VAL V 209 " pdb=" CA VAL V 209 " pdb=" CG1 VAL V 209 " pdb=" CG2 VAL V 209 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 5510 not shown) Planarity restraints: 5991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.032 2.00e-02 2.50e+03 6.24e-02 3.89e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.12e-02 3.74e+01 pdb=" C ALA Y 503 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA T 296 " -0.053 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO T 297 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO T 297 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO T 297 " -0.045 5.00e-02 4.00e+02 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 261 2.52 - 3.11: 23810 3.11 - 3.71: 54020 3.71 - 4.30: 79823 4.30 - 4.90: 132098 Nonbonded interactions: 290012 Sorted by model distance: nonbonded pdb=" CZ PHE G 107 " pdb=" OE1 GLU G 111 " model vdw 1.921 3.340 nonbonded pdb=" O ALA X 499 " pdb=" CB ALA X 503 " model vdw 2.003 2.768 nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.237 2.170 nonbonded pdb=" OG1 THR Z 190 " pdb="MG MG Z 602 " model vdw 2.240 2.170 nonbonded pdb=" OH TYR U 259 " pdb=" OD2 ASP U 325 " model vdw 2.255 3.040 ... (remaining 290007 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: 12.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.780 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.009 0.093 34384 Z= 0.400 Angle : 1.000 20.447 46598 Z= 0.576 Chirality : 0.059 0.379 5513 Planarity : 0.007 0.079 5991 Dihedral : 15.159 176.107 12560 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.27 % Favored : 94.48 % Rotamer: Outliers : 0.45 % Allowed : 10.22 % Favored : 89.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.10), residues: 4457 helix: -3.11 (0.08), residues: 2129 sheet: -1.87 (0.20), residues: 531 loop : -2.33 (0.12), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 454 TYR 0.027 0.003 TYR V 393 PHE 0.028 0.003 PHE S 249 TRP 0.020 0.003 TRP Y 141 HIS 0.014 0.002 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.40 (34384) covalent geometry : angle 1.00029 / 0.58 (46598) hydrogen bonds : bond 0.17549 / 11.46 ( 1654) hydrogen bonds : angle 8.02201 / 5.53 ( 4800) *********************** 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 583 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 567 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.1913 (tt) cc_final: 0.1708 (mp) REVERT: J 119 LEU cc_start: 0.5770 (tt) cc_final: 0.5339 (pp) REVERT: P 39 LEU cc_start: 0.8034 (mp) cc_final: 0.7791 (mt) REVERT: R 111 LEU cc_start: 0.7224 (mp) cc_final: 0.7010 (mp) REVERT: S 234 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6406 (tm-30) REVERT: T 282 MET cc_start: 0.8534 (tpp) cc_final: 0.8154 (tpt) REVERT: T 325 ASP cc_start: 0.8197 (t70) cc_final: 0.7852 (t0) REVERT: T 558 LYS cc_start: 0.7859 (mppt) cc_final: 0.7612 (mmmm) REVERT: V 61 HIS cc_start: 0.7422 (t70) cc_final: 0.7094 (t-90) REVERT: V 112 ASP cc_start: 0.8265 (p0) cc_final: 0.8012 (p0) REVERT: V 325 ASP cc_start: 0.8133 (t0) cc_final: 0.7860 (t0) REVERT: V 506 LYS cc_start: 0.6958 (mmtm) cc_final: 0.6491 (mmmt) REVERT: X 488 MET cc_start: 0.7718 (mmt) cc_final: 0.7325 (mmm) REVERT: Y 195 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6390 (tm-30) REVERT: Y 317 ASP cc_start: 0.8003 (m-30) cc_final: 0.7752 (m-30) REVERT: Z 90 MET cc_start: 0.8663 (mmt) cc_final: 0.8433 (mmt) REVERT: Z 195 GLU cc_start: 0.6991 (tp30) cc_final: 0.6638 (tp30) REVERT: Z 385 ARG cc_start: 0.7207 (mmt180) cc_final: 0.7006 (mpt-90) REVERT: Z 448 GLN cc_start: 0.6405 (tm-30) cc_final: 0.5893 (mt0) REVERT: Z 488 MET cc_start: 0.7789 (mmt) cc_final: 0.7580 (mmt) outliers start: 16 outliers final: 5 residues processed: 580 average time/residue: 0.2353 time to fit residues: 213.8959 Evaluate side-chains 408 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 403 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain Z residue 314 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 ASN B 98 GLN D 92 ASN I 94 ASN P 66 GLN P 71 GLN Q 46 HIS R 66 HIS R 104 HIS R 137 HIS R 181 ASN S 186 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS T 104 GLN T 134 ASN T 152 ASN T 241 HIS T 358 HIS T 386 GLN T 452 GLN U 104 GLN U 140 GLN U 196 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 264 GLN U 319 HIS U 441 GLN V 123 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 242 GLN V 244 ASN V 264 GLN V 278 GLN V 386 GLN V 486 GLN V 497 GLN X 174 GLN X 199 ASN X 322 GLN X 337 GLN X 414 GLN Y 199 ASN Y 278 GLN Y 412 ASN Z 174 GLN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.162603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128332 restraints weight = 50649.577| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.91 r_work: 0.3303 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1675 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= 0.148 Angle : 0.601 9.773 46598 Z= 0.312 Chirality : 0.044 0.178 5513 Planarity : 0.005 0.059 5991 Dihedral : 6.592 172.690 4828 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.43 % Favored : 96.37 % Rotamer: Outliers : 1.74 % Allowed : 13.93 % Favored : 84.33 % 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: -2.47 (0.12), residues: 4457 helix: -1.40 (0.10), residues: 2150 sheet: -1.49 (0.21), residues: 579 loop : -1.77 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 437 TYR 0.024 0.001 TYR P 75 PHE 0.026 0.001 PHE A 107 TRP 0.007 0.001 TRP Y 141 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (34384) covalent geometry : angle 0.60124 / 0.31 (46598) hydrogen bonds : bond 0.04037 / 2.71 ( 1654) hydrogen bonds : angle 5.29503 / 3.65 ( 4800) *********************** 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 562 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 500 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5355 (tpp) cc_final: 0.5149 (tpt) REVERT: B 82 PHE cc_start: 0.5652 (m-10) cc_final: 0.5133 (m-10) REVERT: C 105 LEU cc_start: 0.1205 (tt) cc_final: 0.0986 (mp) REVERT: D 61 MET cc_start: 0.6492 (mpp) cc_final: 0.5617 (mpp) REVERT: H 61 MET cc_start: 0.4721 (mmt) cc_final: 0.3780 (mtt) REVERT: I 61 MET cc_start: 0.4950 (mtm) cc_final: 0.4478 (ttm) REVERT: J 123 LEU cc_start: 0.1344 (tp) cc_final: 0.0914 (mt) REVERT: J 124 ILE cc_start: 0.5076 (mt) cc_final: 0.4625 (mt) REVERT: P 39 LEU cc_start: 0.8138 (mp) cc_final: 0.7756 (mt) REVERT: R 86 LYS cc_start: 0.6067 (mmtm) cc_final: 0.5559 (mmtm) REVERT: S 127 LEU cc_start: 0.6483 (mp) cc_final: 0.6269 (mm) REVERT: S 234 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6610 (tm-30) REVERT: T 227 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7955 (ttp-110) REVERT: T 282 MET cc_start: 0.8660 (tpp) cc_final: 0.8025 (tpt) REVERT: T 390 VAL cc_start: 0.9124 (p) cc_final: 0.8899 (t) REVERT: T 407 PHE cc_start: 0.8044 (t80) cc_final: 0.7834 (t80) REVERT: T 558 LYS cc_start: 0.8095 (mppt) cc_final: 0.7646 (mmmm) REVERT: U 220 ARG cc_start: 0.8801 (mpp80) cc_final: 0.8457 (mtm110) REVERT: U 282 MET cc_start: 0.9142 (mmt) cc_final: 0.8727 (mmt) REVERT: V 61 HIS cc_start: 0.8086 (t70) cc_final: 0.7602 (t-90) REVERT: V 112 ASP cc_start: 0.8336 (p0) cc_final: 0.7958 (p0) REVERT: V 282 MET cc_start: 0.8741 (tpt) cc_final: 0.8491 (tpt) REVERT: V 445 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7184 (t) REVERT: V 506 LYS cc_start: 0.7130 (mmtm) cc_final: 0.6660 (mmmt) REVERT: X 337 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8339 (mt0) REVERT: X 488 MET cc_start: 0.8419 (mmt) cc_final: 0.7911 (ttp) REVERT: X 541 GLU cc_start: 0.4606 (OUTLIER) cc_final: 0.4056 (tp30) REVERT: Y 168 ASP cc_start: 0.8315 (m-30) cc_final: 0.8108 (m-30) REVERT: Y 195 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7326 (tm-30) REVERT: Y 199 ASN cc_start: 0.8809 (m-40) cc_final: 0.8146 (m110) REVERT: Y 317 ASP cc_start: 0.8303 (m-30) cc_final: 0.8094 (m-30) REVERT: Y 547 GLU cc_start: 0.7968 (mp0) cc_final: 0.7746 (mt-10) REVERT: Z 149 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7507 (mm-30) REVERT: Z 448 GLN cc_start: 0.6689 (tm-30) cc_final: 0.5917 (mt0) REVERT: Z 572 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6948 (tmmt) outliers start: 62 outliers final: 37 residues processed: 542 average time/residue: 0.2159 time to fit residues: 190.3872 Evaluate side-chains 460 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 420 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 337 GLN Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [328, 388, 269, 435, 294, 130, 253, 145, 310, 262, 193] chunk 328 optimal weight: 0.4980 chunk 388 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 145 optimal weight: 0.0170 chunk 310 optimal weight: 0.0970 chunk 262 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 83 GLN Q 21 ASN R 73 ASN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN T 134 ASN T 452 GLN T 461 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 61 HIS ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS X 286 ASN X 322 GLN Y 292 GLN Z 83 ASN Z 408 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.164719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130372 restraints weight = 50594.200| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.77 r_work: 0.3349 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34384 Z= 0.109 Angle : 0.543 9.389 46598 Z= 0.280 Chirality : 0.042 0.177 5513 Planarity : 0.004 0.049 5991 Dihedral : 6.117 176.795 4824 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 2.05 % Allowed : 15.89 % Favored : 82.06 % 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: -1.61 (0.12), residues: 4457 helix: -0.57 (0.11), residues: 2160 sheet: -1.25 (0.21), residues: 574 loop : -1.47 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 496 TYR 0.022 0.001 TYR S 158 PHE 0.022 0.001 PHE C 107 TRP 0.006 0.001 TRP U 73 HIS 0.009 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (34384) covalent geometry : angle 0.54283 / 0.28 (46598) hydrogen bonds : bond 0.03463 / 2.33 ( 1654) hydrogen bonds : angle 4.74637 / 3.27 ( 4800) *********************** 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 552 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 479 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.6490 (ppp) cc_final: 0.6287 (ppp) REVERT: B 82 PHE cc_start: 0.4638 (OUTLIER) cc_final: 0.4391 (m-10) REVERT: H 61 MET cc_start: 0.4689 (mmt) cc_final: 0.3929 (mtt) REVERT: I 61 MET cc_start: 0.4660 (mtm) cc_final: 0.4321 (ttm) REVERT: J 95 ILE cc_start: 0.2037 (OUTLIER) cc_final: 0.1474 (tp) REVERT: J 119 LEU cc_start: 0.5730 (tt) cc_final: 0.5152 (pp) REVERT: J 123 LEU cc_start: 0.1147 (tp) cc_final: 0.0786 (mt) REVERT: J 124 ILE cc_start: 0.4667 (mt) cc_final: 0.3978 (mt) REVERT: P 63 LYS cc_start: 0.8585 (tptt) cc_final: 0.8239 (ttmm) REVERT: P 71 GLN cc_start: 0.7541 (tt0) cc_final: 0.7324 (tt0) REVERT: Q 49 GLN cc_start: 0.6003 (pt0) cc_final: 0.5728 (pt0) REVERT: R 119 HIS cc_start: 0.5760 (m-70) cc_final: 0.5011 (m90) REVERT: R 137 HIS cc_start: 0.3620 (m90) cc_final: 0.2963 (m-70) REVERT: S 185 HIS cc_start: 0.5129 (m90) cc_final: 0.4662 (m90) REVERT: S 219 GLN cc_start: 0.6210 (mp10) cc_final: 0.5242 (tp-100) REVERT: S 234 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6548 (tm-30) REVERT: T 325 ASP cc_start: 0.8661 (t0) cc_final: 0.8451 (t0) REVERT: T 467 ASP cc_start: 0.8204 (t70) cc_final: 0.7775 (t0) REVERT: T 481 THR cc_start: 0.8749 (m) cc_final: 0.8502 (p) REVERT: T 558 LYS cc_start: 0.8031 (mppt) cc_final: 0.7617 (mmmm) REVERT: U 283 ARG cc_start: 0.7799 (mtp180) cc_final: 0.7523 (ttp-110) REVERT: U 439 MET cc_start: 0.8922 (tpp) cc_final: 0.8586 (tpt) REVERT: V 445 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7312 (t) REVERT: V 506 LYS cc_start: 0.7082 (mmtm) cc_final: 0.6749 (mmmt) REVERT: X 381 ASP cc_start: 0.8158 (m-30) cc_final: 0.7848 (t0) REVERT: X 488 MET cc_start: 0.8406 (mmt) cc_final: 0.7924 (ttp) REVERT: Y 195 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7325 (tm-30) REVERT: Y 199 ASN cc_start: 0.8535 (m-40) cc_final: 0.7946 (m110) REVERT: Y 317 ASP cc_start: 0.8217 (m-30) cc_final: 0.8008 (m-30) REVERT: Y 538 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7248 (t) REVERT: Y 547 GLU cc_start: 0.7998 (mp0) cc_final: 0.7791 (mt-10) REVERT: Z 387 LEU cc_start: 0.8707 (tp) cc_final: 0.8495 (tp) REVERT: Z 429 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.6057 (t70) REVERT: Z 448 GLN cc_start: 0.6689 (tm-30) cc_final: 0.5903 (mt0) outliers start: 73 outliers final: 38 residues processed: 532 average time/residue: 0.2082 time to fit residues: 180.3717 Evaluate side-chains 441 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 398 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 182 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 551 LYS Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [96, 148, 414, 255, 21, 312, 310, 387, 273, 217, 184] chunk 96 optimal weight: 10.0000 chunk 148 optimal weight: 0.5980 chunk 414 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 312 optimal weight: 1.9990 chunk 310 optimal weight: 0.0470 chunk 387 optimal weight: 0.9990 chunk 273 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN R 73 ASN ** R 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 405 GLN T 452 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN X 286 ASN X 322 GLN X 337 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126969 restraints weight = 50509.681| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.85 r_work: 0.3312 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34384 Z= 0.152 Angle : 0.575 9.675 46598 Z= 0.295 Chirality : 0.044 0.179 5513 Planarity : 0.004 0.047 5991 Dihedral : 6.014 174.695 4824 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 2.92 % Allowed : 16.68 % Favored : 80.40 % 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 (0.13), residues: 4457 helix: -0.24 (0.11), residues: 2178 sheet: -1.30 (0.21), residues: 586 loop : -1.20 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 496 TYR 0.022 0.002 TYR Z 397 PHE 0.025 0.001 PHE P 122 TRP 0.009 0.001 TRP U 73 HIS 0.006 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (34384) covalent geometry : angle 0.57513 / 0.30 (46598) hydrogen bonds : bond 0.03610 / 2.43 ( 1654) hydrogen bonds : angle 4.62738 / 3.19 ( 4800) *********************** 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 528 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 424 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.6803 (ppp) cc_final: 0.6598 (ppp) REVERT: B 118 LEU cc_start: 0.4732 (OUTLIER) cc_final: 0.4404 (mt) REVERT: D 69 ILE cc_start: 0.7008 (tp) cc_final: 0.6696 (tp) REVERT: D 81 MET cc_start: 0.6088 (tmm) cc_final: 0.5713 (tmm) REVERT: G 61 MET cc_start: 0.5706 (tpp) cc_final: 0.5333 (tpp) REVERT: J 95 ILE cc_start: 0.2146 (OUTLIER) cc_final: 0.1345 (tp) REVERT: J 124 ILE cc_start: 0.4672 (mt) cc_final: 0.4466 (mt) REVERT: P 39 LEU cc_start: 0.7810 (mp) cc_final: 0.7589 (mt) REVERT: P 63 LYS cc_start: 0.8625 (tptt) cc_final: 0.8174 (ttmm) REVERT: Q 45 ILE cc_start: 0.6309 (mp) cc_final: 0.6057 (mp) REVERT: R 119 HIS cc_start: 0.5722 (m-70) cc_final: 0.4815 (m90) REVERT: S 158 TYR cc_start: 0.3664 (t80) cc_final: 0.3219 (t80) REVERT: S 216 LEU cc_start: 0.5391 (tp) cc_final: 0.4750 (tp) REVERT: S 219 GLN cc_start: 0.6362 (mp10) cc_final: 0.5479 (tp-100) REVERT: S 234 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6581 (tm-30) REVERT: T 325 ASP cc_start: 0.8582 (t0) cc_final: 0.8319 (t0) REVERT: T 537 LYS cc_start: 0.8124 (tptt) cc_final: 0.7697 (tppt) REVERT: T 558 LYS cc_start: 0.8067 (mppt) cc_final: 0.7656 (mmmm) REVERT: U 70 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7114 (t) REVERT: U 220 ARG cc_start: 0.8855 (mpp80) cc_final: 0.8543 (mtm110) REVERT: U 282 MET cc_start: 0.9216 (mmt) cc_final: 0.8826 (mmt) REVERT: U 283 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7583 (ttp-110) REVERT: U 439 MET cc_start: 0.8925 (tpp) cc_final: 0.8585 (tpt) REVERT: V 50 LYS cc_start: 0.8045 (tptp) cc_final: 0.7733 (tmmt) REVERT: V 445 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7364 (t) REVERT: V 506 LYS cc_start: 0.7069 (mmtm) cc_final: 0.6732 (mmmt) REVERT: V 550 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6830 (mt) REVERT: X 381 ASP cc_start: 0.8247 (m-30) cc_final: 0.7906 (t0) REVERT: X 488 MET cc_start: 0.8400 (mmt) cc_final: 0.7927 (ttp) REVERT: X 541 GLU cc_start: 0.4682 (OUTLIER) cc_final: 0.4105 (tp30) REVERT: Y 195 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7338 (tm-30) REVERT: Y 199 ASN cc_start: 0.8554 (m-40) cc_final: 0.7859 (m110) REVERT: Y 538 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.7104 (t) REVERT: Y 547 GLU cc_start: 0.8153 (mp0) cc_final: 0.7809 (mt-10) REVERT: Z 345 ASP cc_start: 0.8291 (t0) cc_final: 0.7995 (t0) REVERT: Z 429 ASP cc_start: 0.6284 (OUTLIER) cc_final: 0.5944 (t70) REVERT: Z 448 GLN cc_start: 0.6584 (tm-30) cc_final: 0.5848 (mt0) outliers start: 104 outliers final: 63 residues processed: 502 average time/residue: 0.2066 time to fit residues: 170.9017 Evaluate side-chains 469 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 398 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 182 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 506 ILE Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 533 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [3, 137, 125, 288, 260, 124, 266, 85, 221, 428, 40] chunk 3 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 260 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 428 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 ASN J 98 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN U 539 ASN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN Z 278 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124954 restraints weight = 50974.042| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.84 r_work: 0.3283 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34384 Z= 0.194 Angle : 0.608 9.092 46598 Z= 0.311 Chirality : 0.045 0.267 5513 Planarity : 0.004 0.043 5991 Dihedral : 6.034 164.983 4824 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 3.26 % Allowed : 17.41 % Favored : 79.33 % 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: -1.12 (0.13), residues: 4457 helix: -0.17 (0.11), residues: 2184 sheet: -1.38 (0.21), residues: 590 loop : -1.06 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 496 TYR 0.028 0.002 TYR Z 248 PHE 0.040 0.002 PHE J 126 TRP 0.014 0.001 TRP U 73 HIS 0.007 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (34384) covalent geometry : angle 0.60780 / 0.31 (46598) hydrogen bonds : bond 0.03807 / 2.55 ( 1654) hydrogen bonds : angle 4.70166 / 3.24 ( 4800) *********************** 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 537 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 421 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5443 (mmm) cc_final: 0.4972 (tpt) REVERT: B 81 MET cc_start: 0.7097 (ppp) cc_final: 0.6876 (ppp) REVERT: B 105 LEU cc_start: 0.3311 (tt) cc_final: 0.2664 (mp) REVERT: B 118 LEU cc_start: 0.4679 (OUTLIER) cc_final: 0.4213 (mt) REVERT: C 119 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.4870 (pp) REVERT: D 81 MET cc_start: 0.6184 (tmm) cc_final: 0.5865 (tmm) REVERT: D 104 LEU cc_start: 0.2101 (mt) cc_final: 0.1725 (tt) REVERT: I 60 LYS cc_start: 0.5730 (mtpt) cc_final: 0.5431 (mmmt) REVERT: I 61 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4848 (ttm) REVERT: I 85 LEU cc_start: 0.6680 (mt) cc_final: 0.6478 (mt) REVERT: J 95 ILE cc_start: 0.1835 (OUTLIER) cc_final: 0.1116 (tt) REVERT: J 124 ILE cc_start: 0.4462 (mt) cc_final: 0.4086 (mt) REVERT: P 63 LYS cc_start: 0.8546 (tptt) cc_final: 0.8169 (tttm) REVERT: Q 45 ILE cc_start: 0.6483 (mp) cc_final: 0.6209 (mp) REVERT: R 119 HIS cc_start: 0.5681 (m-70) cc_final: 0.5043 (m90) REVERT: R 139 ASN cc_start: 0.2063 (p0) cc_final: 0.1668 (p0) REVERT: S 158 TYR cc_start: 0.4162 (t80) cc_final: 0.3779 (t80) REVERT: S 216 LEU cc_start: 0.5422 (tp) cc_final: 0.5177 (tp) REVERT: T 227 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8059 (ttp-110) REVERT: T 325 ASP cc_start: 0.8638 (t0) cc_final: 0.8322 (t0) REVERT: T 537 LYS cc_start: 0.8106 (tptt) cc_final: 0.7880 (tptt) REVERT: T 558 LYS cc_start: 0.8086 (mppt) cc_final: 0.7716 (mmmm) REVERT: U 220 ARG cc_start: 0.8867 (mpp80) cc_final: 0.8541 (mtm110) REVERT: U 439 MET cc_start: 0.8862 (tpp) cc_final: 0.8603 (tpt) REVERT: V 445 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7292 (t) REVERT: V 506 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6759 (mmmt) REVERT: X 488 MET cc_start: 0.8430 (mmt) cc_final: 0.7922 (ttp) REVERT: X 497 GLU cc_start: 0.7446 (mp0) cc_final: 0.7210 (mp0) REVERT: X 539 ILE cc_start: 0.7302 (mm) cc_final: 0.7089 (mt) REVERT: X 541 GLU cc_start: 0.4497 (OUTLIER) cc_final: 0.4037 (tp30) REVERT: Y 155 THR cc_start: 0.8216 (p) cc_final: 0.7942 (p) REVERT: Y 195 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7386 (tm-30) REVERT: Y 199 ASN cc_start: 0.8594 (m-40) cc_final: 0.7849 (m110) REVERT: Y 538 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7157 (t) REVERT: Y 547 GLU cc_start: 0.8148 (mp0) cc_final: 0.7914 (mt-10) REVERT: Z 429 ASP cc_start: 0.6282 (OUTLIER) cc_final: 0.5967 (t70) REVERT: Z 448 GLN cc_start: 0.6595 (tm-30) cc_final: 0.5826 (mt0) outliers start: 116 outliers final: 83 residues processed: 504 average time/residue: 0.2041 time to fit residues: 170.0552 Evaluate side-chains 489 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 398 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 61 MET Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 118 THR Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 285 THR Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain V residue 535 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 337 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 506 ILE Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [158, 36, 24, 371, 337, 239, 33, 429, 52, 252, 50] chunk 158 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 371 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 239 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 429 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 GLN D 92 ASN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN U 539 ASN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 GLN X 337 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.158421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124575 restraints weight = 50711.794| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.93 r_work: 0.3276 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 34384 Z= 0.197 Angle : 0.607 11.233 46598 Z= 0.310 Chirality : 0.045 0.177 5513 Planarity : 0.004 0.041 5991 Dihedral : 5.988 157.342 4824 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.40 % Rotamer: Outliers : 3.40 % Allowed : 18.65 % Favored : 77.96 % 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: -1.02 (0.13), residues: 4457 helix: -0.11 (0.11), residues: 2179 sheet: -1.37 (0.21), residues: 578 loop : -0.97 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 51 TYR 0.024 0.002 TYR Z 248 PHE 0.030 0.002 PHE J 126 TRP 0.015 0.002 TRP U 73 HIS 0.005 0.001 HIS S 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (34384) covalent geometry : angle 0.60745 / 0.31 (46598) hydrogen bonds : bond 0.03820 / 2.57 ( 1654) hydrogen bonds : angle 4.68144 / 3.23 ( 4800) *********************** 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 523 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 402 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5901 (mmm) cc_final: 0.5389 (tpt) REVERT: B 81 MET cc_start: 0.7173 (ppp) cc_final: 0.6970 (ppp) REVERT: B 82 PHE cc_start: 0.4846 (OUTLIER) cc_final: 0.4360 (m-80) REVERT: B 118 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4591 (mt) REVERT: D 104 LEU cc_start: 0.2547 (mt) cc_final: 0.1905 (tt) REVERT: J 95 ILE cc_start: 0.1714 (OUTLIER) cc_final: 0.0810 (tt) REVERT: J 124 ILE cc_start: 0.4754 (mt) cc_final: 0.4456 (mt) REVERT: R 119 HIS cc_start: 0.5740 (m-70) cc_final: 0.5213 (m90) REVERT: S 158 TYR cc_start: 0.4330 (t80) cc_final: 0.3815 (t80) REVERT: S 216 LEU cc_start: 0.5396 (tp) cc_final: 0.5166 (tp) REVERT: T 227 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8077 (ttp-110) REVERT: T 325 ASP cc_start: 0.8651 (t0) cc_final: 0.8364 (t0) REVERT: T 537 LYS cc_start: 0.8198 (tptt) cc_final: 0.7795 (tppt) REVERT: T 558 LYS cc_start: 0.8073 (mppt) cc_final: 0.7708 (mmmm) REVERT: U 220 ARG cc_start: 0.8869 (mpp80) cc_final: 0.8540 (mtm110) REVERT: U 282 MET cc_start: 0.9191 (mmt) cc_final: 0.8827 (mmt) REVERT: U 283 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7745 (ttp-110) REVERT: U 439 MET cc_start: 0.8887 (tpp) cc_final: 0.8617 (tpt) REVERT: V 445 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7211 (t) REVERT: V 506 LYS cc_start: 0.7048 (mmtm) cc_final: 0.6724 (mmmt) REVERT: X 337 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: X 488 MET cc_start: 0.8462 (mmt) cc_final: 0.7973 (ttp) REVERT: X 497 GLU cc_start: 0.7459 (mp0) cc_final: 0.7186 (mp0) REVERT: X 539 ILE cc_start: 0.7307 (mm) cc_final: 0.7094 (mt) REVERT: X 541 GLU cc_start: 0.4880 (OUTLIER) cc_final: 0.4185 (tp30) REVERT: Y 155 THR cc_start: 0.8228 (p) cc_final: 0.7941 (p) REVERT: Y 193 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8969 (tt) REVERT: Y 195 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: Y 199 ASN cc_start: 0.8623 (m-40) cc_final: 0.7859 (m110) REVERT: Y 538 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.7122 (t) REVERT: Y 547 GLU cc_start: 0.8167 (mp0) cc_final: 0.7937 (mt-10) REVERT: Z 429 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.6134 (t70) REVERT: Z 448 GLN cc_start: 0.6514 (tm-30) cc_final: 0.5781 (mt0) outliers start: 121 outliers final: 92 residues processed: 488 average time/residue: 0.2078 time to fit residues: 167.4739 Evaluate side-chains 482 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 380 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 285 THR Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 535 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 337 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 506 ILE Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 195 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [440, 30, 173, 364, 300, 102, 344, 184, 43, 57, 150] chunk 440 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 364 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 344 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 GLN D 92 ASN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 GLN X 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.160685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126271 restraints weight = 50588.239| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.72 r_work: 0.3311 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34384 Z= 0.151 Angle : 0.574 12.592 46598 Z= 0.292 Chirality : 0.044 0.179 5513 Planarity : 0.004 0.040 5991 Dihedral : 5.828 151.854 4824 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 3.06 % Allowed : 19.43 % 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: -0.82 (0.13), residues: 4457 helix: 0.08 (0.11), residues: 2174 sheet: -1.31 (0.21), residues: 578 loop : -0.91 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 42 TYR 0.019 0.001 TYR Z 248 PHE 0.027 0.001 PHE J 126 TRP 0.018 0.002 TRP V 73 HIS 0.004 0.001 HIS S 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (34384) covalent geometry : angle 0.57381 / 0.29 (46598) hydrogen bonds : bond 0.03526 / 2.37 ( 1654) hydrogen bonds : angle 4.54667 / 3.13 ( 4800) *********************** 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 504 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 395 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5847 (mmm) cc_final: 0.5329 (tpt) REVERT: B 82 PHE cc_start: 0.4809 (OUTLIER) cc_final: 0.4341 (m-80) REVERT: B 118 LEU cc_start: 0.4804 (OUTLIER) cc_final: 0.4319 (mt) REVERT: D 81 MET cc_start: 0.6318 (tmm) cc_final: 0.6110 (tmm) REVERT: D 104 LEU cc_start: 0.2511 (mt) cc_final: 0.2004 (tt) REVERT: E 81 MET cc_start: 0.5167 (tpp) cc_final: 0.4965 (ttt) REVERT: J 95 ILE cc_start: 0.1691 (OUTLIER) cc_final: 0.0821 (tt) REVERT: Q 45 ILE cc_start: 0.6615 (mp) cc_final: 0.6262 (mp) REVERT: Q 63 TYR cc_start: 0.6639 (m-80) cc_final: 0.6314 (m-80) REVERT: R 119 HIS cc_start: 0.5902 (m-70) cc_final: 0.5328 (m90) REVERT: S 158 TYR cc_start: 0.4229 (t80) cc_final: 0.3490 (t80) REVERT: S 216 LEU cc_start: 0.5417 (tp) cc_final: 0.5191 (tp) REVERT: S 274 MET cc_start: 0.8634 (mmp) cc_final: 0.8354 (mmp) REVERT: T 227 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8040 (ttp-110) REVERT: T 325 ASP cc_start: 0.8624 (t0) cc_final: 0.8365 (t0) REVERT: T 407 PHE cc_start: 0.7913 (t80) cc_final: 0.7597 (m-80) REVERT: T 558 LYS cc_start: 0.8042 (mppt) cc_final: 0.7694 (mmmm) REVERT: U 220 ARG cc_start: 0.8848 (mpp80) cc_final: 0.8536 (mtm110) REVERT: U 283 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7705 (ttp-110) REVERT: U 439 MET cc_start: 0.8883 (tpp) cc_final: 0.8528 (tpt) REVERT: V 50 LYS cc_start: 0.8115 (tptp) cc_final: 0.7841 (tmmt) REVERT: V 445 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7243 (t) REVERT: V 506 LYS cc_start: 0.7049 (mmtm) cc_final: 0.6800 (mmmt) REVERT: X 488 MET cc_start: 0.8413 (mmt) cc_final: 0.7926 (ttp) REVERT: X 497 GLU cc_start: 0.7376 (mp0) cc_final: 0.7099 (mp0) REVERT: X 541 GLU cc_start: 0.4847 (OUTLIER) cc_final: 0.4222 (tp30) REVERT: Y 155 THR cc_start: 0.8241 (p) cc_final: 0.7966 (p) REVERT: Y 193 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8932 (tt) REVERT: Y 195 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: Y 199 ASN cc_start: 0.8526 (m-40) cc_final: 0.7830 (m110) REVERT: Y 538 VAL cc_start: 0.7300 (OUTLIER) cc_final: 0.7096 (t) REVERT: Z 387 LEU cc_start: 0.8579 (tp) cc_final: 0.8369 (tp) REVERT: Z 429 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5955 (t70) REVERT: Z 448 GLN cc_start: 0.6419 (tm-30) cc_final: 0.5760 (mt0) outliers start: 109 outliers final: 86 residues processed: 471 average time/residue: 0.2051 time to fit residues: 159.2108 Evaluate side-chains 474 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 379 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 337 GLN Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 195 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [241, 169, 61, 415, 39, 94, 376, 386, 72, 346, 177] chunk 241 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 415 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 376 optimal weight: 2.9990 chunk 386 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 71 GLN Q 40 GLN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.161737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127717 restraints weight = 50390.445| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.69 r_work: 0.3323 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34384 Z= 0.135 Angle : 0.566 12.805 46598 Z= 0.288 Chirality : 0.043 0.187 5513 Planarity : 0.004 0.040 5991 Dihedral : 5.657 143.759 4824 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.89 % Rotamer: Outliers : 2.86 % Allowed : 19.94 % Favored : 77.20 % 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: -0.64 (0.13), residues: 4457 helix: 0.21 (0.12), residues: 2173 sheet: -1.22 (0.21), residues: 577 loop : -0.79 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 42 TYR 0.017 0.001 TYR Z 248 PHE 0.023 0.001 PHE E 107 TRP 0.013 0.001 TRP U 73 HIS 0.005 0.001 HIS R 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (34384) covalent geometry : angle 0.56647 / 0.29 (46598) hydrogen bonds : bond 0.03435 / 2.31 ( 1654) hydrogen bonds : angle 4.47453 / 3.08 ( 4800) *********************** 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 502 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 400 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5864 (mmm) cc_final: 0.5325 (tpt) REVERT: B 82 PHE cc_start: 0.4789 (OUTLIER) cc_final: 0.4571 (m-80) REVERT: B 118 LEU cc_start: 0.4800 (OUTLIER) cc_final: 0.4456 (mt) REVERT: D 104 LEU cc_start: 0.2608 (mt) cc_final: 0.2050 (tt) REVERT: G 81 MET cc_start: 0.5473 (tpp) cc_final: 0.5269 (tpt) REVERT: J 95 ILE cc_start: 0.1634 (OUTLIER) cc_final: 0.0789 (tt) REVERT: J 119 LEU cc_start: 0.5312 (tt) cc_final: 0.4753 (pt) REVERT: P 110 LYS cc_start: 0.7272 (ptpp) cc_final: 0.7011 (ptmm) REVERT: Q 45 ILE cc_start: 0.6600 (mp) cc_final: 0.6301 (mp) REVERT: Q 63 TYR cc_start: 0.6614 (m-80) cc_final: 0.6321 (m-80) REVERT: Q 70 PRO cc_start: 0.3493 (Cg_endo) cc_final: 0.2939 (Cg_exo) REVERT: R 119 HIS cc_start: 0.5989 (m-70) cc_final: 0.5472 (m90) REVERT: S 158 TYR cc_start: 0.4346 (t80) cc_final: 0.3678 (t80) REVERT: S 190 TYR cc_start: 0.5561 (m-80) cc_final: 0.5133 (m-80) REVERT: S 216 LEU cc_start: 0.5423 (tp) cc_final: 0.5208 (tp) REVERT: T 325 ASP cc_start: 0.8620 (t0) cc_final: 0.8296 (t0) REVERT: T 407 PHE cc_start: 0.7943 (t80) cc_final: 0.7614 (m-80) REVERT: T 481 THR cc_start: 0.8800 (m) cc_final: 0.8542 (p) REVERT: T 558 LYS cc_start: 0.8034 (mppt) cc_final: 0.7603 (mmmm) REVERT: U 220 ARG cc_start: 0.8846 (mpp80) cc_final: 0.8548 (mtm110) REVERT: U 283 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7644 (ttp-110) REVERT: U 439 MET cc_start: 0.8884 (tpp) cc_final: 0.8511 (tpt) REVERT: V 50 LYS cc_start: 0.8118 (tptp) cc_final: 0.7882 (tmmt) REVERT: V 445 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7334 (t) REVERT: V 506 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6574 (mmmt) REVERT: X 219 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8073 (mt-10) REVERT: X 488 MET cc_start: 0.8422 (mmt) cc_final: 0.7928 (ttp) REVERT: X 541 GLU cc_start: 0.4840 (OUTLIER) cc_final: 0.4224 (tp30) REVERT: Y 155 THR cc_start: 0.8225 (p) cc_final: 0.7949 (p) REVERT: Y 193 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8912 (tt) REVERT: Y 195 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: Y 199 ASN cc_start: 0.8516 (m-40) cc_final: 0.7860 (m110) REVERT: Y 538 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.7062 (t) REVERT: Z 178 LYS cc_start: 0.8872 (mttt) cc_final: 0.8559 (mtpt) REVERT: Z 429 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.6095 (t70) REVERT: Z 448 GLN cc_start: 0.6456 (tm-30) cc_final: 0.5751 (mt0) outliers start: 102 outliers final: 89 residues processed: 475 average time/residue: 0.1990 time to fit residues: 156.5386 Evaluate side-chains 482 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 384 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 399 ILE Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 541 GLU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 195 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 506 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 429 ASP Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [332, 90, 249, 44, 384, 5, 418, 258, 162, 214, 172] chunk 332 optimal weight: 0.0370 chunk 90 optimal weight: 0.2980 chunk 249 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 384 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 418 optimal weight: 0.0070 chunk 258 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 GLN D 94 ASN F 92 ASN P 71 GLN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 GLN T 452 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN U 549 HIS ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.164362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130043 restraints weight = 50335.852| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.60 r_work: 0.3397 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 34384 Z= 0.102 Angle : 0.546 11.259 46598 Z= 0.276 Chirality : 0.042 0.230 5513 Planarity : 0.003 0.040 5991 Dihedral : 5.189 125.113 4824 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 2.27 % Allowed : 20.89 % Favored : 76.83 % 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: -0.33 (0.13), residues: 4457 helix: 0.45 (0.12), residues: 2172 sheet: -0.97 (0.22), residues: 568 loop : -0.65 (0.16), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 42 TYR 0.021 0.001 TYR Z 397 PHE 0.023 0.001 PHE E 107 TRP 0.008 0.001 TRP U 73 HIS 0.004 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (34384) covalent geometry : angle 0.54587 / 0.28 (46598) hydrogen bonds : bond 0.03101 / 2.09 ( 1654) hydrogen bonds : angle 4.27111 / 2.93 ( 4800) *********************** 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 550 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 469 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6026 (tpp) cc_final: 0.5811 (mmm) REVERT: B 61 MET cc_start: 0.5856 (mmm) cc_final: 0.5216 (tpt) REVERT: D 61 MET cc_start: 0.6917 (mpp) cc_final: 0.5824 (mpp) REVERT: D 69 ILE cc_start: 0.6845 (tp) cc_final: 0.6384 (tp) REVERT: D 81 MET cc_start: 0.6257 (tmm) cc_final: 0.5967 (tmm) REVERT: D 104 LEU cc_start: 0.2411 (mt) cc_final: 0.1981 (tt) REVERT: D 105 LEU cc_start: 0.4537 (OUTLIER) cc_final: 0.3120 (mp) REVERT: D 119 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.4418 (tt) REVERT: F 92 ASN cc_start: 0.5928 (OUTLIER) cc_final: 0.5642 (m-40) REVERT: J 95 ILE cc_start: 0.1886 (OUTLIER) cc_final: 0.1202 (tt) REVERT: P 135 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8406 (mm) REVERT: Q 42 ARG cc_start: 0.6096 (ptt90) cc_final: 0.5637 (ptm160) REVERT: Q 45 ILE cc_start: 0.6333 (mp) cc_final: 0.6043 (mp) REVERT: Q 63 TYR cc_start: 0.6620 (m-80) cc_final: 0.6336 (m-80) REVERT: R 119 HIS cc_start: 0.5943 (m-70) cc_final: 0.5497 (m90) REVERT: S 158 TYR cc_start: 0.4103 (t80) cc_final: 0.3607 (t80) REVERT: S 190 TYR cc_start: 0.5509 (m-80) cc_final: 0.5272 (m-80) REVERT: T 325 ASP cc_start: 0.8688 (t0) cc_final: 0.8320 (t0) REVERT: T 407 PHE cc_start: 0.7828 (t80) cc_final: 0.7531 (m-80) REVERT: T 467 ASP cc_start: 0.8145 (t70) cc_final: 0.7652 (t0) REVERT: T 474 LEU cc_start: 0.7600 (tt) cc_final: 0.7282 (mp) REVERT: T 558 LYS cc_start: 0.7989 (mppt) cc_final: 0.7607 (mmmm) REVERT: U 220 ARG cc_start: 0.8714 (mpp80) cc_final: 0.8410 (mtm110) REVERT: U 282 MET cc_start: 0.9030 (mmt) cc_final: 0.8734 (mmt) REVERT: V 50 LYS cc_start: 0.8054 (tptp) cc_final: 0.7823 (tmmt) REVERT: V 445 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7220 (t) REVERT: X 381 ASP cc_start: 0.8083 (m-30) cc_final: 0.7748 (t0) REVERT: X 488 MET cc_start: 0.8304 (mmt) cc_final: 0.7827 (ttp) REVERT: Y 193 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8826 (tt) REVERT: Y 195 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7335 (tm-30) REVERT: Y 199 ASN cc_start: 0.8358 (m-40) cc_final: 0.7773 (m110) REVERT: Y 538 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.7018 (t) REVERT: Z 310 TYR cc_start: 0.7543 (m-80) cc_final: 0.7310 (m-80) REVERT: Z 365 SER cc_start: 0.8253 (p) cc_final: 0.8031 (m) REVERT: Z 411 LYS cc_start: 0.6997 (mptt) cc_final: 0.6688 (mmtt) REVERT: Z 448 GLN cc_start: 0.6308 (tm-30) cc_final: 0.5774 (mt0) outliers start: 81 outliers final: 54 residues processed: 529 average time/residue: 0.2050 time to fit residues: 177.2094 Evaluate side-chains 482 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 420 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [146, 399, 93, 31, 144, 151, 413, 164, 434, 364, 222] chunk 146 optimal weight: 1.9990 chunk 399 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 144 optimal weight: 0.0270 chunk 151 optimal weight: 0.7980 chunk 413 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 434 optimal weight: 1.9990 chunk 364 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 71 GLN R 181 ASN S 156 GLN ** S 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN T 497 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.163612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129853 restraints weight = 50490.522| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.62 r_work: 0.3355 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34384 Z= 0.130 Angle : 0.578 11.281 46598 Z= 0.291 Chirality : 0.044 0.184 5513 Planarity : 0.004 0.041 5991 Dihedral : 5.223 111.360 4824 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.86 % Favored : 96.03 % Rotamer: Outliers : 1.99 % Allowed : 21.57 % Favored : 76.44 % 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: -0.33 (0.13), residues: 4457 helix: 0.45 (0.12), residues: 2163 sheet: -1.00 (0.22), residues: 565 loop : -0.63 (0.16), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 91 TYR 0.023 0.001 TYR Z 397 PHE 0.023 0.001 PHE A 107 TRP 0.009 0.001 TRP U 73 HIS 0.003 0.001 HIS V 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (34384) covalent geometry : angle 0.57807 / 0.29 (46598) hydrogen bonds : bond 0.03299 / 2.22 ( 1654) hydrogen bonds : angle 4.32079 / 2.97 ( 4800) ********************** 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 481 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 410 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6057 (tpp) cc_final: 0.5793 (mmm) REVERT: B 61 MET cc_start: 0.5844 (mmm) cc_final: 0.5205 (tpt) REVERT: D 61 MET cc_start: 0.6960 (mpp) cc_final: 0.5925 (mpp) REVERT: D 81 MET cc_start: 0.6450 (tmm) cc_final: 0.6199 (tmm) REVERT: D 104 LEU cc_start: 0.2445 (mt) cc_final: 0.1960 (tt) REVERT: D 105 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.3129 (mp) REVERT: D 119 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.4442 (tt) REVERT: J 95 ILE cc_start: 0.1969 (OUTLIER) cc_final: 0.1229 (tt) REVERT: P 135 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8450 (mm) REVERT: Q 42 ARG cc_start: 0.6037 (ptt90) cc_final: 0.5605 (ptm160) REVERT: Q 63 TYR cc_start: 0.6653 (m-80) cc_final: 0.6424 (m-80) REVERT: R 119 HIS cc_start: 0.6083 (m-70) cc_final: 0.5544 (m90) REVERT: S 158 TYR cc_start: 0.4294 (t80) cc_final: 0.3685 (t80) REVERT: S 190 TYR cc_start: 0.5488 (m-80) cc_final: 0.5134 (m-80) REVERT: T 325 ASP cc_start: 0.8603 (t0) cc_final: 0.8230 (t0) REVERT: T 407 PHE cc_start: 0.7845 (t80) cc_final: 0.7480 (m-80) REVERT: T 467 ASP cc_start: 0.8313 (t70) cc_final: 0.7851 (t0) REVERT: T 558 LYS cc_start: 0.7962 (mppt) cc_final: 0.7543 (mmmm) REVERT: U 220 ARG cc_start: 0.8761 (mpp80) cc_final: 0.8518 (mtm110) REVERT: U 439 MET cc_start: 0.8865 (tpp) cc_final: 0.8557 (tpt) REVERT: V 50 LYS cc_start: 0.8144 (tptp) cc_final: 0.7875 (tmmt) REVERT: V 445 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7244 (t) REVERT: X 381 ASP cc_start: 0.8139 (m-30) cc_final: 0.7848 (t0) REVERT: X 488 MET cc_start: 0.8410 (mmt) cc_final: 0.7920 (ttp) REVERT: Y 193 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8886 (tt) REVERT: Y 385 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7896 (mtm-85) REVERT: Y 448 GLN cc_start: 0.8643 (tt0) cc_final: 0.7968 (tt0) REVERT: Y 538 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.7086 (t) REVERT: Z 178 LYS cc_start: 0.8830 (mttt) cc_final: 0.8536 (mtpt) REVERT: Z 365 SER cc_start: 0.8443 (p) cc_final: 0.8132 (m) REVERT: Z 411 LYS cc_start: 0.7100 (mptt) cc_final: 0.6746 (mmtt) REVERT: Z 448 GLN cc_start: 0.6374 (tm-30) cc_final: 0.5730 (mt0) outliers start: 71 outliers final: 60 residues processed: 467 average time/residue: 0.2026 time to fit residues: 155.0924 Evaluate side-chains 461 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 394 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 148 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 212 SER Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 278 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 354 THR Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 208 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 314 LEU Chi-restraints excluded: chain Z residue 390 ASN Chi-restraints excluded: chain Z residue 492 ILE Chi-restraints excluded: chain Z residue 494 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: [277, 323, 384, 108, 410, 114, 330, 348, 396, 407, 387] chunk 277 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 384 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 410 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 330 optimal weight: 6.9990 chunk 348 optimal weight: 0.2980 chunk 396 optimal weight: 0.8980 chunk 407 optimal weight: 4.9990 chunk 387 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 71 GLN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN T 452 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Y 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.163603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129918 restraints weight = 50497.957| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.64 r_work: 0.3374 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34384 Z= 0.115 Angle : 0.564 11.533 46598 Z= 0.284 Chirality : 0.043 0.184 5513 Planarity : 0.004 0.041 5991 Dihedral : 5.087 86.510 4824 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.25 % Rotamer: Outliers : 2.02 % Allowed : 21.71 % Favored : 76.27 % 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: -0.24 (0.13), residues: 4457 helix: 0.53 (0.12), residues: 2168 sheet: -0.97 (0.22), residues: 569 loop : -0.60 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 42 TYR 0.022 0.001 TYR Z 397 PHE 0.024 0.001 PHE G 107 TRP 0.009 0.001 TRP U 73 HIS 0.003 0.001 HIS S 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (34384) covalent geometry : angle 0.56367 / 0.28 (46598) hydrogen bonds : bond 0.03190 / 2.15 ( 1654) hydrogen bonds : angle 4.27330 / 2.94 ( 4800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9980.19 seconds wall clock time: 171 minutes 0.73 seconds (10260.73 seconds total)