Starting phenix.real_space_refine on Fri Mar 6 19:06:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6re1_4838/03_2026/6re1_4838.cif Found real_map, /net/cci-nas-00/data/ceres_data/6re1_4838/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6re1_4838/03_2026/6re1_4838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6re1_4838/03_2026/6re1_4838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6re1_4838/03_2026/6re1_4838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6re1_4838/03_2026/6re1_4838.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33863 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.99, per 1000 atoms: 0.24 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 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: 1.22 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: 9.42 Time building geometry restraints manager: 3.69 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: 20320 35.22 - 70.44: 442 70.44 - 105.66: 39 105.66 - 140.89: 1 140.89 - 176.11: 1 Dihedral angle restraints: 20803 sinusoidal: 8060 harmonic: 12743 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -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 20800 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: 10.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 34.300 Find NCS groups from input model: 0.770 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: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 15.257 176.107 12653 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.00 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 covalent geometry : bond 0.00902 (34384) covalent geometry : angle 1.00029 (46598) hydrogen bonds : bond 0.17549 ( 1654) hydrogen bonds : angle 8.02201 ( 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 : 1.298 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: 0.2371 time to fit residues: 213.5202 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 : 1.177 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: 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 292 GLN Y 412 ASN Z 174 GLN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.162855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128724 restraints weight = 50650.036| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.90 r_work: 0.3310 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1763 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= 0.146 Angle : 0.594 10.000 46598 Z= 0.308 Chirality : 0.043 0.167 5513 Planarity : 0.005 0.057 5991 Dihedral : 7.242 172.047 4921 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.34 % Favored : 96.46 % Rotamer: Outliers : 1.80 % Allowed : 13.98 % Favored : 84.22 % 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: -2.40 (0.12), residues: 4457 helix: -1.35 (0.10), residues: 2146 sheet: -1.47 (0.21), residues: 579 loop : -1.75 (0.14), residues: 1732 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 0.008 0.001 TRP U 73 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00325 (34384) covalent geometry : angle 0.59362 (46598) hydrogen bonds : bond 0.03905 ( 1654) hydrogen bonds : angle 5.21706 ( 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 573 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 509 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5391 (tpp) cc_final: 0.5158 (tpt) REVERT: B 82 PHE cc_start: 0.5683 (m-10) cc_final: 0.5152 (m-10) REVERT: B 118 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4439 (pp) REVERT: D 61 MET cc_start: 0.6433 (mpp) cc_final: 0.5589 (mpp) REVERT: D 126 PHE cc_start: 0.5196 (m-80) cc_final: 0.4968 (m-80) REVERT: H 61 MET cc_start: 0.4821 (mmt) cc_final: 0.3879 (mtt) REVERT: J 123 LEU cc_start: 0.1105 (tp) cc_final: 0.0693 (mt) REVERT: J 124 ILE cc_start: 0.5096 (mt) cc_final: 0.4760 (mt) REVERT: P 39 LEU cc_start: 0.8136 (mp) cc_final: 0.7735 (mt) REVERT: R 86 LYS cc_start: 0.6120 (mmtm) cc_final: 0.5694 (mmtm) REVERT: R 119 HIS cc_start: 0.4825 (m-70) cc_final: 0.3863 (m90) REVERT: S 234 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6602 (tm-30) REVERT: T 227 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7951 (ttp-110) REVERT: T 282 MET cc_start: 0.8655 (tpp) cc_final: 0.8022 (tpt) REVERT: T 390 VAL cc_start: 0.9102 (p) cc_final: 0.8887 (t) REVERT: T 558 LYS cc_start: 0.8083 (mppt) cc_final: 0.7636 (mmmm) REVERT: U 282 MET cc_start: 0.9161 (mmt) cc_final: 0.8750 (mmt) REVERT: V 61 HIS cc_start: 0.8086 (t70) cc_final: 0.7606 (t-90) REVERT: V 73 TRP cc_start: 0.8370 (m-10) cc_final: 0.8059 (m-10) REVERT: V 112 ASP cc_start: 0.8324 (p0) cc_final: 0.7951 (p0) REVERT: V 282 MET cc_start: 0.8737 (tpt) cc_final: 0.8443 (tpt) REVERT: V 445 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7195 (t) REVERT: V 506 LYS cc_start: 0.7098 (mmtm) cc_final: 0.6645 (mmmt) REVERT: X 337 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: X 488 MET cc_start: 0.8396 (mmt) cc_final: 0.7903 (ttp) REVERT: X 535 LYS cc_start: 0.6978 (mptt) cc_final: 0.6772 (mppt) REVERT: X 541 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.4058 (tp30) REVERT: Y 168 ASP cc_start: 0.8319 (m-30) cc_final: 0.8102 (m-30) REVERT: Y 195 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7335 (tm-30) REVERT: Y 199 ASN cc_start: 0.8806 (m-40) cc_final: 0.8148 (m110) REVERT: Y 317 ASP cc_start: 0.8325 (m-30) cc_final: 0.8113 (m-30) REVERT: Y 547 GLU cc_start: 0.7977 (mp0) cc_final: 0.7748 (mt-10) REVERT: Z 149 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7527 (mm-30) REVERT: Z 178 LYS cc_start: 0.8892 (mttt) cc_final: 0.8533 (mtpt) REVERT: Z 448 GLN cc_start: 0.6677 (tm-30) cc_final: 0.5911 (mt0) REVERT: Z 572 LYS cc_start: 0.7192 (mmmt) cc_final: 0.6949 (tmmt) outliers start: 64 outliers final: 36 residues processed: 552 average time/residue: 0.2129 time to fit residues: 189.6076 Evaluate side-chains 458 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 418 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 70 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 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: chunk 328 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 435 optimal weight: 0.0670 chunk 294 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 310 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN P 83 GLN 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 539 ASN V 61 HIS ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 286 ASN X 322 GLN Z 83 ASN Z 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.162828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128109 restraints weight = 50591.054| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.71 r_work: 0.3325 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34384 Z= 0.138 Angle : 0.566 9.211 46598 Z= 0.293 Chirality : 0.043 0.208 5513 Planarity : 0.004 0.049 5991 Dihedral : 6.833 178.872 4917 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 2.53 % Allowed : 15.95 % Favored : 81.52 % 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: -1.59 (0.12), residues: 4457 helix: -0.57 (0.11), residues: 2151 sheet: -1.30 (0.21), residues: 579 loop : -1.41 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 496 TYR 0.021 0.001 TYR I 102 PHE 0.024 0.001 PHE C 107 TRP 0.008 0.001 TRP U 73 HIS 0.009 0.001 HIS V 61 Details of bonding type rmsd covalent geometry : bond 0.00313 (34384) covalent geometry : angle 0.56563 (46598) hydrogen bonds : bond 0.03648 ( 1654) hydrogen bonds : angle 4.77657 ( 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 544 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 454 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5118 (mp) REVERT: B 82 PHE cc_start: 0.5332 (m-10) cc_final: 0.5036 (m-10) REVERT: B 118 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4575 (mt) REVERT: C 119 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.4673 (mt) REVERT: J 123 LEU cc_start: 0.0966 (tp) cc_final: 0.0633 (mt) REVERT: J 124 ILE cc_start: 0.4769 (mt) cc_final: 0.4319 (mt) REVERT: P 55 THR cc_start: 0.9065 (m) cc_final: 0.8725 (m) REVERT: P 81 PHE cc_start: 0.7954 (m-10) cc_final: 0.7741 (m-10) REVERT: R 119 HIS cc_start: 0.5448 (m-70) cc_final: 0.4813 (m90) REVERT: R 137 HIS cc_start: 0.3552 (m90) cc_final: 0.2824 (m-70) REVERT: S 158 TYR cc_start: 0.4004 (t80) cc_final: 0.3252 (t80) REVERT: S 185 HIS cc_start: 0.5195 (m90) cc_final: 0.4696 (m90) REVERT: S 193 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7319 (mt) REVERT: S 201 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7889 (tt) REVERT: S 219 GLN cc_start: 0.6330 (mp10) cc_final: 0.5306 (tp-100) REVERT: S 234 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6420 (tm-30) REVERT: S 274 MET cc_start: 0.8720 (mmp) cc_final: 0.8220 (mmt) REVERT: T 282 MET cc_start: 0.8687 (tpp) cc_final: 0.8025 (tpt) REVERT: T 325 ASP cc_start: 0.8635 (t0) cc_final: 0.8376 (t0) REVERT: T 407 PHE cc_start: 0.8048 (t80) cc_final: 0.7834 (t80) REVERT: T 537 LYS cc_start: 0.8143 (tptt) cc_final: 0.7639 (tppt) REVERT: T 558 LYS cc_start: 0.8059 (mppt) cc_final: 0.7647 (mmmm) REVERT: U 439 MET cc_start: 0.8930 (tpp) cc_final: 0.8640 (tpt) REVERT: V 112 ASP cc_start: 0.8256 (p0) cc_final: 0.7906 (p0) REVERT: V 282 MET cc_start: 0.8677 (tpt) cc_final: 0.8450 (tpt) REVERT: V 326 ASP cc_start: 0.8340 (m-30) cc_final: 0.7987 (m-30) REVERT: V 329 LYS cc_start: 0.8354 (mttp) cc_final: 0.8119 (mttm) REVERT: V 445 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7254 (t) REVERT: V 506 LYS cc_start: 0.7108 (mmtm) cc_final: 0.6694 (mmmt) REVERT: X 488 MET cc_start: 0.8362 (mmt) cc_final: 0.7905 (ttp) REVERT: X 541 GLU cc_start: 0.4686 (OUTLIER) cc_final: 0.4104 (tp30) REVERT: Y 195 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7302 (tm-30) REVERT: Y 199 ASN cc_start: 0.8501 (m-40) cc_final: 0.7851 (m110) REVERT: Y 538 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7262 (t) REVERT: Y 547 GLU cc_start: 0.8122 (mp0) cc_final: 0.7868 (mt-10) REVERT: Z 387 LEU cc_start: 0.8746 (tp) cc_final: 0.8468 (tp) REVERT: Z 429 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.6081 (t70) REVERT: Z 448 GLN cc_start: 0.6660 (tm-30) cc_final: 0.5891 (mt0) REVERT: Z 451 GLU cc_start: 0.6944 (tt0) cc_final: 0.6662 (tp30) outliers start: 90 outliers final: 47 residues processed: 520 average time/residue: 0.2065 time to fit residues: 174.2961 Evaluate side-chains 449 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 393 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU 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 C residue 119 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 123 LEU Chi-restraints excluded: chain I residue 56 LEU 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 135 LEU Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 182 LEU 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 246 LEU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 271 GLN 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 84 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 178 THR Chi-restraints excluded: chain U residue 202 LEU 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 456 VAL Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 532 VAL 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 326 THR 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: chunk 96 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 414 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 312 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 chunk 387 optimal weight: 0.0770 chunk 273 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN E 98 GLN Q 21 ASN R 73 ASN ** R 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 452 GLN U 539 ASN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 GLN X 337 GLN X 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125808 restraints weight = 50454.172| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.76 r_work: 0.3301 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34384 Z= 0.164 Angle : 0.580 9.183 46598 Z= 0.298 Chirality : 0.044 0.173 5513 Planarity : 0.004 0.050 5991 Dihedral : 6.625 169.805 4917 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.11 % Favored : 95.76 % Rotamer: Outliers : 3.06 % Allowed : 16.96 % Favored : 79.98 % 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: -1.27 (0.13), residues: 4457 helix: -0.30 (0.11), residues: 2181 sheet: -1.33 (0.21), residues: 578 loop : -1.19 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 496 TYR 0.020 0.002 TYR U 57 PHE 0.022 0.001 PHE A 107 TRP 0.009 0.001 TRP U 73 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00381 (34384) covalent geometry : angle 0.57964 (46598) hydrogen bonds : bond 0.03678 ( 1654) hydrogen bonds : angle 4.67040 ( 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 524 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 415 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.5025 (mp) REVERT: B 118 LEU cc_start: 0.4614 (OUTLIER) cc_final: 0.4145 (mt) REVERT: C 119 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.4776 (mt) REVERT: D 81 MET cc_start: 0.6151 (tmm) cc_final: 0.5813 (tmm) REVERT: P 63 LYS cc_start: 0.8504 (tptt) cc_final: 0.8271 (tttm) REVERT: P 71 GLN cc_start: 0.7531 (tt0) cc_final: 0.7273 (tt0) REVERT: P 127 ASP cc_start: 0.7494 (m-30) cc_final: 0.7151 (m-30) REVERT: Q 45 ILE cc_start: 0.6430 (mp) cc_final: 0.6169 (mp) REVERT: Q 49 GLN cc_start: 0.5743 (pt0) cc_final: 0.5533 (pt0) REVERT: R 119 HIS cc_start: 0.5643 (m-70) cc_final: 0.4727 (m90) REVERT: S 158 TYR cc_start: 0.3884 (t80) cc_final: 0.3501 (t80) REVERT: S 219 GLN cc_start: 0.6431 (mp10) cc_final: 0.5597 (tp-100) REVERT: T 227 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8005 (ttp-110) REVERT: T 282 MET cc_start: 0.8689 (tpp) cc_final: 0.8045 (tpt) REVERT: T 325 ASP cc_start: 0.8659 (t0) cc_final: 0.8336 (t0) REVERT: T 537 LYS cc_start: 0.8119 (tptt) cc_final: 0.7846 (tptt) REVERT: T 558 LYS cc_start: 0.8072 (mppt) cc_final: 0.7676 (mmmm) REVERT: U 282 MET cc_start: 0.9185 (mmt) cc_final: 0.8830 (mmt) REVERT: U 439 MET cc_start: 0.8914 (tpp) cc_final: 0.8611 (tpt) REVERT: V 112 ASP cc_start: 0.8289 (p0) cc_final: 0.7936 (p0) REVERT: V 445 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7247 (t) REVERT: V 506 LYS cc_start: 0.7119 (mmtm) cc_final: 0.6739 (mmmt) REVERT: X 337 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: X 488 MET cc_start: 0.8401 (mmt) cc_final: 0.7912 (ttp) REVERT: X 539 ILE cc_start: 0.7203 (mm) cc_final: 0.6975 (mt) REVERT: X 541 GLU cc_start: 0.4661 (OUTLIER) cc_final: 0.4143 (tp30) REVERT: Y 195 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7311 (tm-30) REVERT: Y 199 ASN cc_start: 0.8577 (m-40) cc_final: 0.7859 (m110) REVERT: Y 538 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.7110 (t) REVERT: Y 547 GLU cc_start: 0.8133 (mp0) cc_final: 0.7811 (mt-10) REVERT: Z 429 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.5937 (t70) REVERT: Z 448 GLN cc_start: 0.6600 (tm-30) cc_final: 0.5860 (mt0) REVERT: Z 451 GLU cc_start: 0.6909 (tt0) cc_final: 0.6679 (tp30) outliers start: 109 outliers final: 68 residues processed: 497 average time/residue: 0.2004 time to fit residues: 163.7066 Evaluate side-chains 459 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 383 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 78 LEU 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 C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU 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 56 LEU 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 148 HIS 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 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 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 378 THR 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 390 VAL 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 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 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 131 GLU Chi-restraints excluded: chain Z residue 160 LEU 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 533 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 3 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 288 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 266 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 428 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN J 98 GLN ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127571 restraints weight = 50839.063| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.86 r_work: 0.3325 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2667 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= 0.128 Angle : 0.558 11.583 46598 Z= 0.286 Chirality : 0.043 0.179 5513 Planarity : 0.004 0.046 5991 Dihedral : 6.311 164.292 4917 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.25 % Rotamer: Outliers : 2.75 % Allowed : 18.28 % Favored : 78.97 % 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: -0.96 (0.13), residues: 4457 helix: -0.02 (0.11), residues: 2183 sheet: -1.28 (0.21), residues: 582 loop : -1.05 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 42 TYR 0.020 0.001 TYR Z 248 PHE 0.033 0.001 PHE J 126 TRP 0.010 0.001 TRP U 73 HIS 0.006 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00291 (34384) covalent geometry : angle 0.55826 (46598) hydrogen bonds : bond 0.03400 ( 1654) hydrogen bonds : angle 4.53730 ( 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 522 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 424 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4727 (mp) REVERT: B 118 LEU cc_start: 0.4498 (OUTLIER) cc_final: 0.4211 (mt) REVERT: D 69 ILE cc_start: 0.6935 (tp) cc_final: 0.6443 (tp) REVERT: D 81 MET cc_start: 0.6264 (tmm) cc_final: 0.5998 (tmm) REVERT: D 104 LEU cc_start: 0.2156 (mt) cc_final: 0.1856 (tt) REVERT: J 61 MET cc_start: 0.2058 (mmm) cc_final: 0.1715 (mmm) REVERT: J 95 ILE cc_start: 0.1931 (OUTLIER) cc_final: 0.1250 (tt) REVERT: P 63 LYS cc_start: 0.8457 (tptt) cc_final: 0.8108 (tttm) REVERT: Q 45 ILE cc_start: 0.6373 (mp) cc_final: 0.6048 (mp) REVERT: Q 49 GLN cc_start: 0.5949 (pt0) cc_final: 0.5406 (pm20) REVERT: R 119 HIS cc_start: 0.5572 (m-70) cc_final: 0.4807 (m90) REVERT: S 158 TYR cc_start: 0.3854 (t80) cc_final: 0.3534 (t80) REVERT: S 193 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7492 (mt) REVERT: T 325 ASP cc_start: 0.8707 (t0) cc_final: 0.8322 (t0) REVERT: T 481 THR cc_start: 0.8763 (m) cc_final: 0.8536 (p) REVERT: T 537 LYS cc_start: 0.8170 (tptt) cc_final: 0.7773 (tppt) REVERT: T 558 LYS cc_start: 0.8074 (mppt) cc_final: 0.7630 (mmmm) REVERT: U 70 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7025 (t) REVERT: U 282 MET cc_start: 0.9200 (mmt) cc_final: 0.8880 (mmt) REVERT: U 439 MET cc_start: 0.8901 (tpp) cc_final: 0.8589 (tpt) REVERT: V 50 LYS cc_start: 0.8111 (tptp) cc_final: 0.7811 (tmmt) REVERT: V 445 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7321 (t) REVERT: V 506 LYS cc_start: 0.7041 (mmtm) cc_final: 0.6766 (mmmt) REVERT: X 488 MET cc_start: 0.8395 (mmt) cc_final: 0.7897 (ttp) REVERT: X 497 GLU cc_start: 0.7454 (mp0) cc_final: 0.7156 (mp0) REVERT: Y 193 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8900 (tt) REVERT: Y 195 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7380 (tm-30) REVERT: Y 199 ASN cc_start: 0.8518 (m-40) cc_final: 0.7848 (m110) REVERT: Y 538 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.7122 (t) REVERT: Y 547 GLU cc_start: 0.8188 (mp0) cc_final: 0.7881 (mt-10) REVERT: Z 178 LYS cc_start: 0.8918 (mttt) cc_final: 0.8594 (mtpt) REVERT: Z 429 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5933 (t70) REVERT: Z 448 GLN cc_start: 0.6492 (tm-30) cc_final: 0.5800 (mt0) REVERT: Z 494 GLU cc_start: 0.5544 (tt0) cc_final: 0.5221 (mp0) outliers start: 98 outliers final: 69 residues processed: 495 average time/residue: 0.2050 time to fit residues: 166.6747 Evaluate side-chains 471 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 393 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU 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 F residue 81 MET 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 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 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 246 LEU 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 390 VAL 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 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 465 ASP 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 316 THR Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 390 VAL 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 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 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 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 538 VAL Chi-restraints excluded: chain Z residue 160 LEU 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: chunk 158 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 371 optimal weight: 0.5980 chunk 337 optimal weight: 0.6980 chunk 239 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 429 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN D 92 ASN ** R 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 185 HIS ** 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 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125178 restraints weight = 50586.657| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.71 r_work: 0.3306 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34384 Z= 0.173 Angle : 0.591 11.735 46598 Z= 0.301 Chirality : 0.044 0.176 5513 Planarity : 0.004 0.040 5991 Dihedral : 6.350 156.478 4917 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.31 % Favored : 95.56 % Rotamer: Outliers : 3.15 % Allowed : 18.53 % Favored : 78.32 % 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: -0.84 (0.13), residues: 4457 helix: 0.06 (0.11), residues: 2180 sheet: -1.30 (0.21), residues: 576 loop : -0.90 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 42 TYR 0.017 0.002 TYR U 57 PHE 0.029 0.001 PHE P 122 TRP 0.014 0.002 TRP V 73 HIS 0.004 0.001 HIS T 319 Details of bonding type rmsd covalent geometry : bond 0.00402 (34384) covalent geometry : angle 0.59060 (46598) hydrogen bonds : bond 0.03654 ( 1654) hydrogen bonds : angle 4.58785 ( 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 517 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 405 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.4782 (OUTLIER) cc_final: 0.4370 (mt) REVERT: D 104 LEU cc_start: 0.2321 (mt) cc_final: 0.1861 (tt) REVERT: D 113 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4724 (tp) REVERT: J 61 MET cc_start: 0.2144 (mmm) cc_final: 0.1927 (mmm) REVERT: J 95 ILE cc_start: 0.1804 (OUTLIER) cc_final: 0.0937 (tt) REVERT: J 119 LEU cc_start: 0.5163 (tt) cc_final: 0.4616 (pt) REVERT: Q 45 ILE cc_start: 0.6513 (mp) cc_final: 0.6234 (mp) REVERT: Q 63 TYR cc_start: 0.6747 (m-80) cc_final: 0.6442 (m-80) REVERT: Q 70 PRO cc_start: 0.3671 (Cg_endo) cc_final: 0.3116 (Cg_exo) REVERT: R 119 HIS cc_start: 0.5544 (m-70) cc_final: 0.5017 (m90) REVERT: R 139 ASN cc_start: 0.2066 (p0) cc_final: 0.1712 (p0) REVERT: S 158 TYR cc_start: 0.3783 (t80) cc_final: 0.3516 (t80) REVERT: S 191 GLN cc_start: 0.5945 (mm-40) cc_final: 0.5647 (mm110) REVERT: T 227 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8036 (ttp-110) REVERT: T 325 ASP cc_start: 0.8668 (t0) cc_final: 0.8306 (t0) REVERT: T 558 LYS cc_start: 0.8050 (mppt) cc_final: 0.7613 (mmmm) REVERT: U 282 MET cc_start: 0.9195 (mmt) cc_final: 0.8876 (mmt) REVERT: V 50 LYS cc_start: 0.8100 (tptp) cc_final: 0.7817 (tmmt) REVERT: V 112 ASP cc_start: 0.8448 (p0) cc_final: 0.8219 (p0) REVERT: V 445 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7276 (t) REVERT: V 506 LYS cc_start: 0.7017 (mmtm) cc_final: 0.6635 (mmmt) REVERT: X 488 MET cc_start: 0.8396 (mmt) cc_final: 0.7904 (ttp) REVERT: X 497 GLU cc_start: 0.7416 (mp0) cc_final: 0.7182 (mp0) REVERT: X 541 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.4053 (tp30) REVERT: Y 193 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8948 (tt) REVERT: Y 195 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: Y 199 ASN cc_start: 0.8564 (m-40) cc_final: 0.7806 (m110) REVERT: Y 538 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.7146 (t) REVERT: Y 547 GLU cc_start: 0.8111 (mp0) cc_final: 0.7899 (mt-10) REVERT: Z 429 ASP cc_start: 0.6301 (OUTLIER) cc_final: 0.5994 (t70) REVERT: Z 448 GLN cc_start: 0.6518 (tm-30) cc_final: 0.5794 (mt0) REVERT: Z 451 GLU cc_start: 0.6856 (tp30) cc_final: 0.6078 (tp30) outliers start: 112 outliers final: 81 residues processed: 490 average time/residue: 0.2029 time to fit residues: 163.0798 Evaluate side-chains 475 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 385 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE 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 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 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 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 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 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 390 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 440 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 364 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 344 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN R 181 ASN ** S 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN U 539 ASN ** 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 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126063 restraints weight = 50560.573| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.66 r_work: 0.3309 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34384 Z= 0.175 Angle : 0.594 13.076 46598 Z= 0.303 Chirality : 0.045 0.178 5513 Planarity : 0.004 0.040 5991 Dihedral : 6.331 150.886 4917 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 3.20 % Allowed : 19.07 % Favored : 77.73 % 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: -0.77 (0.13), residues: 4457 helix: 0.12 (0.11), residues: 2168 sheet: -1.30 (0.21), residues: 581 loop : -0.87 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 199 TYR 0.015 0.002 TYR V 324 PHE 0.031 0.002 PHE P 122 TRP 0.016 0.002 TRP V 73 HIS 0.005 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00409 (34384) covalent geometry : angle 0.59391 (46598) hydrogen bonds : bond 0.03664 ( 1654) hydrogen bonds : angle 4.56738 ( 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 500 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 386 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6024 (tpp) cc_final: 0.4739 (mmt) REVERT: B 118 LEU cc_start: 0.4841 (OUTLIER) cc_final: 0.4394 (mt) REVERT: D 81 MET cc_start: 0.6292 (tmm) cc_final: 0.6029 (tmm) REVERT: D 104 LEU cc_start: 0.2491 (mt) cc_final: 0.1991 (tt) REVERT: J 95 ILE cc_start: 0.1711 (OUTLIER) cc_final: 0.0806 (tt) REVERT: P 81 PHE cc_start: 0.7921 (m-10) cc_final: 0.7557 (m-10) REVERT: Q 45 ILE cc_start: 0.6577 (mp) cc_final: 0.6293 (mp) REVERT: Q 63 TYR cc_start: 0.6815 (m-80) cc_final: 0.6515 (m-80) REVERT: Q 70 PRO cc_start: 0.3502 (Cg_endo) cc_final: 0.2959 (Cg_exo) REVERT: R 119 HIS cc_start: 0.5631 (m-70) cc_final: 0.5048 (m90) REVERT: S 72 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7248 (mt0) REVERT: S 191 GLN cc_start: 0.5754 (mm-40) cc_final: 0.5518 (mm110) REVERT: T 227 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8038 (ttp-110) REVERT: T 325 ASP cc_start: 0.8658 (t0) cc_final: 0.8310 (t0) REVERT: T 558 LYS cc_start: 0.8053 (mppt) cc_final: 0.7710 (mmmm) REVERT: U 282 MET cc_start: 0.9179 (mmt) cc_final: 0.8895 (mmt) REVERT: V 50 LYS cc_start: 0.8117 (tptp) cc_final: 0.7843 (tmmt) REVERT: V 445 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7254 (t) REVERT: V 506 LYS cc_start: 0.6996 (mmtm) cc_final: 0.6629 (mmmt) REVERT: X 488 MET cc_start: 0.8411 (mmt) cc_final: 0.7920 (ttp) REVERT: X 497 GLU cc_start: 0.7378 (mp0) cc_final: 0.7167 (mp0) REVERT: X 541 GLU cc_start: 0.4791 (OUTLIER) cc_final: 0.4181 (tp30) REVERT: Y 193 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8939 (tt) REVERT: Y 195 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: Y 199 ASN cc_start: 0.8565 (m-40) cc_final: 0.7823 (m110) REVERT: Y 538 VAL cc_start: 0.7325 (OUTLIER) cc_final: 0.7102 (t) REVERT: Z 429 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.5933 (t70) REVERT: Z 448 GLN cc_start: 0.6443 (tm-30) cc_final: 0.5891 (mt0) REVERT: Z 451 GLU cc_start: 0.6897 (tp30) cc_final: 0.6283 (tp30) outliers start: 114 outliers final: 94 residues processed: 473 average time/residue: 0.2059 time to fit residues: 160.9518 Evaluate side-chains 481 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 378 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL 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 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 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 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 72 GLN 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 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 185 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 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 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 390 VAL 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 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 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 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: chunk 241 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 415 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 376 optimal weight: 0.7980 chunk 386 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 346 optimal weight: 0.0870 chunk 177 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 71 GLN Q 40 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127918 restraints weight = 50284.708| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.59 r_work: 0.3349 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3011 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= 0.126 Angle : 0.565 11.540 46598 Z= 0.286 Chirality : 0.043 0.204 5513 Planarity : 0.004 0.040 5991 Dihedral : 6.101 143.216 4917 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 2.98 % Allowed : 19.74 % Favored : 77.28 % 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: -0.58 (0.13), residues: 4457 helix: 0.28 (0.12), residues: 2174 sheet: -1.18 (0.21), residues: 577 loop : -0.80 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 51 TYR 0.015 0.001 TYR U 57 PHE 0.022 0.001 PHE J 126 TRP 0.012 0.001 TRP U 73 HIS 0.003 0.001 HIS S 250 Details of bonding type rmsd covalent geometry : bond 0.00288 (34384) covalent geometry : angle 0.56463 (46598) hydrogen bonds : bond 0.03383 ( 1654) hydrogen bonds : angle 4.44296 ( 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 516 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 410 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6037 (tpp) cc_final: 0.4855 (mmt) REVERT: B 118 LEU cc_start: 0.4723 (OUTLIER) cc_final: 0.4421 (mt) REVERT: D 69 ILE cc_start: 0.6920 (tp) cc_final: 0.6484 (tp) REVERT: D 81 MET cc_start: 0.6185 (tmm) cc_final: 0.5930 (tmm) REVERT: D 104 LEU cc_start: 0.2512 (mt) cc_final: 0.1977 (tt) REVERT: D 113 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.4777 (tp) REVERT: J 95 ILE cc_start: 0.1801 (OUTLIER) cc_final: 0.0950 (tt) REVERT: P 81 PHE cc_start: 0.7903 (m-10) cc_final: 0.7539 (m-10) REVERT: Q 45 ILE cc_start: 0.6571 (mp) cc_final: 0.6278 (mp) REVERT: Q 63 TYR cc_start: 0.6664 (m-80) cc_final: 0.6417 (m-80) REVERT: Q 70 PRO cc_start: 0.3529 (Cg_endo) cc_final: 0.2973 (Cg_exo) REVERT: R 119 HIS cc_start: 0.5594 (m-70) cc_final: 0.5125 (m90) REVERT: S 191 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5495 (mm110) REVERT: T 325 ASP cc_start: 0.8648 (t0) cc_final: 0.8292 (t0) REVERT: T 481 THR cc_start: 0.8783 (m) cc_final: 0.8541 (p) REVERT: T 558 LYS cc_start: 0.8034 (mppt) cc_final: 0.7613 (mmmm) REVERT: U 220 ARG cc_start: 0.8762 (mpp80) cc_final: 0.8415 (mtm180) REVERT: V 445 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7315 (t) REVERT: V 506 LYS cc_start: 0.6938 (mmtm) cc_final: 0.6663 (mmmt) REVERT: X 219 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8040 (mt-10) REVERT: X 488 MET cc_start: 0.8392 (mmt) cc_final: 0.7907 (ttp) REVERT: X 541 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.4193 (tp30) REVERT: Y 193 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8886 (tt) REVERT: Y 195 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: Y 199 ASN cc_start: 0.8491 (m-40) cc_final: 0.7838 (m110) REVERT: Y 538 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.7024 (t) REVERT: Z 178 LYS cc_start: 0.8886 (mttt) cc_final: 0.8550 (mtpt) REVERT: Z 422 MET cc_start: 0.6768 (mtm) cc_final: 0.6440 (mtp) REVERT: Z 429 ASP cc_start: 0.6312 (OUTLIER) cc_final: 0.5970 (t70) REVERT: Z 448 GLN cc_start: 0.6370 (tm-30) cc_final: 0.5819 (mt0) REVERT: Z 451 GLU cc_start: 0.6944 (tp30) cc_final: 0.6194 (tp30) outliers start: 106 outliers final: 87 residues processed: 488 average time/residue: 0.2076 time to fit residues: 166.8489 Evaluate side-chains 481 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 385 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain F residue 81 MET 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 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 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 223 VAL Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 271 MET Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 120 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 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 405 GLN 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 316 THR 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 390 VAL 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 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 74 LEU 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 390 ASN Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 332 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 384 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 418 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN T 452 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.158589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124585 restraints weight = 50383.200| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.68 r_work: 0.3280 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 34384 Z= 0.222 Angle : 0.643 11.707 46598 Z= 0.327 Chirality : 0.046 0.209 5513 Planarity : 0.004 0.043 5991 Dihedral : 6.419 131.707 4917 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.04 % Rotamer: Outliers : 3.06 % Allowed : 20.02 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4457 helix: 0.08 (0.11), residues: 2173 sheet: -1.31 (0.21), residues: 584 loop : -0.80 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 199 TYR 0.018 0.002 TYR V 324 PHE 0.036 0.002 PHE P 122 TRP 0.019 0.002 TRP U 73 HIS 0.004 0.001 HIS T 319 Details of bonding type rmsd covalent geometry : bond 0.00522 (34384) covalent geometry : angle 0.64292 (46598) hydrogen bonds : bond 0.03979 ( 1654) hydrogen bonds : angle 4.68166 ( 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 498 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 389 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 GLU cc_start: 0.4434 (tp30) cc_final: 0.4233 (tp30) REVERT: B 118 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4379 (pp) REVERT: D 81 MET cc_start: 0.6448 (tmm) cc_final: 0.6216 (tmm) REVERT: D 113 ILE cc_start: 0.5369 (OUTLIER) cc_final: 0.5040 (tp) REVERT: G 61 MET cc_start: 0.5226 (tmm) cc_final: 0.4657 (tmm) REVERT: J 95 ILE cc_start: 0.1791 (OUTLIER) cc_final: 0.0801 (tt) REVERT: J 119 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4657 (pt) REVERT: P 110 LYS cc_start: 0.7207 (ptpp) cc_final: 0.6925 (ptmm) REVERT: Q 63 TYR cc_start: 0.6837 (m-80) cc_final: 0.6559 (m-80) REVERT: Q 70 PRO cc_start: 0.3639 (Cg_endo) cc_final: 0.3063 (Cg_exo) REVERT: Q 71 LYS cc_start: 0.5605 (mttp) cc_final: 0.4689 (ttpt) REVERT: R 97 TYR cc_start: 0.6028 (m-80) cc_final: 0.5806 (m-80) REVERT: R 119 HIS cc_start: 0.5696 (m-70) cc_final: 0.5109 (m90) REVERT: S 72 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: S 141 SER cc_start: 0.7503 (p) cc_final: 0.7210 (p) REVERT: S 190 TYR cc_start: 0.5709 (m-80) cc_final: 0.5201 (m-80) REVERT: T 227 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8059 (ttp-110) REVERT: T 325 ASP cc_start: 0.8736 (t0) cc_final: 0.8371 (t0) REVERT: T 558 LYS cc_start: 0.8068 (mppt) cc_final: 0.7701 (mmmm) REVERT: V 445 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7304 (t) REVERT: V 456 VAL cc_start: 0.6314 (OUTLIER) cc_final: 0.5791 (m) REVERT: V 506 LYS cc_start: 0.7028 (mmtm) cc_final: 0.6637 (mmmt) REVERT: X 488 MET cc_start: 0.8438 (mmt) cc_final: 0.7931 (ttp) REVERT: X 541 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.4149 (tp30) REVERT: Y 193 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8991 (tt) REVERT: Y 195 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: Y 538 VAL cc_start: 0.7394 (OUTLIER) cc_final: 0.7162 (t) REVERT: Z 429 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6056 (t70) REVERT: Z 448 GLN cc_start: 0.6572 (tm-30) cc_final: 0.5835 (mt0) REVERT: Z 451 GLU cc_start: 0.6914 (tp30) cc_final: 0.6287 (tp30) REVERT: Z 494 GLU cc_start: 0.5786 (tt0) cc_final: 0.5316 (mp0) outliers start: 109 outliers final: 91 residues processed: 476 average time/residue: 0.2056 time to fit residues: 161.3861 Evaluate side-chains 478 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 375 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL 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 D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE 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 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 65 VAL 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 72 GLN 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 201 ILE Chi-restraints excluded: chain S residue 212 SER 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 120 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 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 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 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 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 74 LEU Chi-restraints excluded: chain Z residue 131 GLU 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 390 ASN Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 146 optimal weight: 3.9990 chunk 399 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 413 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 434 optimal weight: 0.9990 chunk 364 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 71 GLN R 181 ASN ** 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** S 191 GLN 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** Z 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.160829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126697 restraints weight = 50437.853| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.61 r_work: 0.3318 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34384 Z= 0.154 Angle : 0.597 11.356 46598 Z= 0.302 Chirality : 0.044 0.204 5513 Planarity : 0.004 0.042 5991 Dihedral : 6.168 121.198 4917 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 2.86 % Allowed : 20.19 % Favored : 76.94 % 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: -0.63 (0.13), residues: 4457 helix: 0.21 (0.11), residues: 2176 sheet: -1.22 (0.21), residues: 577 loop : -0.76 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 199 TYR 0.015 0.001 TYR U 57 PHE 0.027 0.001 PHE P 122 TRP 0.014 0.001 TRP U 73 HIS 0.004 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00359 (34384) covalent geometry : angle 0.59651 (46598) hydrogen bonds : bond 0.03581 ( 1654) hydrogen bonds : angle 4.54919 ( 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 494 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 392 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 GLU cc_start: 0.4268 (tp30) cc_final: 0.4034 (tp30) REVERT: B 118 LEU cc_start: 0.5029 (OUTLIER) cc_final: 0.4537 (mt) REVERT: D 81 MET cc_start: 0.6237 (tmm) cc_final: 0.6026 (tmm) REVERT: G 61 MET cc_start: 0.5196 (tmm) cc_final: 0.4677 (tmm) REVERT: J 95 ILE cc_start: 0.1660 (OUTLIER) cc_final: 0.0789 (tt) REVERT: J 119 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4621 (pt) REVERT: P 110 LYS cc_start: 0.7204 (ptpp) cc_final: 0.6996 (ptmm) REVERT: Q 70 PRO cc_start: 0.3688 (Cg_endo) cc_final: 0.3082 (Cg_exo) REVERT: Q 71 LYS cc_start: 0.5557 (mttp) cc_final: 0.4737 (ttpt) REVERT: R 119 HIS cc_start: 0.5540 (m-70) cc_final: 0.4992 (m90) REVERT: S 72 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: S 158 TYR cc_start: 0.4032 (t80) cc_final: 0.3540 (t80) REVERT: S 190 TYR cc_start: 0.5375 (m-80) cc_final: 0.5017 (m-80) REVERT: T 325 ASP cc_start: 0.8637 (t0) cc_final: 0.8261 (t0) REVERT: T 558 LYS cc_start: 0.8056 (mppt) cc_final: 0.7697 (mmmm) REVERT: U 220 ARG cc_start: 0.8775 (mpp80) cc_final: 0.8433 (mtm180) REVERT: V 445 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7229 (t) REVERT: V 456 VAL cc_start: 0.6241 (OUTLIER) cc_final: 0.5683 (m) REVERT: V 506 LYS cc_start: 0.6933 (mmtm) cc_final: 0.6621 (mmmt) REVERT: X 219 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8062 (mt-10) REVERT: X 488 MET cc_start: 0.8431 (mmt) cc_final: 0.7935 (ttp) REVERT: X 511 GLU cc_start: 0.3672 (OUTLIER) cc_final: 0.3393 (pm20) REVERT: Y 193 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8904 (tt) REVERT: Y 195 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: Y 199 ASN cc_start: 0.8542 (m-40) cc_final: 0.7834 (m110) REVERT: Y 538 VAL cc_start: 0.7333 (OUTLIER) cc_final: 0.7114 (t) REVERT: Z 178 LYS cc_start: 0.8862 (mttt) cc_final: 0.8536 (mtpt) REVERT: Z 429 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.6079 (t70) REVERT: Z 448 GLN cc_start: 0.6370 (tm-30) cc_final: 0.5832 (mt0) REVERT: Z 451 GLU cc_start: 0.6928 (tp30) cc_final: 0.6314 (tp30) REVERT: Z 494 GLU cc_start: 0.5709 (tt0) cc_final: 0.5294 (mp0) outliers start: 102 outliers final: 84 residues processed: 470 average time/residue: 0.2059 time to fit residues: 159.9177 Evaluate side-chains 482 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 387 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 72 GLN 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 212 SER 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 120 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 430 VAL Chi-restraints excluded: chain T residue 473 VAL 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 399 ILE Chi-restraints excluded: chain U residue 405 GLN 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 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 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 511 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 74 LEU 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 390 ASN Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 3.9990 chunk 323 optimal weight: 0.5980 chunk 384 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 410 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 330 optimal weight: 9.9990 chunk 348 optimal weight: 1.9990 chunk 396 optimal weight: 0.9980 chunk 407 optimal weight: 4.9990 chunk 387 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN H 98 GLN ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 GLN R 78 HIS T 452 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN X 144 HIS ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129197 restraints weight = 50304.217| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.55 r_work: 0.3372 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34384 Z= 0.116 Angle : 0.560 11.071 46598 Z= 0.284 Chirality : 0.043 0.185 5513 Planarity : 0.004 0.041 5991 Dihedral : 5.790 96.040 4917 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.89 % Rotamer: Outliers : 2.39 % Allowed : 20.92 % Favored : 76.69 % 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: -0.40 (0.13), residues: 4457 helix: 0.40 (0.12), residues: 2178 sheet: -1.12 (0.21), residues: 586 loop : -0.65 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 199 TYR 0.015 0.001 TYR U 57 PHE 0.023 0.001 PHE A 107 TRP 0.009 0.001 TRP U 73 HIS 0.003 0.001 HIS S 250 Details of bonding type rmsd covalent geometry : bond 0.00264 (34384) covalent geometry : angle 0.56010 (46598) hydrogen bonds : bond 0.03271 ( 1654) hydrogen bonds : angle 4.36776 ( 4800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9809.27 seconds wall clock time: 168 minutes 5.34 seconds (10085.34 seconds total)