Starting phenix.real_space_refine on Wed Jun 18 04:59:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1s_36800/06_2025/8k1s_36800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1s_36800/06_2025/8k1s_36800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1s_36800/06_2025/8k1s_36800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1s_36800/06_2025/8k1s_36800.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1s_36800/06_2025/8k1s_36800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1s_36800/06_2025/8k1s_36800.cif" } resolution = 2.83 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= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 S 76 5.16 5 C 13712 2.51 5 N 3398 2.21 5 O 3794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21000 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "B" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "C" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "D" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "E" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "F" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "I" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.02, per 1000 atoms: 0.62 Number of scatterers: 21000 At special positions: 0 Unit cell: (176.79, 115.37, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 76 16.00 P 16 15.00 O 3794 8.00 N 3398 7.00 C 13712 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: 4.86 Conformation dependent library (CDL) restraints added in 2.7 seconds 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4958 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 68.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.689A pdb=" N GLU A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.546A pdb=" N GLY A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 123 through 139 removed outlier: 3.547A pdb=" N GLY B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 59 through 67 Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 123 through 140 removed outlier: 3.547A pdb=" N GLY C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 59 through 67 Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.546A pdb=" N GLY D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 removed outlier: 3.556A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 67 Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU E 94 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 123 through 140 removed outlier: 3.546A pdb=" N GLY E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 131 " --> pdb=" O ASP E 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.689A pdb=" N GLU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 123 through 139 removed outlier: 3.546A pdb=" N GLY F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 29 removed outlier: 3.558A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 67 Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.689A pdb=" N GLU G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 123 through 140 removed outlier: 3.547A pdb=" N GLY G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS G 131 " --> pdb=" O ASP G 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN G 134 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 29 removed outlier: 3.558A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 67 Processing helix chain 'H' and resid 68 through 71 Processing helix chain 'H' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 123 through 139 removed outlier: 3.547A pdb=" N GLY H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 35 removed outlier: 3.678A pdb=" N ALA I 21 " --> pdb=" O PRO I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 73 through 102 Processing helix chain 'I' and resid 128 through 157 removed outlier: 3.569A pdb=" N VAL I 132 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 157 through 174 Processing helix chain 'I' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL I 189 " --> pdb=" O MET I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 205 Processing helix chain 'I' and resid 208 through 219 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 251 removed outlier: 3.504A pdb=" N LEU I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 275 Processing helix chain 'I' and resid 285 through 289 Processing helix chain 'I' and resid 290 through 303 removed outlier: 3.578A pdb=" N LEU I 299 " --> pdb=" O VAL I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 331 Processing helix chain 'I' and resid 344 through 373 Processing helix chain 'I' and resid 376 through 389 Processing helix chain 'I' and resid 402 through 419 Processing helix chain 'I' and resid 419 through 427 removed outlier: 3.746A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 35 removed outlier: 3.677A pdb=" N ALA J 21 " --> pdb=" O PRO J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 73 through 102 Processing helix chain 'J' and resid 128 through 157 removed outlier: 3.567A pdb=" N VAL J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 157 through 174 Processing helix chain 'J' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL J 189 " --> pdb=" O MET J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 205 Processing helix chain 'J' and resid 208 through 219 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 225 through 251 removed outlier: 3.503A pdb=" N LEU J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 275 Processing helix chain 'J' and resid 285 through 289 Processing helix chain 'J' and resid 290 through 303 removed outlier: 3.578A pdb=" N LEU J 299 " --> pdb=" O VAL J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 331 Processing helix chain 'J' and resid 344 through 373 Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 402 through 419 Processing helix chain 'J' and resid 419 through 427 removed outlier: 3.745A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 35 removed outlier: 3.677A pdb=" N ALA K 21 " --> pdb=" O PRO K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 73 through 102 Processing helix chain 'K' and resid 128 through 157 removed outlier: 3.569A pdb=" N VAL K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix Processing helix chain 'K' and resid 157 through 174 Processing helix chain 'K' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL K 189 " --> pdb=" O MET K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 205 Processing helix chain 'K' and resid 208 through 219 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 225 through 251 removed outlier: 3.504A pdb=" N LEU K 236 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 275 Processing helix chain 'K' and resid 285 through 289 Processing helix chain 'K' and resid 290 through 303 removed outlier: 3.577A pdb=" N LEU K 299 " --> pdb=" O VAL K 295 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 331 Processing helix chain 'K' and resid 344 through 373 Processing helix chain 'K' and resid 376 through 389 Processing helix chain 'K' and resid 402 through 419 Processing helix chain 'K' and resid 419 through 427 removed outlier: 3.745A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 35 removed outlier: 3.677A pdb=" N ALA L 21 " --> pdb=" O PRO L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 73 through 102 Processing helix chain 'L' and resid 128 through 157 removed outlier: 3.569A pdb=" N VAL L 132 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix Processing helix chain 'L' and resid 157 through 174 Processing helix chain 'L' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL L 189 " --> pdb=" O MET L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 205 Processing helix chain 'L' and resid 208 through 219 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 225 through 251 removed outlier: 3.504A pdb=" N LEU L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 275 Processing helix chain 'L' and resid 285 through 289 Processing helix chain 'L' and resid 290 through 303 removed outlier: 3.578A pdb=" N LEU L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 344 through 373 Processing helix chain 'L' and resid 376 through 389 Processing helix chain 'L' and resid 402 through 419 Processing helix chain 'L' and resid 419 through 427 removed outlier: 3.744A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.302A pdb=" N VAL A 32 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL A 53 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA A 34 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.304A pdb=" N VAL B 32 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 53 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA B 34 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL C 32 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL C 53 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 34 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 6.304A pdb=" N VAL D 32 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL D 53 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA D 34 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL E 32 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL E 53 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL F 32 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL F 53 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA F 34 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL G 32 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL G 53 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA G 34 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL H 32 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL H 53 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA H 34 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1358 hydrogen bonds defined for protein. 3978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3301 1.31 - 1.44: 5658 1.44 - 1.56: 12302 1.56 - 1.68: 27 1.68 - 1.81: 140 Bond restraints: 21428 Sorted by residual: bond pdb=" CA LYS J 315 " pdb=" C LYS J 315 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.28e-02 6.10e+03 4.02e+01 bond pdb=" CA LYS L 315 " pdb=" C LYS L 315 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.33e-02 5.65e+03 3.25e+01 bond pdb=" CA ALA J 305 " pdb=" C ALA J 305 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.34e-02 5.57e+03 1.68e+01 bond pdb=" CA GLY I 306 " pdb=" C GLY I 306 " ideal model delta sigma weight residual 1.516 1.468 0.048 1.18e-02 7.18e+03 1.67e+01 bond pdb=" N LYS J 315 " pdb=" CA LYS J 315 " ideal model delta sigma weight residual 1.454 1.407 0.047 1.17e-02 7.31e+03 1.63e+01 ... (remaining 21423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 28909 3.09 - 6.18: 199 6.18 - 9.28: 22 9.28 - 12.37: 1 12.37 - 15.46: 2 Bond angle restraints: 29133 Sorted by residual: angle pdb=" N ILE J 314 " pdb=" CA ILE J 314 " pdb=" C ILE J 314 " ideal model delta sigma weight residual 109.63 94.17 15.46 1.44e+00 4.82e-01 1.15e+02 angle pdb=" N ILE L 314 " pdb=" CA ILE L 314 " pdb=" C ILE L 314 " ideal model delta sigma weight residual 109.30 96.69 12.61 1.31e+00 5.83e-01 9.27e+01 angle pdb=" N ILE I 314 " pdb=" CA ILE I 314 " pdb=" C ILE I 314 " ideal model delta sigma weight residual 109.51 98.85 10.66 1.43e+00 4.89e-01 5.55e+01 angle pdb=" O SER I 312 " pdb=" C SER I 312 " pdb=" N GLY I 313 " ideal model delta sigma weight residual 122.78 114.25 8.53 1.33e+00 5.65e-01 4.12e+01 angle pdb=" CA SER K 312 " pdb=" C SER K 312 " pdb=" N GLY K 313 " ideal model delta sigma weight residual 116.01 125.06 -9.05 1.45e+00 4.76e-01 3.90e+01 ... (remaining 29128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 12333 28.79 - 57.57: 134 57.57 - 86.36: 8 86.36 - 115.14: 4 115.14 - 143.93: 8 Dihedral angle restraints: 12487 sinusoidal: 4782 harmonic: 7705 Sorted by residual: dihedral pdb=" O2A ADP H 301 " pdb=" O3A ADP H 301 " pdb=" PA ADP H 301 " pdb=" PB ADP H 301 " ideal model delta sinusoidal sigma weight residual -60.00 83.93 -143.93 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual -60.00 83.93 -143.93 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP D 301 " pdb=" O3A ADP D 301 " pdb=" PA ADP D 301 " pdb=" PB ADP D 301 " ideal model delta sinusoidal sigma weight residual -60.00 83.89 -143.89 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 12484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3049 0.057 - 0.115: 445 0.115 - 0.172: 35 0.172 - 0.230: 11 0.230 - 0.287: 3 Chirality restraints: 3543 Sorted by residual: chirality pdb=" CA SER J 307 " pdb=" N SER J 307 " pdb=" C SER J 307 " pdb=" CB SER J 307 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA SER L 307 " pdb=" N SER L 307 " pdb=" C SER L 307 " pdb=" CB SER L 307 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA SER K 307 " pdb=" N SER K 307 " pdb=" C SER K 307 " pdb=" CB SER K 307 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3540 not shown) Planarity restraints: 3542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET K 301 " -0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C MET K 301 " 0.064 2.00e-02 2.50e+03 pdb=" O MET K 301 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE K 302 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET J 301 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C MET J 301 " -0.063 2.00e-02 2.50e+03 pdb=" O MET J 301 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE J 302 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 301 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C MET I 301 " -0.057 2.00e-02 2.50e+03 pdb=" O MET I 301 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE I 302 " 0.020 2.00e-02 2.50e+03 ... (remaining 3539 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.85: 7059 2.85 - 3.42: 23835 3.42 - 3.99: 40272 3.99 - 4.57: 58222 4.57 - 5.14: 83422 Nonbonded interactions: 212810 Sorted by model distance: nonbonded pdb=" OE2 GLU E 94 " pdb=" NZ LYS G 115 " model vdw 2.272 3.120 nonbonded pdb=" O ALA L 55 " pdb=" OG1 THR L 59 " model vdw 2.294 3.040 nonbonded pdb=" O ALA I 55 " pdb=" OG1 THR I 59 " model vdw 2.294 3.040 nonbonded pdb=" O ALA K 55 " pdb=" OG1 THR K 59 " model vdw 2.294 3.040 nonbonded pdb=" O ALA J 55 " pdb=" OG1 THR J 59 " model vdw 2.294 3.040 ... (remaining 212805 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 7 through 139 or resid 301)) selection = chain 'D' selection = (chain 'E' and (resid 7 through 139 or resid 301)) selection = chain 'F' selection = (chain 'G' and (resid 7 through 139 or resid 301)) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.860 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 : 0.004 0.081 21428 Z= 0.235 Angle : 0.610 15.459 29133 Z= 0.326 Chirality : 0.043 0.287 3543 Planarity : 0.003 0.037 3542 Dihedral : 10.425 143.931 7529 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 4.10 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 1.13 (0.16), residues: 2663 helix: 1.47 (0.12), residues: 1647 sheet: 0.88 (0.30), residues: 296 loop : -0.93 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 158 HIS 0.003 0.001 HIS E 110 PHE 0.024 0.001 PHE J 202 TYR 0.003 0.001 TYR F 73 ARG 0.002 0.000 ARG I 417 Details of bonding type rmsd hydrogen bonds : bond 0.24391 ( 1358) hydrogen bonds : angle 7.02181 ( 3978) covalent geometry : bond 0.00372 (21428) covalent geometry : angle 0.60951 (29133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 639 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7263 (mp0) REVERT: A 111 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7530 (mmpt) REVERT: B 23 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7738 (mtmm) REVERT: B 126 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7416 (ttpp) REVERT: B 134 GLN cc_start: 0.7508 (tp40) cc_final: 0.7225 (mt0) REVERT: C 35 VAL cc_start: 0.8311 (p) cc_final: 0.8104 (m) REVERT: C 111 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7454 (mmpt) REVERT: E 111 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7592 (mmpt) REVERT: F 23 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7787 (mtpt) REVERT: F 59 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6279 (mt-10) REVERT: F 126 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7356 (ttpp) REVERT: F 127 ASP cc_start: 0.7602 (m-30) cc_final: 0.7354 (m-30) REVERT: G 16 ARG cc_start: 0.8351 (mtm180) cc_final: 0.8070 (mtm-85) REVERT: G 35 VAL cc_start: 0.8303 (p) cc_final: 0.8069 (t) REVERT: G 111 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7381 (mmpt) REVERT: I 158 TRP cc_start: 0.6190 (m100) cc_final: 0.5471 (t60) REVERT: I 331 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7236 (mtm-85) REVERT: I 360 PHE cc_start: 0.6889 (t80) cc_final: 0.6603 (m-10) REVERT: I 394 THR cc_start: 0.8226 (t) cc_final: 0.7854 (t) REVERT: J 81 MET cc_start: 0.7231 (ttm) cc_final: 0.7019 (ttt) REVERT: J 196 LEU cc_start: 0.8001 (mt) cc_final: 0.7445 (tp) REVERT: J 394 THR cc_start: 0.7429 (t) cc_final: 0.6965 (t) REVERT: K 81 MET cc_start: 0.7254 (ttm) cc_final: 0.6979 (ttt) REVERT: K 196 LEU cc_start: 0.8054 (mt) cc_final: 0.7491 (tp) REVERT: K 394 THR cc_start: 0.7357 (t) cc_final: 0.6902 (t) REVERT: L 158 TRP cc_start: 0.6127 (m100) cc_final: 0.5509 (t60) REVERT: L 331 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7175 (mtm-85) REVERT: L 333 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7714 (mmpt) REVERT: L 394 THR cc_start: 0.8366 (t) cc_final: 0.8042 (t) outliers start: 17 outliers final: 2 residues processed: 648 average time/residue: 1.1673 time to fit residues: 865.6152 Evaluate side-chains 441 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 435 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 111 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 206 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 61 ASN B 83 GLN C 38 ASN C 61 ASN C 70 ASN C 110 HIS D 51 HIS E 105 GLN F 61 ASN F 83 GLN F 106 ASN F 110 HIS G 38 ASN G 61 ASN G 70 ASN G 110 HIS H 38 ASN I 174 ASN I 434 ASN J 239 ASN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.209901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.170530 restraints weight = 23842.653| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.29 r_work: 0.3848 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21428 Z= 0.147 Angle : 0.631 7.181 29133 Z= 0.310 Chirality : 0.043 0.159 3543 Planarity : 0.004 0.037 3542 Dihedral : 9.732 131.033 2927 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.48 % Allowed : 14.04 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 2.05 (0.17), residues: 2663 helix: 2.25 (0.12), residues: 1702 sheet: 0.79 (0.29), residues: 288 loop : -0.73 (0.26), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 181 HIS 0.003 0.001 HIS A 110 PHE 0.035 0.002 PHE J 202 TYR 0.013 0.001 TYR I 270 ARG 0.006 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 1358) hydrogen bonds : angle 4.54825 ( 3978) covalent geometry : bond 0.00324 (21428) covalent geometry : angle 0.63106 (29133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 456 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8015 (mt-10) cc_final: 0.6983 (mp0) REVERT: A 111 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7893 (mmpt) REVERT: B 16 ARG cc_start: 0.8997 (mtm180) cc_final: 0.8792 (mtm-85) REVERT: B 23 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8231 (mtpt) REVERT: B 108 TYR cc_start: 0.7707 (m-10) cc_final: 0.7174 (m-80) REVERT: B 127 ASP cc_start: 0.8636 (m-30) cc_final: 0.8325 (m-30) REVERT: C 16 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8368 (mtm-85) REVERT: C 111 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7911 (mmpt) REVERT: C 135 SER cc_start: 0.7892 (m) cc_final: 0.7364 (p) REVERT: D 126 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7196 (mmtp) REVERT: E 41 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7895 (mmtm) REVERT: E 111 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7896 (mmpt) REVERT: E 127 ASP cc_start: 0.8630 (m-30) cc_final: 0.8251 (m-30) REVERT: F 60 GLU cc_start: 0.7889 (tp30) cc_final: 0.7523 (tp30) REVERT: F 108 TYR cc_start: 0.7601 (m-10) cc_final: 0.7093 (m-80) REVERT: F 127 ASP cc_start: 0.8475 (m-30) cc_final: 0.8176 (m-30) REVERT: G 111 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7996 (mmtt) REVERT: G 135 SER cc_start: 0.7849 (m) cc_final: 0.7324 (p) REVERT: G 139 GLU cc_start: 0.6107 (tp30) cc_final: 0.5767 (mp0) REVERT: H 126 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7141 (mmtp) REVERT: I 91 PHE cc_start: 0.7287 (t80) cc_final: 0.7029 (t80) REVERT: I 146 LEU cc_start: 0.7822 (tt) cc_final: 0.7482 (tt) REVERT: I 150 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.6112 (pt) REVERT: I 196 LEU cc_start: 0.7960 (mt) cc_final: 0.7676 (mt) REVERT: I 243 MET cc_start: 0.7764 (ttt) cc_final: 0.7399 (ttp) REVERT: I 267 TRP cc_start: 0.7369 (m100) cc_final: 0.7023 (m100) REVERT: I 331 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7229 (mtm-85) REVERT: I 333 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7766 (mmpt) REVERT: I 394 THR cc_start: 0.8508 (t) cc_final: 0.8237 (t) REVERT: J 196 LEU cc_start: 0.7847 (mt) cc_final: 0.7196 (tp) REVERT: J 331 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7524 (mtt-85) REVERT: J 340 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7686 (mtt-85) REVERT: K 196 LEU cc_start: 0.7830 (mt) cc_final: 0.7166 (tp) REVERT: K 237 MET cc_start: 0.7843 (mmm) cc_final: 0.7583 (tpt) REVERT: K 331 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7406 (mtt-85) REVERT: L 91 PHE cc_start: 0.7188 (t80) cc_final: 0.6931 (t80) REVERT: L 146 LEU cc_start: 0.7284 (mp) cc_final: 0.6835 (tt) REVERT: L 150 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.6015 (pt) REVERT: L 243 MET cc_start: 0.7886 (ttt) cc_final: 0.7522 (ttp) REVERT: L 267 TRP cc_start: 0.7455 (m100) cc_final: 0.7179 (m100) REVERT: L 331 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7106 (mtm-85) REVERT: L 333 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7572 (mmpt) outliers start: 78 outliers final: 22 residues processed: 506 average time/residue: 1.2902 time to fit residues: 741.3414 Evaluate side-chains 436 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 407 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 150 ILE Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 12 optimal weight: 0.6980 chunk 189 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 106 ASN E 105 GLN F 51 HIS I 434 ASN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN L 434 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.207583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.167635 restraints weight = 23898.415| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.44 r_work: 0.3821 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21428 Z= 0.139 Angle : 0.605 6.771 29133 Z= 0.294 Chirality : 0.043 0.169 3543 Planarity : 0.004 0.036 3542 Dihedral : 9.505 128.840 2923 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.30 % Allowed : 16.45 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 2.19 (0.17), residues: 2663 helix: 2.48 (0.12), residues: 1686 sheet: 0.76 (0.29), residues: 285 loop : -0.91 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 181 HIS 0.003 0.001 HIS H 110 PHE 0.033 0.001 PHE J 202 TYR 0.010 0.001 TYR B 107 ARG 0.005 0.001 ARG G 16 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1358) hydrogen bonds : angle 4.29018 ( 3978) covalent geometry : bond 0.00316 (21428) covalent geometry : angle 0.60550 (29133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 432 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7063 (mp0) REVERT: A 111 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7826 (mmpt) REVERT: A 127 ASP cc_start: 0.8296 (m-30) cc_final: 0.7878 (m-30) REVERT: B 23 LYS cc_start: 0.8252 (mtpp) cc_final: 0.8042 (mtpt) REVERT: B 60 GLU cc_start: 0.7697 (tp30) cc_final: 0.7275 (tp30) REVERT: B 108 TYR cc_start: 0.7465 (m-80) cc_final: 0.6945 (m-80) REVERT: B 127 ASP cc_start: 0.8273 (m-30) cc_final: 0.7934 (m-30) REVERT: B 128 MET cc_start: 0.9043 (mmm) cc_final: 0.8744 (mmp) REVERT: C 16 ARG cc_start: 0.8604 (mtm180) cc_final: 0.8273 (mtm-85) REVERT: C 60 GLU cc_start: 0.7613 (tp30) cc_final: 0.7275 (tp30) REVERT: C 62 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7269 (mt-10) REVERT: C 111 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8205 (mtpt) REVERT: C 135 SER cc_start: 0.7729 (m) cc_final: 0.7290 (p) REVERT: D 56 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7589 (t0) REVERT: D 126 LYS cc_start: 0.7593 (ttpt) cc_final: 0.6988 (mmtp) REVERT: E 111 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7783 (mmpt) REVERT: E 127 ASP cc_start: 0.8305 (m-30) cc_final: 0.7900 (m-30) REVERT: F 60 GLU cc_start: 0.7742 (tp30) cc_final: 0.7388 (tp30) REVERT: F 108 TYR cc_start: 0.7383 (m-80) cc_final: 0.6898 (m-80) REVERT: F 127 ASP cc_start: 0.8293 (m-30) cc_final: 0.7936 (m-30) REVERT: F 128 MET cc_start: 0.8950 (mmm) cc_final: 0.8705 (mmp) REVERT: G 60 GLU cc_start: 0.7611 (tp30) cc_final: 0.7139 (tp30) REVERT: G 111 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7802 (mmpt) REVERT: G 135 SER cc_start: 0.7836 (m) cc_final: 0.7237 (p) REVERT: H 59 GLU cc_start: 0.7943 (mp0) cc_final: 0.7374 (mp0) REVERT: H 83 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: H 126 LYS cc_start: 0.7602 (ttpt) cc_final: 0.7018 (mmtp) REVERT: I 81 MET cc_start: 0.5287 (ttp) cc_final: 0.4976 (mtp) REVERT: I 94 PHE cc_start: 0.7762 (t80) cc_final: 0.7501 (t80) REVERT: I 100 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5411 (ttt) REVERT: I 151 ARG cc_start: 0.6731 (tpt-90) cc_final: 0.6391 (tpt-90) REVERT: I 196 LEU cc_start: 0.8011 (mt) cc_final: 0.7748 (mt) REVERT: I 243 MET cc_start: 0.7692 (ttt) cc_final: 0.7328 (ttp) REVERT: I 267 TRP cc_start: 0.7333 (m100) cc_final: 0.6986 (m100) REVERT: I 331 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7169 (mtm-85) REVERT: I 333 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7658 (mmpt) REVERT: I 355 SER cc_start: 0.8461 (t) cc_final: 0.8196 (m) REVERT: I 394 THR cc_start: 0.8531 (t) cc_final: 0.8268 (t) REVERT: J 134 PHE cc_start: 0.6502 (t80) cc_final: 0.6294 (t80) REVERT: J 143 ILE cc_start: 0.8157 (mt) cc_final: 0.7921 (mm) REVERT: J 196 LEU cc_start: 0.7781 (mt) cc_final: 0.7184 (tp) REVERT: J 331 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7633 (mtp85) REVERT: J 334 LYS cc_start: 0.7742 (pttt) cc_final: 0.7432 (mptt) REVERT: J 340 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7705 (mtp85) REVERT: K 81 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5970 (ttm) REVERT: K 143 ILE cc_start: 0.8196 (mt) cc_final: 0.7946 (mm) REVERT: K 196 LEU cc_start: 0.7788 (mt) cc_final: 0.7185 (tp) REVERT: K 331 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7495 (mtp85) REVERT: K 395 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7760 (mtp) REVERT: L 81 MET cc_start: 0.5426 (ttp) cc_final: 0.5081 (mtp) REVERT: L 100 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.5235 (ttt) REVERT: L 146 LEU cc_start: 0.7254 (mp) cc_final: 0.6934 (tt) REVERT: L 243 MET cc_start: 0.7735 (ttt) cc_final: 0.7372 (ttp) REVERT: L 267 TRP cc_start: 0.7458 (m100) cc_final: 0.7131 (m100) REVERT: L 331 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7186 (mtm-85) REVERT: L 333 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7627 (mmtt) REVERT: L 355 SER cc_start: 0.8465 (t) cc_final: 0.8222 (m) outliers start: 74 outliers final: 30 residues processed: 475 average time/residue: 1.3803 time to fit residues: 742.6429 Evaluate side-chains 434 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 393 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 395 MET Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 118 optimal weight: 6.9990 chunk 226 optimal weight: 50.0000 chunk 119 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.198403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146174 restraints weight = 24111.115| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.30 r_work: 0.3681 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21428 Z= 0.206 Angle : 0.665 8.218 29133 Z= 0.326 Chirality : 0.045 0.174 3543 Planarity : 0.004 0.037 3542 Dihedral : 9.871 130.904 2923 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.90 % Allowed : 15.83 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 1.93 (0.17), residues: 2663 helix: 2.33 (0.12), residues: 1689 sheet: 0.52 (0.29), residues: 288 loop : -1.13 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 181 HIS 0.004 0.001 HIS F 51 PHE 0.034 0.002 PHE K 202 TYR 0.010 0.001 TYR I 270 ARG 0.007 0.001 ARG G 16 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 1358) hydrogen bonds : angle 4.35611 ( 3978) covalent geometry : bond 0.00495 (21428) covalent geometry : angle 0.66492 (29133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 411 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7929 (mt-10) cc_final: 0.6733 (mp0) REVERT: A 111 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7395 (mmpt) REVERT: A 127 ASP cc_start: 0.8464 (m-30) cc_final: 0.7864 (m-30) REVERT: B 23 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7793 (mtpt) REVERT: B 93 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7879 (mmtm) REVERT: B 108 TYR cc_start: 0.7602 (m-10) cc_final: 0.7010 (m-80) REVERT: B 115 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7877 (tppt) REVERT: B 128 MET cc_start: 0.8907 (mmm) cc_final: 0.8582 (mmp) REVERT: C 60 GLU cc_start: 0.7646 (tp30) cc_final: 0.7445 (tp30) REVERT: C 111 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7975 (mtpt) REVERT: C 127 ASP cc_start: 0.8161 (m-30) cc_final: 0.7908 (m-30) REVERT: D 56 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7418 (t0) REVERT: D 59 GLU cc_start: 0.7665 (mp0) cc_final: 0.7401 (mp0) REVERT: D 83 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: D 126 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6462 (mmtp) REVERT: E 111 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7347 (mmpt) REVERT: E 127 ASP cc_start: 0.8372 (m-30) cc_final: 0.7800 (m-30) REVERT: F 59 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6345 (mm-30) REVERT: F 93 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7858 (mmtm) REVERT: F 108 TYR cc_start: 0.7549 (m-10) cc_final: 0.6956 (m-80) REVERT: F 115 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7877 (tppt) REVERT: F 128 MET cc_start: 0.8831 (mmm) cc_final: 0.8492 (mmp) REVERT: G 16 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.8216 (mtp180) REVERT: G 111 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7983 (mtpt) REVERT: G 127 ASP cc_start: 0.8187 (m-30) cc_final: 0.7987 (m-30) REVERT: H 56 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7753 (t0) REVERT: H 83 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: H 126 LYS cc_start: 0.7214 (ttpt) cc_final: 0.6480 (mttp) REVERT: I 81 MET cc_start: 0.5145 (ttp) cc_final: 0.4754 (ttp) REVERT: I 100 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.5434 (ttt) REVERT: I 181 TRP cc_start: 0.7136 (m-10) cc_final: 0.6862 (m-90) REVERT: I 188 TYR cc_start: 0.6923 (m-80) cc_final: 0.6444 (m-10) REVERT: I 267 TRP cc_start: 0.7146 (m100) cc_final: 0.6785 (m100) REVERT: I 331 ARG cc_start: 0.7765 (mtp85) cc_final: 0.6913 (mtm-85) REVERT: I 333 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7334 (mmpt) REVERT: I 340 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6777 (mtp-110) REVERT: I 355 SER cc_start: 0.8230 (t) cc_final: 0.7960 (m) REVERT: J 196 LEU cc_start: 0.7534 (mt) cc_final: 0.7013 (tp) REVERT: J 213 PHE cc_start: 0.7267 (t80) cc_final: 0.6959 (OUTLIER) REVERT: J 331 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7480 (mtp85) REVERT: J 334 LYS cc_start: 0.7855 (pttt) cc_final: 0.7218 (mptt) REVERT: K 24 PHE cc_start: 0.5283 (m-80) cc_final: 0.4579 (t80) REVERT: K 81 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5653 (ttm) REVERT: K 213 PHE cc_start: 0.7218 (t80) cc_final: 0.6925 (t80) REVERT: K 331 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7371 (mtp85) REVERT: L 81 MET cc_start: 0.5236 (ttp) cc_final: 0.4817 (ttp) REVERT: L 94 PHE cc_start: 0.7814 (t80) cc_final: 0.7579 (t80) REVERT: L 146 LEU cc_start: 0.7356 (mp) cc_final: 0.6933 (tt) REVERT: L 181 TRP cc_start: 0.7210 (m-10) cc_final: 0.6982 (m-90) REVERT: L 188 TYR cc_start: 0.6975 (m-80) cc_final: 0.6450 (m-10) REVERT: L 191 ASP cc_start: 0.7834 (t0) cc_final: 0.7313 (m-30) REVERT: L 196 LEU cc_start: 0.7576 (mt) cc_final: 0.7325 (mt) REVERT: L 267 TRP cc_start: 0.7282 (m100) cc_final: 0.6862 (m100) REVERT: L 331 ARG cc_start: 0.7749 (mtp85) cc_final: 0.6817 (mtm-85) REVERT: L 333 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7141 (mmpt) REVERT: L 340 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6747 (mtp-110) REVERT: L 355 SER cc_start: 0.8274 (t) cc_final: 0.8029 (m) outliers start: 110 outliers final: 45 residues processed: 484 average time/residue: 1.3896 time to fit residues: 757.0915 Evaluate side-chains 449 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 388 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 262 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS B 106 ASN C 105 GLN F 51 HIS G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.201083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149395 restraints weight = 24134.051| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.32 r_work: 0.3717 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21428 Z= 0.139 Angle : 0.616 7.440 29133 Z= 0.297 Chirality : 0.043 0.168 3543 Planarity : 0.004 0.035 3542 Dihedral : 9.557 125.574 2923 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.97 % Allowed : 17.34 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 2.14 (0.17), residues: 2663 helix: 2.51 (0.12), residues: 1693 sheet: 0.38 (0.29), residues: 288 loop : -1.01 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 181 HIS 0.003 0.001 HIS H 110 PHE 0.032 0.001 PHE I 94 TYR 0.013 0.001 TYR I 270 ARG 0.010 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1358) hydrogen bonds : angle 4.18058 ( 3978) covalent geometry : bond 0.00320 (21428) covalent geometry : angle 0.61570 (29133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 402 time to evaluate : 2.391 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7976 (mt-10) cc_final: 0.6767 (mp0) REVERT: A 111 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7634 (mmpt) REVERT: A 127 ASP cc_start: 0.8447 (m-30) cc_final: 0.7888 (m-30) REVERT: B 23 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7941 (mtmp) REVERT: B 108 TYR cc_start: 0.7639 (m-10) cc_final: 0.7009 (m-80) REVERT: B 128 MET cc_start: 0.9017 (mmm) cc_final: 0.8788 (mmp) REVERT: C 111 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8063 (mtpt) REVERT: C 128 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8475 (mmm) REVERT: D 56 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7460 (t0) REVERT: D 59 GLU cc_start: 0.7739 (mp0) cc_final: 0.6969 (mp0) REVERT: D 126 LYS cc_start: 0.7325 (ttpt) cc_final: 0.6601 (mmtp) REVERT: E 111 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7499 (mmpt) REVERT: E 127 ASP cc_start: 0.8444 (m-30) cc_final: 0.7905 (m-30) REVERT: F 59 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6501 (mm-30) REVERT: F 108 TYR cc_start: 0.7570 (m-10) cc_final: 0.7022 (m-80) REVERT: F 128 MET cc_start: 0.8921 (mmm) cc_final: 0.8583 (mmp) REVERT: G 16 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8218 (mtp180) REVERT: G 60 GLU cc_start: 0.7831 (tp30) cc_final: 0.7571 (tp30) REVERT: G 111 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7557 (mmpt) REVERT: G 127 ASP cc_start: 0.8251 (m-30) cc_final: 0.8016 (m-30) REVERT: H 59 GLU cc_start: 0.7690 (mp0) cc_final: 0.6943 (mp0) REVERT: H 126 LYS cc_start: 0.7288 (ttpt) cc_final: 0.6629 (mmtp) REVERT: I 196 LEU cc_start: 0.7792 (mt) cc_final: 0.7556 (mt) REVERT: I 243 MET cc_start: 0.7426 (ttt) cc_final: 0.7116 (ttp) REVERT: I 267 TRP cc_start: 0.7223 (m100) cc_final: 0.6843 (m100) REVERT: I 331 ARG cc_start: 0.7858 (mtp85) cc_final: 0.6994 (mtm-85) REVERT: I 333 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7362 (mmpt) REVERT: I 340 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7099 (mtm-85) REVERT: I 355 SER cc_start: 0.8370 (t) cc_final: 0.8045 (m) REVERT: J 213 PHE cc_start: 0.7266 (t80) cc_final: 0.7048 (OUTLIER) REVERT: J 331 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7505 (mtp85) REVERT: J 334 LYS cc_start: 0.7947 (pttt) cc_final: 0.7290 (mptt) REVERT: K 213 PHE cc_start: 0.7237 (t80) cc_final: 0.6972 (OUTLIER) REVERT: K 253 ASN cc_start: 0.8370 (t0) cc_final: 0.8079 (t0) REVERT: K 331 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7448 (mtp85) REVERT: L 81 MET cc_start: 0.5249 (ttp) cc_final: 0.4841 (ttp) REVERT: L 94 PHE cc_start: 0.7749 (t80) cc_final: 0.7538 (t80) REVERT: L 146 LEU cc_start: 0.7456 (mp) cc_final: 0.7001 (tt) REVERT: L 191 ASP cc_start: 0.7695 (t0) cc_final: 0.7290 (m-30) REVERT: L 243 MET cc_start: 0.7452 (ttt) cc_final: 0.7096 (ttp) REVERT: L 267 TRP cc_start: 0.7339 (m100) cc_final: 0.6931 (m100) REVERT: L 331 ARG cc_start: 0.7809 (mtp85) cc_final: 0.6946 (mtm-85) REVERT: L 333 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7343 (mmtt) REVERT: L 340 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6920 (mtm-85) REVERT: L 355 SER cc_start: 0.8375 (t) cc_final: 0.8102 (m) outliers start: 89 outliers final: 35 residues processed: 459 average time/residue: 1.3385 time to fit residues: 694.6492 Evaluate side-chains 424 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 382 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 239 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 230 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 105 GLN E 105 GLN G 105 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.200014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148856 restraints weight = 23898.805| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.29 r_work: 0.3722 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21428 Z= 0.130 Angle : 0.615 8.073 29133 Z= 0.294 Chirality : 0.043 0.185 3543 Planarity : 0.004 0.035 3542 Dihedral : 9.404 120.525 2923 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.21 % Allowed : 19.26 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 2.23 (0.17), residues: 2663 helix: 2.57 (0.12), residues: 1698 sheet: 0.34 (0.30), residues: 285 loop : -0.90 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 181 HIS 0.003 0.001 HIS H 110 PHE 0.030 0.001 PHE K 202 TYR 0.014 0.001 TYR I 270 ARG 0.009 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 1358) hydrogen bonds : angle 4.11494 ( 3978) covalent geometry : bond 0.00295 (21428) covalent geometry : angle 0.61486 (29133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 400 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7953 (mt-10) cc_final: 0.6759 (mp0) REVERT: A 111 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7619 (mmpt) REVERT: A 127 ASP cc_start: 0.8449 (m-30) cc_final: 0.7896 (m-30) REVERT: B 23 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7903 (mtmp) REVERT: B 108 TYR cc_start: 0.7578 (m-10) cc_final: 0.6958 (m-80) REVERT: C 27 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7107 (ttp80) REVERT: C 60 GLU cc_start: 0.7801 (tp30) cc_final: 0.7430 (tp30) REVERT: C 83 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7655 (mm110) REVERT: C 111 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8042 (mtpt) REVERT: C 127 ASP cc_start: 0.8055 (m-30) cc_final: 0.7695 (m-30) REVERT: D 59 GLU cc_start: 0.7774 (mp0) cc_final: 0.7062 (mp0) REVERT: D 126 LYS cc_start: 0.7267 (ttpt) cc_final: 0.6606 (mttp) REVERT: E 111 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7493 (mmpt) REVERT: E 127 ASP cc_start: 0.8430 (m-30) cc_final: 0.7882 (m-30) REVERT: F 59 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6482 (mm-30) REVERT: F 108 TYR cc_start: 0.7504 (m-10) cc_final: 0.6940 (m-80) REVERT: F 128 MET cc_start: 0.8912 (mmm) cc_final: 0.8606 (mmp) REVERT: G 16 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8154 (mtp180) REVERT: G 27 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7197 (ttt-90) REVERT: G 83 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7633 (mm110) REVERT: G 111 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7985 (mtpt) REVERT: G 127 ASP cc_start: 0.8151 (m-30) cc_final: 0.7917 (m-30) REVERT: G 139 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5586 (mt-10) REVERT: H 59 GLU cc_start: 0.7713 (mp0) cc_final: 0.6967 (mp0) REVERT: H 126 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6606 (mmtp) REVERT: I 196 LEU cc_start: 0.7734 (mt) cc_final: 0.7498 (mt) REVERT: I 243 MET cc_start: 0.7428 (ttt) cc_final: 0.7113 (ttp) REVERT: I 267 TRP cc_start: 0.7273 (m100) cc_final: 0.6895 (m100) REVERT: I 331 ARG cc_start: 0.7819 (mtp85) cc_final: 0.6949 (mtm-85) REVERT: I 333 LYS cc_start: 0.7695 (mmpt) cc_final: 0.7292 (mmpt) REVERT: I 340 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7117 (mtm-85) REVERT: I 355 SER cc_start: 0.8378 (t) cc_final: 0.8037 (m) REVERT: J 213 PHE cc_start: 0.7246 (t80) cc_final: 0.7015 (t80) REVERT: J 267 TRP cc_start: 0.7332 (m100) cc_final: 0.6960 (m-10) REVERT: J 331 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7585 (mtp85) REVERT: J 334 LYS cc_start: 0.7928 (pttt) cc_final: 0.7281 (mptt) REVERT: K 196 LEU cc_start: 0.7455 (mm) cc_final: 0.7217 (mm) REVERT: K 213 PHE cc_start: 0.7185 (t80) cc_final: 0.6950 (t80) REVERT: K 267 TRP cc_start: 0.7303 (m100) cc_final: 0.6748 (m-10) REVERT: K 331 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7417 (mtp85) REVERT: L 81 MET cc_start: 0.5156 (ttp) cc_final: 0.4715 (ttp) REVERT: L 94 PHE cc_start: 0.7612 (t80) cc_final: 0.7400 (t80) REVERT: L 146 LEU cc_start: 0.7460 (mp) cc_final: 0.7006 (tt) REVERT: L 191 ASP cc_start: 0.7600 (t0) cc_final: 0.7296 (m-30) REVERT: L 243 MET cc_start: 0.7405 (ttt) cc_final: 0.7034 (ttp) REVERT: L 267 TRP cc_start: 0.7362 (m100) cc_final: 0.7016 (m100) REVERT: L 331 ARG cc_start: 0.7804 (mtp85) cc_final: 0.6932 (mtm-85) REVERT: L 333 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7358 (mmtt) REVERT: L 340 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6948 (mtm-85) REVERT: L 355 SER cc_start: 0.8384 (t) cc_final: 0.8106 (m) outliers start: 72 outliers final: 35 residues processed: 445 average time/residue: 1.3832 time to fit residues: 698.9990 Evaluate side-chains 435 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 393 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 400 GLU Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 143 optimal weight: 0.0980 chunk 241 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN F 70 ASN F 106 ASN G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.194247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141675 restraints weight = 24018.030| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.32 r_work: 0.3645 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 21428 Z= 0.335 Angle : 0.789 9.228 29133 Z= 0.391 Chirality : 0.050 0.199 3543 Planarity : 0.004 0.041 3542 Dihedral : 10.435 145.912 2923 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.37 % Allowed : 19.04 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.26 (0.17), residues: 2663 helix: 1.82 (0.12), residues: 1705 sheet: -0.04 (0.29), residues: 288 loop : -1.34 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 181 HIS 0.006 0.002 HIS B 30 PHE 0.042 0.002 PHE I 94 TYR 0.017 0.002 TYR I 270 ARG 0.008 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 1358) hydrogen bonds : angle 4.59025 ( 3978) covalent geometry : bond 0.00818 (21428) covalent geometry : angle 0.78917 (29133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 411 time to evaluate : 2.364 Fit side-chains revert: symmetry clash REVERT: A 20 SER cc_start: 0.8061 (t) cc_final: 0.7820 (m) REVERT: A 24 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: A 31 GLU cc_start: 0.7941 (mt-10) cc_final: 0.6701 (mp0) REVERT: A 41 LYS cc_start: 0.7825 (mmtp) cc_final: 0.7598 (mmtm) REVERT: A 111 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7447 (mmpt) REVERT: A 127 ASP cc_start: 0.8502 (m-30) cc_final: 0.7913 (m-30) REVERT: B 23 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7859 (mtpt) REVERT: B 39 GLU cc_start: 0.7383 (pt0) cc_final: 0.6739 (pm20) REVERT: B 59 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6652 (mt-10) REVERT: B 70 ASN cc_start: 0.7583 (p0) cc_final: 0.7263 (p0) REVERT: B 108 TYR cc_start: 0.7504 (m-10) cc_final: 0.6873 (m-80) REVERT: B 128 MET cc_start: 0.8890 (mmm) cc_final: 0.8524 (mmp) REVERT: B 134 GLN cc_start: 0.7207 (tp40) cc_final: 0.6640 (mt0) REVERT: C 27 ARG cc_start: 0.7439 (ttp80) cc_final: 0.6936 (ttp80) REVERT: C 60 GLU cc_start: 0.7707 (tp30) cc_final: 0.7447 (tp30) REVERT: C 127 ASP cc_start: 0.7930 (m-30) cc_final: 0.7575 (m-30) REVERT: C 139 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5034 (mt-10) REVERT: D 56 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7742 (t0) REVERT: D 83 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: D 126 LYS cc_start: 0.7289 (ttpt) cc_final: 0.6458 (mttp) REVERT: E 111 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7431 (mmpt) REVERT: E 127 ASP cc_start: 0.8567 (m-30) cc_final: 0.8005 (m-30) REVERT: F 39 GLU cc_start: 0.7776 (pt0) cc_final: 0.7522 (pt0) REVERT: F 108 TYR cc_start: 0.7461 (m-10) cc_final: 0.6850 (m-80) REVERT: F 128 MET cc_start: 0.8846 (mmm) cc_final: 0.8571 (mmp) REVERT: F 134 GLN cc_start: 0.7161 (tp40) cc_final: 0.6599 (mt0) REVERT: G 16 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8201 (mtp180) REVERT: G 27 ARG cc_start: 0.7521 (ttp80) cc_final: 0.6972 (ttp80) REVERT: G 111 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8057 (mtpt) REVERT: G 139 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5150 (mt-10) REVERT: H 126 LYS cc_start: 0.7254 (ttpt) cc_final: 0.6411 (mttp) REVERT: I 81 MET cc_start: 0.5260 (ttp) cc_final: 0.4828 (ttp) REVERT: I 267 TRP cc_start: 0.7343 (m100) cc_final: 0.6920 (m100) REVERT: I 331 ARG cc_start: 0.7756 (mtp85) cc_final: 0.6991 (mtm-85) REVERT: I 340 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7055 (mtp-110) REVERT: I 355 SER cc_start: 0.8210 (t) cc_final: 0.7997 (m) REVERT: J 213 PHE cc_start: 0.7419 (t80) cc_final: 0.7112 (t80) REVERT: J 331 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7460 (mtp85) REVERT: J 400 GLU cc_start: 0.7112 (mp0) cc_final: 0.6839 (mp0) REVERT: K 213 PHE cc_start: 0.7380 (t80) cc_final: 0.7085 (t80) REVERT: K 331 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7312 (mtp85) REVERT: K 341 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7717 (mmm160) REVERT: L 81 MET cc_start: 0.5252 (ttp) cc_final: 0.4846 (ttp) REVERT: L 267 TRP cc_start: 0.7345 (m100) cc_final: 0.6976 (m100) REVERT: L 331 ARG cc_start: 0.7790 (mtp85) cc_final: 0.6965 (mtm-85) REVERT: L 333 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7313 (mmtt) REVERT: L 340 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7017 (mtp-110) REVERT: L 355 SER cc_start: 0.8268 (t) cc_final: 0.8060 (m) outliers start: 98 outliers final: 51 residues processed: 480 average time/residue: 1.4119 time to fit residues: 763.4866 Evaluate side-chains 454 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 393 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 422 THR Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 226 optimal weight: 50.0000 chunk 77 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN G 105 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 434 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.199493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149462 restraints weight = 23913.014| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.22 r_work: 0.3716 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21428 Z= 0.132 Angle : 0.646 9.741 29133 Z= 0.310 Chirality : 0.044 0.213 3543 Planarity : 0.004 0.036 3542 Dihedral : 9.671 127.655 2919 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.90 % Allowed : 20.73 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 1.90 (0.17), residues: 2663 helix: 2.37 (0.12), residues: 1699 sheet: -0.04 (0.29), residues: 285 loop : -1.07 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 181 HIS 0.003 0.001 HIS I 259 PHE 0.041 0.001 PHE L 94 TYR 0.013 0.001 TYR I 270 ARG 0.010 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 1358) hydrogen bonds : angle 4.24104 ( 3978) covalent geometry : bond 0.00299 (21428) covalent geometry : angle 0.64570 (29133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 404 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7877 (mt-10) cc_final: 0.6583 (mp0) REVERT: A 111 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7491 (mmpt) REVERT: A 127 ASP cc_start: 0.8443 (m-30) cc_final: 0.7878 (m-30) REVERT: B 23 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7863 (mtmm) REVERT: B 59 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6651 (mt-10) REVERT: B 70 ASN cc_start: 0.7596 (p0) cc_final: 0.7364 (p0) REVERT: B 108 TYR cc_start: 0.7501 (m-10) cc_final: 0.6852 (m-80) REVERT: B 114 GLU cc_start: 0.8250 (tt0) cc_final: 0.7855 (mt-10) REVERT: C 27 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7101 (ttp80) REVERT: C 60 GLU cc_start: 0.7743 (tp30) cc_final: 0.7397 (tp30) REVERT: C 83 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7530 (mm110) REVERT: C 127 ASP cc_start: 0.7957 (m-30) cc_final: 0.7580 (m-30) REVERT: C 139 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5331 (mt-10) REVERT: D 41 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7749 (mmtt) REVERT: D 59 GLU cc_start: 0.7661 (mp0) cc_final: 0.7027 (mp0) REVERT: D 126 LYS cc_start: 0.7118 (ttpt) cc_final: 0.6433 (mmtp) REVERT: E 111 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7466 (mmpt) REVERT: E 127 ASP cc_start: 0.8429 (m-30) cc_final: 0.7857 (m-30) REVERT: F 39 GLU cc_start: 0.7744 (pt0) cc_final: 0.6880 (pm20) REVERT: F 40 GLU cc_start: 0.8014 (mp0) cc_final: 0.7661 (mp0) REVERT: F 108 TYR cc_start: 0.7452 (m-10) cc_final: 0.6850 (m-80) REVERT: F 114 GLU cc_start: 0.8232 (tt0) cc_final: 0.7861 (mt-10) REVERT: F 128 MET cc_start: 0.8851 (mmm) cc_final: 0.8558 (mmp) REVERT: G 16 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8054 (mtp180) REVERT: G 27 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7155 (ttp80) REVERT: G 60 GLU cc_start: 0.7688 (tp30) cc_final: 0.7458 (tp30) REVERT: G 83 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7546 (mm110) REVERT: G 111 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: G 139 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5404 (mt-10) REVERT: H 41 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7766 (mmtt) REVERT: H 56 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7709 (t0) REVERT: H 126 LYS cc_start: 0.7119 (ttpt) cc_final: 0.6464 (mmtp) REVERT: I 81 MET cc_start: 0.5097 (ttp) cc_final: 0.4626 (ttp) REVERT: I 196 LEU cc_start: 0.7606 (mt) cc_final: 0.7332 (mt) REVERT: I 243 MET cc_start: 0.7283 (ttt) cc_final: 0.6988 (ttp) REVERT: I 267 TRP cc_start: 0.7185 (m100) cc_final: 0.6869 (m100) REVERT: I 331 ARG cc_start: 0.7807 (mtp85) cc_final: 0.6964 (mtp180) REVERT: I 333 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7502 (mmpt) REVERT: I 355 SER cc_start: 0.8255 (t) cc_final: 0.7950 (m) REVERT: J 196 LEU cc_start: 0.7379 (mm) cc_final: 0.7085 (OUTLIER) REVERT: J 213 PHE cc_start: 0.7375 (t80) cc_final: 0.7103 (t80) REVERT: J 267 TRP cc_start: 0.7240 (m100) cc_final: 0.6604 (m-10) REVERT: J 331 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7442 (mtp85) REVERT: K 213 PHE cc_start: 0.7333 (t80) cc_final: 0.7053 (OUTLIER) REVERT: K 267 TRP cc_start: 0.7167 (m100) cc_final: 0.6744 (m-10) REVERT: K 331 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7254 (mtp85) REVERT: L 81 MET cc_start: 0.5041 (ttp) cc_final: 0.4596 (ttp) REVERT: L 243 MET cc_start: 0.7317 (ttt) cc_final: 0.6950 (ttp) REVERT: L 293 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8137 (p) REVERT: L 331 ARG cc_start: 0.7766 (mtp85) cc_final: 0.6932 (mtp180) REVERT: L 333 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7347 (mmtt) REVERT: L 355 SER cc_start: 0.8308 (t) cc_final: 0.8029 (m) outliers start: 65 outliers final: 31 residues processed: 449 average time/residue: 1.3475 time to fit residues: 682.6549 Evaluate side-chains 423 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 387 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 244 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 256 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN G 105 GLN I 155 GLN I 195 ASN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN L 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.198225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146367 restraints weight = 23858.033| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.28 r_work: 0.3696 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21428 Z= 0.158 Angle : 0.662 10.418 29133 Z= 0.319 Chirality : 0.044 0.215 3543 Planarity : 0.004 0.096 3542 Dihedral : 9.687 127.114 2919 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.59 % Allowed : 21.62 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 1.94 (0.17), residues: 2663 helix: 2.39 (0.12), residues: 1702 sheet: -0.01 (0.30), residues: 285 loop : -1.08 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP I 181 HIS 0.003 0.001 HIS D 110 PHE 0.063 0.002 PHE I 94 TYR 0.018 0.001 TYR I 188 ARG 0.010 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 1358) hydrogen bonds : angle 4.24637 ( 3978) covalent geometry : bond 0.00374 (21428) covalent geometry : angle 0.66217 (29133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 390 time to evaluate : 2.396 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6806 (mp0) REVERT: A 111 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7596 (mmpt) REVERT: A 127 ASP cc_start: 0.8429 (m-30) cc_final: 0.8055 (m-30) REVERT: B 23 LYS cc_start: 0.8260 (mtpp) cc_final: 0.8013 (mtmm) REVERT: B 59 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6711 (mt-10) REVERT: B 70 ASN cc_start: 0.7662 (p0) cc_final: 0.7405 (p0) REVERT: B 108 TYR cc_start: 0.7575 (m-10) cc_final: 0.6945 (m-80) REVERT: B 128 MET cc_start: 0.8987 (mmm) cc_final: 0.8659 (mmp) REVERT: C 83 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7594 (mm110) REVERT: C 93 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8033 (mmmt) REVERT: C 127 ASP cc_start: 0.8031 (m-30) cc_final: 0.7656 (m-30) REVERT: C 139 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5406 (mt-10) REVERT: D 56 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7628 (t0) REVERT: D 59 GLU cc_start: 0.7719 (mp0) cc_final: 0.6959 (mp0) REVERT: D 126 LYS cc_start: 0.7250 (ttpt) cc_final: 0.6598 (mmtp) REVERT: E 111 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7516 (mmpt) REVERT: E 127 ASP cc_start: 0.8540 (m-30) cc_final: 0.7987 (m-30) REVERT: F 39 GLU cc_start: 0.7768 (pt0) cc_final: 0.6939 (pm20) REVERT: F 40 GLU cc_start: 0.8121 (mp0) cc_final: 0.7754 (mp0) REVERT: F 70 ASN cc_start: 0.7739 (p0) cc_final: 0.7191 (p0) REVERT: F 108 TYR cc_start: 0.7567 (m-10) cc_final: 0.6999 (m-80) REVERT: F 114 GLU cc_start: 0.8282 (tt0) cc_final: 0.7917 (mt-10) REVERT: F 128 MET cc_start: 0.8938 (mmm) cc_final: 0.8635 (mmp) REVERT: G 16 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8149 (mtp180) REVERT: G 27 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7190 (ttp80) REVERT: G 83 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7606 (mm110) REVERT: G 111 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8040 (mtpt) REVERT: G 139 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5484 (mt-10) REVERT: H 56 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7783 (t0) REVERT: H 126 LYS cc_start: 0.7286 (ttpt) cc_final: 0.6631 (mmtp) REVERT: I 81 MET cc_start: 0.5172 (ttp) cc_final: 0.4732 (ttp) REVERT: I 196 LEU cc_start: 0.7730 (mt) cc_final: 0.7448 (mt) REVERT: I 243 MET cc_start: 0.7495 (ttt) cc_final: 0.7144 (ttp) REVERT: I 267 TRP cc_start: 0.7290 (m100) cc_final: 0.6972 (m100) REVERT: I 331 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7013 (mtp180) REVERT: I 333 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7604 (mmpt) REVERT: I 355 SER cc_start: 0.8373 (t) cc_final: 0.8094 (m) REVERT: J 196 LEU cc_start: 0.7435 (mm) cc_final: 0.7211 (mm) REVERT: J 213 PHE cc_start: 0.7428 (t80) cc_final: 0.7157 (t80) REVERT: J 267 TRP cc_start: 0.7272 (m100) cc_final: 0.6683 (m-10) REVERT: J 331 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7526 (mtp85) REVERT: J 400 GLU cc_start: 0.7070 (mp0) cc_final: 0.6831 (mp0) REVERT: K 36 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.3928 (mtt) REVERT: K 213 PHE cc_start: 0.7458 (t80) cc_final: 0.7180 (t80) REVERT: K 267 TRP cc_start: 0.7252 (m100) cc_final: 0.6843 (m-10) REVERT: K 331 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7348 (mtp85) REVERT: L 81 MET cc_start: 0.5101 (ttp) cc_final: 0.4683 (ttp) REVERT: L 146 LEU cc_start: 0.7479 (mp) cc_final: 0.7006 (tt) REVERT: L 243 MET cc_start: 0.7514 (ttt) cc_final: 0.7154 (ttp) REVERT: L 293 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8239 (p) REVERT: L 331 ARG cc_start: 0.7822 (mtp85) cc_final: 0.6990 (mtp180) REVERT: L 333 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7419 (mmtt) REVERT: L 355 SER cc_start: 0.8384 (t) cc_final: 0.8113 (m) REVERT: L 397 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6733 (tm) outliers start: 58 outliers final: 35 residues processed: 432 average time/residue: 1.3843 time to fit residues: 683.2710 Evaluate side-chains 439 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 393 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 422 THR Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 214 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 105 GLN E 105 GLN G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN K 434 ASN L 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.198765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147114 restraints weight = 23944.062| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.27 r_work: 0.3709 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 21428 Z= 0.155 Angle : 0.665 10.662 29133 Z= 0.321 Chirality : 0.044 0.250 3543 Planarity : 0.004 0.078 3542 Dihedral : 9.624 125.715 2919 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.41 % Allowed : 22.02 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 1.95 (0.17), residues: 2663 helix: 2.37 (0.12), residues: 1706 sheet: -0.02 (0.30), residues: 285 loop : -1.02 (0.27), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 181 HIS 0.004 0.001 HIS C 30 PHE 0.085 0.002 PHE I 94 TYR 0.019 0.001 TYR I 270 ARG 0.010 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 1358) hydrogen bonds : angle 4.24788 ( 3978) covalent geometry : bond 0.00367 (21428) covalent geometry : angle 0.66455 (29133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 401 time to evaluate : 2.142 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7964 (mt-10) cc_final: 0.6797 (mp0) REVERT: A 111 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7594 (mmpt) REVERT: A 127 ASP cc_start: 0.8421 (m-30) cc_final: 0.8044 (m-30) REVERT: B 23 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7889 (mtmp) REVERT: B 59 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6778 (mt-10) REVERT: B 70 ASN cc_start: 0.7652 (p0) cc_final: 0.7438 (p0) REVERT: B 108 TYR cc_start: 0.7545 (m-10) cc_final: 0.6948 (m-80) REVERT: B 114 GLU cc_start: 0.8286 (tt0) cc_final: 0.7919 (mt-10) REVERT: B 128 MET cc_start: 0.8994 (mmm) cc_final: 0.8732 (mmp) REVERT: C 60 GLU cc_start: 0.7728 (tp30) cc_final: 0.7469 (tp30) REVERT: C 83 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7601 (mm110) REVERT: C 93 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8056 (mmmt) REVERT: C 127 ASP cc_start: 0.8032 (m-30) cc_final: 0.7648 (m-30) REVERT: C 139 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5514 (mt-10) REVERT: D 56 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7620 (t0) REVERT: D 59 GLU cc_start: 0.7730 (mp0) cc_final: 0.6978 (mp0) REVERT: D 126 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6600 (mmtp) REVERT: E 111 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7582 (mmpt) REVERT: E 127 ASP cc_start: 0.8537 (m-30) cc_final: 0.7983 (m-30) REVERT: F 39 GLU cc_start: 0.7756 (pt0) cc_final: 0.6934 (pm20) REVERT: F 40 GLU cc_start: 0.8150 (mp0) cc_final: 0.7930 (mp0) REVERT: F 70 ASN cc_start: 0.7730 (p0) cc_final: 0.7205 (p0) REVERT: F 108 TYR cc_start: 0.7534 (m-10) cc_final: 0.6950 (m-80) REVERT: F 114 GLU cc_start: 0.8278 (tt0) cc_final: 0.7919 (mt-10) REVERT: F 128 MET cc_start: 0.8934 (mmm) cc_final: 0.8634 (mmp) REVERT: G 16 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8146 (mtp180) REVERT: G 83 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7650 (mm110) REVERT: G 111 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7998 (mtpt) REVERT: G 139 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5514 (mt-10) REVERT: H 56 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7762 (t0) REVERT: H 126 LYS cc_start: 0.7360 (ttpt) cc_final: 0.6709 (mmtp) REVERT: I 196 LEU cc_start: 0.7717 (mt) cc_final: 0.7438 (mt) REVERT: I 243 MET cc_start: 0.7437 (ttt) cc_final: 0.7114 (ttp) REVERT: I 267 TRP cc_start: 0.7383 (m100) cc_final: 0.7054 (m100) REVERT: I 331 ARG cc_start: 0.7860 (mtp85) cc_final: 0.6970 (mtm-85) REVERT: I 333 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7541 (mmpt) REVERT: I 355 SER cc_start: 0.8381 (t) cc_final: 0.8089 (m) REVERT: J 196 LEU cc_start: 0.7401 (mm) cc_final: 0.7193 (mm) REVERT: J 213 PHE cc_start: 0.7423 (t80) cc_final: 0.7162 (t80) REVERT: J 267 TRP cc_start: 0.7255 (m100) cc_final: 0.6781 (m-10) REVERT: J 331 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7529 (mtp85) REVERT: J 400 GLU cc_start: 0.7360 (mp0) cc_final: 0.7096 (mp0) REVERT: K 36 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.3866 (mtt) REVERT: K 213 PHE cc_start: 0.7445 (t80) cc_final: 0.7176 (t80) REVERT: K 267 TRP cc_start: 0.7230 (m100) cc_final: 0.6865 (m-10) REVERT: K 331 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7334 (mtp85) REVERT: L 81 MET cc_start: 0.5068 (ttp) cc_final: 0.4657 (ttp) REVERT: L 98 ILE cc_start: 0.7744 (mm) cc_final: 0.7458 (mp) REVERT: L 146 LEU cc_start: 0.7477 (mp) cc_final: 0.7109 (tt) REVERT: L 243 MET cc_start: 0.7466 (ttt) cc_final: 0.7132 (ttp) REVERT: L 293 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8218 (p) REVERT: L 331 ARG cc_start: 0.7811 (mtp85) cc_final: 0.6978 (mtp180) REVERT: L 333 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7483 (mmtt) REVERT: L 355 SER cc_start: 0.8409 (t) cc_final: 0.8137 (m) outliers start: 54 outliers final: 34 residues processed: 439 average time/residue: 1.3427 time to fit residues: 665.8041 Evaluate side-chains 435 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 391 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 422 THR Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 105 GLN E 105 GLN G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN K 434 ASN L 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.199988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149810 restraints weight = 23721.589| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.22 r_work: 0.3723 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21428 Z= 0.133 Angle : 0.652 11.276 29133 Z= 0.311 Chirality : 0.044 0.249 3543 Planarity : 0.004 0.066 3542 Dihedral : 9.441 121.282 2919 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.59 % Allowed : 21.80 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 2.08 (0.17), residues: 2663 helix: 2.49 (0.12), residues: 1706 sheet: -0.03 (0.30), residues: 285 loop : -0.97 (0.27), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I 181 HIS 0.004 0.001 HIS C 30 PHE 0.041 0.001 PHE I 94 TYR 0.018 0.001 TYR I 270 ARG 0.010 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 1358) hydrogen bonds : angle 4.17465 ( 3978) covalent geometry : bond 0.00305 (21428) covalent geometry : angle 0.65220 (29133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19412.77 seconds wall clock time: 329 minutes 50.00 seconds (19790.00 seconds total)