Starting phenix.real_space_refine on Thu Jun 26 06:37:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ve2_21152/06_2025/6ve2_21152.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ve2_21152/06_2025/6ve2_21152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ve2_21152/06_2025/6ve2_21152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ve2_21152/06_2025/6ve2_21152.map" model { file = "/net/cci-nas-00/data/ceres_data/6ve2_21152/06_2025/6ve2_21152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ve2_21152/06_2025/6ve2_21152.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.072 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: 3 Type Number sf(0) Gaussians C 17892 2.51 5 N 6153 2.21 5 O 6153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "O" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1102 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 9, 'TRANS': 215} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 7, 'ASN:plan1': 8, 'ASP:plan': 16, 'PHE:plan': 8, 'GLU:plan': 15, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 352 Restraints were copied for chains: Q, P, S, R, U, T, C, B, E, D, G, F, I, H, K, J, M, L, N Time building chain proxies: 7.76, per 1000 atoms: 0.26 Number of scatterers: 30198 At special positions: 0 Unit cell: (179.8, 179.8, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 6153 8.00 N 6153 7.00 C 17892 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: 9.41 Conformation dependent library (CDL) restraints added in 6.0 seconds 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11172 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 71 sheets defined 23.1% alpha, 59.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.703A pdb=" N GLY A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.699A pdb=" N LYS A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 removed outlier: 3.804A pdb=" N VAL A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.277A pdb=" N ARG A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'B' and resid 12 through 27 removed outlier: 3.702A pdb=" N GLY B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.698A pdb=" N LYS B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.803A pdb=" N VAL B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.715A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'C' and resid 12 through 27 removed outlier: 3.702A pdb=" N GLY C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.699A pdb=" N LYS C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 3.803A pdb=" N VAL C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 139 " --> pdb=" O PHE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG C 297 " --> pdb=" O PRO C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'D' and resid 12 through 27 removed outlier: 3.702A pdb=" N GLY D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.698A pdb=" N LYS D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 139 " --> pdb=" O PHE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG D 297 " --> pdb=" O PRO D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'E' and resid 12 through 27 removed outlier: 3.702A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 59 Processing helix chain 'E' and resid 103 through 115 removed outlier: 3.698A pdb=" N LYS E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 removed outlier: 3.801A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 246 Processing helix chain 'E' and resid 286 through 292 removed outlier: 3.715A pdb=" N LEU E 292 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG E 297 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'F' and resid 12 through 27 removed outlier: 3.701A pdb=" N GLY F 27 " --> pdb=" O VAL F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 59 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.699A pdb=" N LYS F 107 " --> pdb=" O ASN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG F 297 " --> pdb=" O PRO F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'G' and resid 12 through 27 removed outlier: 3.700A pdb=" N GLY G 27 " --> pdb=" O VAL G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 59 Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.699A pdb=" N LYS G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL G 136 " --> pdb=" O PRO G 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 246 Processing helix chain 'G' and resid 286 through 292 removed outlier: 3.715A pdb=" N LEU G 292 " --> pdb=" O PHE G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 297 removed outlier: 4.277A pdb=" N ARG G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 325 Processing helix chain 'H' and resid 12 through 27 removed outlier: 3.702A pdb=" N GLY H 27 " --> pdb=" O VAL H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 59 Processing helix chain 'H' and resid 103 through 115 removed outlier: 3.697A pdb=" N LYS H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL H 136 " --> pdb=" O PRO H 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 246 Processing helix chain 'H' and resid 286 through 292 removed outlier: 3.713A pdb=" N LEU H 292 " --> pdb=" O PHE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 325 Processing helix chain 'I' and resid 12 through 27 removed outlier: 3.702A pdb=" N GLY I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 59 Processing helix chain 'I' and resid 103 through 115 removed outlier: 3.697A pdb=" N LYS I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL I 136 " --> pdb=" O PRO I 132 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 246 Processing helix chain 'I' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU I 292 " --> pdb=" O PHE I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG I 297 " --> pdb=" O PRO I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 325 Processing helix chain 'J' and resid 12 through 27 removed outlier: 3.702A pdb=" N GLY J 27 " --> pdb=" O VAL J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 59 Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.698A pdb=" N LYS J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 246 Processing helix chain 'J' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU J 292 " --> pdb=" O PHE J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG J 297 " --> pdb=" O PRO J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 325 Processing helix chain 'K' and resid 12 through 27 removed outlier: 3.701A pdb=" N GLY K 27 " --> pdb=" O VAL K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 59 Processing helix chain 'K' and resid 103 through 115 removed outlier: 3.699A pdb=" N LYS K 107 " --> pdb=" O ASN K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL K 136 " --> pdb=" O PRO K 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 246 Processing helix chain 'K' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 297 removed outlier: 4.277A pdb=" N ARG K 297 " --> pdb=" O PRO K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'L' and resid 12 through 27 removed outlier: 3.701A pdb=" N GLY L 27 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 59 Processing helix chain 'L' and resid 103 through 115 removed outlier: 3.698A pdb=" N LYS L 107 " --> pdb=" O ASN L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL L 136 " --> pdb=" O PRO L 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 286 through 292 removed outlier: 3.715A pdb=" N LEU L 292 " --> pdb=" O PHE L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 297 removed outlier: 4.278A pdb=" N ARG L 297 " --> pdb=" O PRO L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 325 Processing helix chain 'M' and resid 12 through 27 removed outlier: 3.703A pdb=" N GLY M 27 " --> pdb=" O VAL M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 103 through 115 removed outlier: 3.697A pdb=" N LYS M 107 " --> pdb=" O ASN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL M 136 " --> pdb=" O PRO M 132 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY M 139 " --> pdb=" O PHE M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 246 Processing helix chain 'M' and resid 286 through 292 removed outlier: 3.715A pdb=" N LEU M 292 " --> pdb=" O PHE M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 297 removed outlier: 4.277A pdb=" N ARG M 297 " --> pdb=" O PRO M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 325 Processing helix chain 'N' and resid 12 through 27 removed outlier: 3.701A pdb=" N GLY N 27 " --> pdb=" O VAL N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 103 through 115 removed outlier: 3.698A pdb=" N LYS N 107 " --> pdb=" O ASN N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 142 removed outlier: 3.802A pdb=" N VAL N 136 " --> pdb=" O PRO N 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY N 139 " --> pdb=" O PHE N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 Processing helix chain 'N' and resid 286 through 292 removed outlier: 3.714A pdb=" N LEU N 292 " --> pdb=" O PHE N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 297 removed outlier: 4.277A pdb=" N ARG N 297 " --> pdb=" O PRO N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 325 Processing helix chain 'O' and resid 2 through 12 Processing helix chain 'O' and resid 17 through 24 removed outlier: 4.151A pdb=" N PHE O 21 " --> pdb=" O ASP O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 52 removed outlier: 4.112A pdb=" N ASP O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 124 removed outlier: 3.905A pdb=" N PHE O 123 " --> pdb=" O ASN O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 165 Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 17 through 24 removed outlier: 4.151A pdb=" N PHE P 21 " --> pdb=" O ASP P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 52 removed outlier: 4.112A pdb=" N ASP P 51 " --> pdb=" O GLY P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.906A pdb=" N PHE P 123 " --> pdb=" O ASN P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 165 Processing helix chain 'Q' and resid 2 through 12 Processing helix chain 'Q' and resid 17 through 24 removed outlier: 4.152A pdb=" N PHE Q 21 " --> pdb=" O ASP Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 52 removed outlier: 4.113A pdb=" N ASP Q 51 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 124 removed outlier: 3.904A pdb=" N PHE Q 123 " --> pdb=" O ASN Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 165 Processing helix chain 'R' and resid 2 through 12 Processing helix chain 'R' and resid 17 through 24 removed outlier: 4.152A pdb=" N PHE R 21 " --> pdb=" O ASP R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 52 removed outlier: 4.112A pdb=" N ASP R 51 " --> pdb=" O GLY R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 124 removed outlier: 3.907A pdb=" N PHE R 123 " --> pdb=" O ASN R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 165 Processing helix chain 'S' and resid 2 through 12 Processing helix chain 'S' and resid 17 through 24 removed outlier: 4.152A pdb=" N PHE S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 52 removed outlier: 4.111A pdb=" N ASP S 51 " --> pdb=" O GLY S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 124 removed outlier: 3.906A pdb=" N PHE S 123 " --> pdb=" O ASN S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 155 through 165 Processing helix chain 'T' and resid 2 through 12 Processing helix chain 'T' and resid 17 through 24 removed outlier: 4.151A pdb=" N PHE T 21 " --> pdb=" O ASP T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 52 removed outlier: 4.110A pdb=" N ASP T 51 " --> pdb=" O GLY T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 120 through 124 removed outlier: 3.906A pdb=" N PHE T 123 " --> pdb=" O ASN T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 155 through 165 Processing helix chain 'U' and resid 2 through 12 Processing helix chain 'U' and resid 17 through 24 removed outlier: 4.152A pdb=" N PHE U 21 " --> pdb=" O ASP U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 52 removed outlier: 4.110A pdb=" N ASP U 51 " --> pdb=" O GLY U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 124 removed outlier: 3.904A pdb=" N PHE U 123 " --> pdb=" O ASN U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 155 through 165 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL A 84 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG A 300 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 272 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 315 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL A 270 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 271 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 166 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.500A pdb=" N ALA B 69 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL B 84 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG B 300 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 272 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 315 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 270 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 271 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 166 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 152 removed outlier: 3.500A pdb=" N ALA C 69 " --> pdb=" O PRO C 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL C 84 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG C 300 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 272 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 315 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL C 270 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE C 271 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 166 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 146 through 152 Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL D 84 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG D 300 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 272 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU D 315 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 270 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 271 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 166 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 146 through 152 Processing sheet with id=AB2, first strand: chain 'E' and resid 93 through 95 removed outlier: 5.131A pdb=" N VAL E 84 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG E 300 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY E 272 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU E 315 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL E 270 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE E 271 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU F 166 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 146 through 152 Processing sheet with id=AB4, first strand: chain 'F' and resid 93 through 95 removed outlier: 5.131A pdb=" N VAL F 84 " --> pdb=" O ARG F 300 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG F 300 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY F 272 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU F 315 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL F 270 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE F 271 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU G 166 " --> pdb=" O LYS F 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 146 through 152 Processing sheet with id=AB6, first strand: chain 'G' and resid 93 through 95 removed outlier: 5.132A pdb=" N VAL G 84 " --> pdb=" O ARG G 300 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG G 300 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY G 272 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU G 315 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL G 270 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE G 271 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU H 166 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 146 through 152 Processing sheet with id=AB8, first strand: chain 'H' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL H 84 " --> pdb=" O ARG H 300 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG H 300 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY H 272 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU H 315 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL H 270 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE H 271 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU I 166 " --> pdb=" O LYS H 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 146 through 152 Processing sheet with id=AC1, first strand: chain 'I' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL I 84 " --> pdb=" O ARG I 300 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG I 300 " --> pdb=" O VAL I 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY I 272 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU I 315 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL I 270 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE I 271 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU J 166 " --> pdb=" O LYS I 285 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 146 through 152 Processing sheet with id=AC3, first strand: chain 'J' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL J 84 " --> pdb=" O ARG J 300 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG J 300 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY J 272 " --> pdb=" O VAL J 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU J 315 " --> pdb=" O VAL J 270 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL J 270 " --> pdb=" O LEU J 315 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE J 271 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU K 166 " --> pdb=" O LYS J 285 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 146 through 152 Processing sheet with id=AC5, first strand: chain 'K' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL K 84 " --> pdb=" O ARG K 300 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG K 300 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY K 272 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU K 315 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL K 270 " --> pdb=" O LEU K 315 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE K 271 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU L 166 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 146 through 152 removed outlier: 3.500A pdb=" N ALA L 69 " --> pdb=" O PRO L 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 93 through 95 removed outlier: 5.130A pdb=" N VAL L 84 " --> pdb=" O ARG L 300 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG L 300 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY L 272 " --> pdb=" O VAL L 313 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU L 315 " --> pdb=" O VAL L 270 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL L 270 " --> pdb=" O LEU L 315 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE L 271 " --> pdb=" O VAL M 180 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU M 166 " --> pdb=" O LYS L 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 146 through 152 Processing sheet with id=AC9, first strand: chain 'M' and resid 93 through 95 removed outlier: 5.131A pdb=" N VAL M 84 " --> pdb=" O ARG M 300 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG M 300 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY M 272 " --> pdb=" O VAL M 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU M 315 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL M 270 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE M 271 " --> pdb=" O VAL N 180 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU N 166 " --> pdb=" O LYS M 285 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 146 through 152 Processing sheet with id=AD2, first strand: chain 'N' and resid 93 through 95 removed outlier: 5.131A pdb=" N VAL N 84 " --> pdb=" O ARG N 300 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG N 300 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY N 272 " --> pdb=" O VAL N 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU N 315 " --> pdb=" O VAL N 270 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL N 270 " --> pdb=" O LEU N 315 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE N 271 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 166 " --> pdb=" O LYS N 285 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AD4, first strand: chain 'A' and resid 187 through 201 removed outlier: 3.910A pdb=" N ARG A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 252 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 252 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG D 228 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 228 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 252 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG F 228 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG G 228 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 252 " --> pdb=" O GLU H 194 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG H 228 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG I 228 " --> pdb=" O THR I 224 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE I 252 " --> pdb=" O GLU J 194 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG J 228 " --> pdb=" O THR J 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE J 252 " --> pdb=" O GLU K 194 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG K 228 " --> pdb=" O THR K 224 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE K 252 " --> pdb=" O GLU L 194 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG L 228 " --> pdb=" O THR L 224 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG M 228 " --> pdb=" O THR M 224 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE M 252 " --> pdb=" O GLU N 194 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AD6, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AD7, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AD8, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AD9, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AE1, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AE2, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AE3, first strand: chain 'E' and resid 117 through 119 Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 117 through 119 Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE8, first strand: chain 'H' and resid 2 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 117 through 119 Processing sheet with id=AF1, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 117 through 119 Processing sheet with id=AF3, first strand: chain 'J' and resid 2 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 117 through 119 Processing sheet with id=AF5, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AF6, first strand: chain 'K' and resid 117 through 119 Processing sheet with id=AF7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 117 through 119 Processing sheet with id=AF9, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AG1, first strand: chain 'M' and resid 117 through 119 Processing sheet with id=AG2, first strand: chain 'N' and resid 2 through 7 Processing sheet with id=AG3, first strand: chain 'N' and resid 117 through 119 Processing sheet with id=AG4, first strand: chain 'O' and resid 14 through 15 removed outlier: 3.580A pdb=" N PHE O 59 " --> pdb=" O ARG O 110 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG O 110 " --> pdb=" O PHE O 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 134 through 137 removed outlier: 3.654A pdb=" N THR O 153 " --> pdb=" O ILE O 137 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER O 206 " --> pdb=" O LEU O 154 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE O 170 " --> pdb=" O ARG O 192 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLY O 194 " --> pdb=" O LEU O 168 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU O 168 " --> pdb=" O GLY O 194 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 14 through 15 removed outlier: 3.581A pdb=" N PHE P 59 " --> pdb=" O ARG P 110 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG P 110 " --> pdb=" O PHE P 59 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 134 through 137 removed outlier: 3.654A pdb=" N THR P 153 " --> pdb=" O ILE P 137 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER P 206 " --> pdb=" O LEU P 154 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE P 170 " --> pdb=" O ARG P 192 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY P 194 " --> pdb=" O LEU P 168 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU P 168 " --> pdb=" O GLY P 194 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 14 through 15 removed outlier: 3.582A pdb=" N PHE Q 59 " --> pdb=" O ARG Q 110 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG Q 110 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 134 through 137 removed outlier: 3.654A pdb=" N THR Q 153 " --> pdb=" O ILE Q 137 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER Q 206 " --> pdb=" O LEU Q 154 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE Q 170 " --> pdb=" O ARG Q 192 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY Q 194 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU Q 168 " --> pdb=" O GLY Q 194 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 14 through 15 removed outlier: 3.581A pdb=" N PHE R 59 " --> pdb=" O ARG R 110 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG R 110 " --> pdb=" O PHE R 59 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 134 through 137 removed outlier: 3.654A pdb=" N THR R 153 " --> pdb=" O ILE R 137 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER R 206 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE R 170 " --> pdb=" O ARG R 192 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY R 194 " --> pdb=" O LEU R 168 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU R 168 " --> pdb=" O GLY R 194 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 14 through 15 removed outlier: 3.582A pdb=" N PHE S 59 " --> pdb=" O ARG S 110 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG S 110 " --> pdb=" O PHE S 59 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 134 through 137 removed outlier: 3.652A pdb=" N THR S 153 " --> pdb=" O ILE S 137 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER S 206 " --> pdb=" O LEU S 154 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE S 170 " --> pdb=" O ARG S 192 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY S 194 " --> pdb=" O LEU S 168 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU S 168 " --> pdb=" O GLY S 194 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 14 through 15 removed outlier: 3.580A pdb=" N PHE T 59 " --> pdb=" O ARG T 110 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG T 110 " --> pdb=" O PHE T 59 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 134 through 137 removed outlier: 3.653A pdb=" N THR T 153 " --> pdb=" O ILE T 137 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER T 206 " --> pdb=" O LEU T 154 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE T 170 " --> pdb=" O ARG T 192 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY T 194 " --> pdb=" O LEU T 168 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU T 168 " --> pdb=" O GLY T 194 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'U' and resid 14 through 15 removed outlier: 3.581A pdb=" N PHE U 59 " --> pdb=" O ARG U 110 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG U 110 " --> pdb=" O PHE U 59 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 134 through 137 removed outlier: 3.653A pdb=" N THR U 153 " --> pdb=" O ILE U 137 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER U 206 " --> pdb=" O LEU U 154 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE U 170 " --> pdb=" O ARG U 192 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY U 194 " --> pdb=" O LEU U 168 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU U 168 " --> pdb=" O GLY U 194 " (cutoff:3.500A) 3265 hydrogen bonds defined for protein. 9042 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: 19.37 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 6153 1.29 - 1.36: 6118 1.36 - 1.42: 0 1.42 - 1.49: 6167 1.49 - 1.55: 11725 Bond restraints: 30163 Sorted by residual: bond pdb=" N THR G 208 " pdb=" CA THR G 208 " ideal model delta sigma weight residual 1.463 1.436 0.027 1.31e-02 5.83e+03 4.36e+00 bond pdb=" N THR A 208 " pdb=" CA THR A 208 " ideal model delta sigma weight residual 1.463 1.436 0.027 1.31e-02 5.83e+03 4.26e+00 bond pdb=" N THR I 208 " pdb=" CA THR I 208 " ideal model delta sigma weight residual 1.463 1.436 0.027 1.31e-02 5.83e+03 4.25e+00 bond pdb=" N THR J 208 " pdb=" CA THR J 208 " ideal model delta sigma weight residual 1.463 1.436 0.027 1.31e-02 5.83e+03 4.23e+00 bond pdb=" CA ALA M 205 " pdb=" CB ALA M 205 " ideal model delta sigma weight residual 1.531 1.463 0.067 3.28e-02 9.30e+02 4.22e+00 ... (remaining 30158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 38595 2.15 - 4.30: 2721 4.30 - 6.45: 411 6.45 - 8.60: 77 8.60 - 10.74: 28 Bond angle restraints: 41832 Sorted by residual: angle pdb=" N THR F 208 " pdb=" CA THR F 208 " pdb=" C THR F 208 " ideal model delta sigma weight residual 108.56 97.82 10.74 1.74e+00 3.30e-01 3.81e+01 angle pdb=" N THR H 208 " pdb=" CA THR H 208 " pdb=" C THR H 208 " ideal model delta sigma weight residual 108.56 97.82 10.74 1.74e+00 3.30e-01 3.81e+01 angle pdb=" N THR C 208 " pdb=" CA THR C 208 " pdb=" C THR C 208 " ideal model delta sigma weight residual 108.56 97.83 10.73 1.74e+00 3.30e-01 3.80e+01 angle pdb=" N THR G 208 " pdb=" CA THR G 208 " pdb=" C THR G 208 " ideal model delta sigma weight residual 108.56 97.84 10.72 1.74e+00 3.30e-01 3.79e+01 angle pdb=" N THR J 208 " pdb=" CA THR J 208 " pdb=" C THR J 208 " ideal model delta sigma weight residual 108.56 97.85 10.71 1.74e+00 3.30e-01 3.79e+01 ... (remaining 41827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.74: 13632 3.74 - 7.48: 2769 7.48 - 11.22: 705 11.22 - 14.96: 164 14.96 - 18.70: 20 Dihedral angle restraints: 17290 sinusoidal: 0 harmonic: 17290 Sorted by residual: dihedral pdb=" CA VAL O 86 " pdb=" C VAL O 86 " pdb=" N VAL O 87 " pdb=" CA VAL O 87 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA VAL U 86 " pdb=" C VAL U 86 " pdb=" N VAL U 87 " pdb=" CA VAL U 87 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA VAL P 86 " pdb=" C VAL P 86 " pdb=" N VAL P 87 " pdb=" CA VAL P 87 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 17287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4004 0.069 - 0.137: 1329 0.137 - 0.206: 188 0.206 - 0.275: 37 0.275 - 0.343: 28 Chirality restraints: 5586 Sorted by residual: chirality pdb=" CA SER N 203 " pdb=" N SER N 203 " pdb=" C SER N 203 " pdb=" CB SER N 203 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA SER J 203 " pdb=" N SER J 203 " pdb=" C SER J 203 " pdb=" CB SER J 203 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA SER M 203 " pdb=" N SER M 203 " pdb=" C SER M 203 " pdb=" CB SER M 203 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 5583 not shown) Planarity restraints: 6118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 201 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C SER D 201 " -0.070 2.00e-02 2.50e+03 pdb=" O SER D 201 " 0.026 2.00e-02 2.50e+03 pdb=" N SER D 202 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 201 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C SER K 201 " 0.070 2.00e-02 2.50e+03 pdb=" O SER K 201 " -0.026 2.00e-02 2.50e+03 pdb=" N SER K 202 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 201 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C SER F 201 " -0.069 2.00e-02 2.50e+03 pdb=" O SER F 201 " 0.026 2.00e-02 2.50e+03 pdb=" N SER F 202 " 0.024 2.00e-02 2.50e+03 ... (remaining 6115 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2426 2.72 - 3.26: 28274 3.26 - 3.81: 45491 3.81 - 4.35: 48213 4.35 - 4.90: 80844 Nonbonded interactions: 205248 Sorted by model distance: nonbonded pdb=" N SER L 203 " pdb=" O SER M 202 " model vdw 2.173 3.120 nonbonded pdb=" N SER F 203 " pdb=" O SER G 202 " model vdw 2.183 3.120 nonbonded pdb=" N SER D 203 " pdb=" O SER E 202 " model vdw 2.185 3.120 nonbonded pdb=" N SER B 203 " pdb=" O SER C 202 " model vdw 2.209 3.120 nonbonded pdb=" O SER A 202 " pdb=" N SER N 203 " model vdw 2.226 3.120 ... (remaining 205243 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: 0.40 Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'N' } 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 group one per residue 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.120 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 72.370 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 : 0.006 0.067 30163 Z= 0.406 Angle : 1.227 10.744 41832 Z= 0.793 Chirality : 0.069 0.343 5586 Planarity : 0.007 0.040 6118 Dihedral : 5.367 18.700 6118 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.69 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 6083 helix: 0.84 (0.15), residues: 1071 sheet: 0.07 (0.09), residues: 2870 loop : -2.33 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.16177 ( 3097) hydrogen bonds : angle 10.03200 ( 9042) covalent geometry : bond 0.00591 (30163) covalent geometry : angle 1.22706 (41832) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.336 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2596 time to fit residues: 48.7477 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 8.9990 chunk 456 optimal weight: 7.9990 chunk 253 optimal weight: 30.0000 chunk 155 optimal weight: 50.0000 chunk 307 optimal weight: 50.0000 chunk 243 optimal weight: 9.9990 chunk 471 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 286 optimal weight: 50.0000 chunk 351 optimal weight: 6.9990 chunk 546 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.058085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.038367 restraints weight = 293031.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.038585 restraints weight = 275182.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.038716 restraints weight = 259826.094| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30163 Z= 0.251 Angle : 0.691 8.684 41832 Z= 0.417 Chirality : 0.052 0.147 5586 Planarity : 0.004 0.021 6118 Dihedral : 6.502 24.759 6118 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.44 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.10), residues: 6083 helix: 0.77 (0.16), residues: 1085 sheet: 0.08 (0.09), residues: 2660 loop : -2.24 (0.11), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 3097) hydrogen bonds : angle 7.55959 ( 9042) covalent geometry : bond 0.00347 (30163) covalent geometry : angle 0.69069 (41832) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2648 time to fit residues: 49.9781 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 404 optimal weight: 7.9990 chunk 283 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 243 optimal weight: 50.0000 chunk 144 optimal weight: 9.9990 chunk 107 optimal weight: 50.0000 chunk 310 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 509 optimal weight: 50.0000 chunk 478 optimal weight: 8.9990 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.054391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.035558 restraints weight = 302299.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.035789 restraints weight = 277331.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.035884 restraints weight = 261998.967| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30163 Z= 0.321 Angle : 0.727 7.658 41832 Z= 0.448 Chirality : 0.053 0.146 5586 Planarity : 0.004 0.022 6118 Dihedral : 6.972 26.995 6118 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.74 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.11), residues: 6083 helix: 0.67 (0.17), residues: 1001 sheet: -0.15 (0.09), residues: 2926 loop : -2.07 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 3097) hydrogen bonds : angle 7.80833 ( 9042) covalent geometry : bond 0.00424 (30163) covalent geometry : angle 0.72717 (41832) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2659 time to fit residues: 49.6370 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 234 optimal weight: 6.9990 chunk 582 optimal weight: 50.0000 chunk 575 optimal weight: 50.0000 chunk 152 optimal weight: 50.0000 chunk 555 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 461 optimal weight: 40.0000 chunk 95 optimal weight: 5.9990 chunk 462 optimal weight: 40.0000 chunk 179 optimal weight: 50.0000 chunk 508 optimal weight: 7.9990 overall best weight: 11.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.053125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034999 restraints weight = 310498.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.035312 restraints weight = 280955.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.035518 restraints weight = 260667.042| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30163 Z= 0.274 Angle : 0.684 9.492 41832 Z= 0.418 Chirality : 0.051 0.142 5586 Planarity : 0.004 0.022 6118 Dihedral : 7.127 27.048 6118 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.50 % Favored : 91.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 6083 helix: 0.71 (0.17), residues: 1015 sheet: -0.45 (0.09), residues: 2933 loop : -2.28 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 3097) hydrogen bonds : angle 7.64065 ( 9042) covalent geometry : bond 0.00378 (30163) covalent geometry : angle 0.68390 (41832) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.063 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2611 time to fit residues: 48.6792 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 517 optimal weight: 50.0000 chunk 220 optimal weight: 30.0000 chunk 568 optimal weight: 50.0000 chunk 136 optimal weight: 50.0000 chunk 340 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 514 optimal weight: 30.0000 chunk 314 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.052437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.034856 restraints weight = 311841.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.035151 restraints weight = 274558.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.035278 restraints weight = 241431.087| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30163 Z= 0.310 Angle : 0.728 10.706 41832 Z= 0.447 Chirality : 0.052 0.146 5586 Planarity : 0.004 0.027 6118 Dihedral : 7.527 29.229 6118 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.54 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.10), residues: 6083 helix: -0.03 (0.15), residues: 1197 sheet: -0.62 (0.09), residues: 2870 loop : -2.94 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 3097) hydrogen bonds : angle 8.06959 ( 9042) covalent geometry : bond 0.00433 (30163) covalent geometry : angle 0.72823 (41832) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.302 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2647 time to fit residues: 49.6838 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 265 optimal weight: 1.9990 chunk 285 optimal weight: 30.0000 chunk 448 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 194 optimal weight: 4.9990 chunk 412 optimal weight: 30.0000 chunk 535 optimal weight: 7.9990 chunk 148 optimal weight: 50.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.052100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.034585 restraints weight = 313870.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034953 restraints weight = 279484.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.035282 restraints weight = 247739.079| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30163 Z= 0.219 Angle : 0.622 8.388 41832 Z= 0.379 Chirality : 0.052 0.142 5586 Planarity : 0.003 0.026 6118 Dihedral : 6.987 29.137 6118 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.47 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.10), residues: 6083 helix: 0.69 (0.16), residues: 1113 sheet: -0.58 (0.10), residues: 2828 loop : -3.11 (0.11), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 3097) hydrogen bonds : angle 7.39736 ( 9042) covalent geometry : bond 0.00307 (30163) covalent geometry : angle 0.62193 (41832) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.419 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2700 time to fit residues: 50.9024 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 491 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 125 optimal weight: 40.0000 chunk 23 optimal weight: 6.9990 chunk 146 optimal weight: 50.0000 chunk 322 optimal weight: 40.0000 chunk 234 optimal weight: 40.0000 chunk 311 optimal weight: 0.0470 chunk 460 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 155 optimal weight: 50.0000 overall best weight: 13.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.051757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.034119 restraints weight = 314272.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.034417 restraints weight = 280567.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.034700 restraints weight = 258183.278| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.8243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30163 Z= 0.301 Angle : 0.720 11.235 41832 Z= 0.442 Chirality : 0.052 0.145 5586 Planarity : 0.004 0.027 6118 Dihedral : 7.531 31.213 6118 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.47 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.10), residues: 6083 helix: 0.25 (0.16), residues: 1155 sheet: -0.66 (0.10), residues: 2506 loop : -3.20 (0.10), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 3097) hydrogen bonds : angle 8.05209 ( 9042) covalent geometry : bond 0.00421 (30163) covalent geometry : angle 0.72048 (41832) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2807 time to fit residues: 52.6667 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 474 optimal weight: 30.0000 chunk 390 optimal weight: 50.0000 chunk 38 optimal weight: 50.0000 chunk 106 optimal weight: 40.0000 chunk 303 optimal weight: 40.0000 chunk 476 optimal weight: 50.0000 chunk 566 optimal weight: 40.0000 chunk 584 optimal weight: 20.0000 chunk 518 optimal weight: 20.0000 chunk 538 optimal weight: 7.9990 chunk 319 optimal weight: 50.0000 overall best weight: 23.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.051488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.033714 restraints weight = 317668.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.034043 restraints weight = 283183.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034209 restraints weight = 260593.522| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.9506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 30163 Z= 0.481 Angle : 0.955 16.784 41832 Z= 0.588 Chirality : 0.054 0.176 5586 Planarity : 0.005 0.037 6118 Dihedral : 9.291 36.191 6118 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.37 % Favored : 85.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.83 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.10), residues: 6083 helix: -0.56 (0.16), residues: 945 sheet: -1.35 (0.10), residues: 2534 loop : -3.59 (0.09), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.05697 ( 3097) hydrogen bonds : angle 9.69065 ( 9042) covalent geometry : bond 0.00671 (30163) covalent geometry : angle 0.95511 (41832) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.647 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2837 time to fit residues: 52.4541 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 336 optimal weight: 40.0000 chunk 437 optimal weight: 5.9990 chunk 563 optimal weight: 50.0000 chunk 275 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 590 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 82 optimal weight: 40.0000 chunk 499 optimal weight: 30.0000 chunk 466 optimal weight: 20.0000 chunk 539 optimal weight: 30.0000 overall best weight: 16.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.051063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.033602 restraints weight = 317754.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.033840 restraints weight = 283728.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.034079 restraints weight = 266081.625| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.9704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30163 Z= 0.356 Angle : 0.798 14.385 41832 Z= 0.487 Chirality : 0.052 0.150 5586 Planarity : 0.004 0.034 6118 Dihedral : 8.306 37.888 6118 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.79 % Favored : 85.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.10), residues: 6083 helix: -0.60 (0.15), residues: 1057 sheet: -1.37 (0.10), residues: 2443 loop : -3.81 (0.09), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 3097) hydrogen bonds : angle 8.73595 ( 9042) covalent geometry : bond 0.00496 (30163) covalent geometry : angle 0.79822 (41832) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.589 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2800 time to fit residues: 52.7622 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 361 optimal weight: 50.0000 chunk 96 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 chunk 505 optimal weight: 50.0000 chunk 595 optimal weight: 7.9990 chunk 481 optimal weight: 40.0000 chunk 67 optimal weight: 40.0000 chunk 548 optimal weight: 8.9990 chunk 380 optimal weight: 50.0000 chunk 27 optimal weight: 50.0000 overall best weight: 23.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.050912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.033315 restraints weight = 319762.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.033535 restraints weight = 287269.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.033790 restraints weight = 268894.754| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 1.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 30163 Z= 0.484 Angle : 0.971 18.178 41832 Z= 0.597 Chirality : 0.054 0.166 5586 Planarity : 0.005 0.039 6118 Dihedral : 9.626 40.049 6118 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.44 % Allowed : 17.94 % Favored : 81.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.10), residues: 6083 helix: -1.39 (0.15), residues: 938 sheet: -1.70 (0.10), residues: 2415 loop : -3.65 (0.10), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.05633 ( 3097) hydrogen bonds : angle 9.85371 ( 9042) covalent geometry : bond 0.00673 (30163) covalent geometry : angle 0.97108 (41832) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12166 Ramachandran restraints generated. 6083 Oldfield, 0 Emsley, 6083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2848 time to fit residues: 53.2820 Evaluate side-chains 91 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 65 optimal weight: 50.0000 chunk 440 optimal weight: 9.9990 chunk 268 optimal weight: 40.0000 chunk 406 optimal weight: 20.0000 chunk 208 optimal weight: 50.0000 chunk 104 optimal weight: 50.0000 chunk 387 optimal weight: 20.0000 chunk 280 optimal weight: 50.0000 chunk 338 optimal weight: 30.0000 chunk 184 optimal weight: 40.0000 chunk 118 optimal weight: 20.0000 overall best weight: 19.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.050618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.033242 restraints weight = 318389.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.033537 restraints weight = 284927.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.033679 restraints weight = 263568.815| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 1.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30163 Z= 0.406 Angle : 0.881 16.294 41832 Z= 0.540 Chirality : 0.052 0.156 5586 Planarity : 0.005 0.036 6118 Dihedral : 9.072 41.377 6118 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 17.29 % Favored : 82.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.10), residues: 6083 helix: -1.55 (0.14), residues: 987 sheet: -1.49 (0.11), residues: 2282 loop : -4.09 (0.09), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 3097) hydrogen bonds : angle 9.37607 ( 9042) covalent geometry : bond 0.00569 (30163) covalent geometry : angle 0.88060 (41832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9182.83 seconds wall clock time: 158 minutes 22.59 seconds (9502.59 seconds total)