Starting phenix.real_space_refine on Sun Aug 24 15:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1s_36800/08_2025/8k1s_36800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1s_36800/08_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_36800/08_2025/8k1s_36800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1s_36800/08_2025/8k1s_36800.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1s_36800/08_2025/8k1s_36800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1s_36800/08_2025/8k1s_36800.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.28, per 1000 atoms: 0.25 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: 1.97 Conformation dependent library (CDL) restraints added in 903.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.76 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: 4.07 Time building geometry restraints manager: 2.54 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: 0.02 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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.940 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG I 417 TYR 0.003 0.001 TYR F 73 PHE 0.024 0.001 PHE J 202 TRP 0.003 0.001 TRP J 158 HIS 0.003 0.001 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00372 (21428) covalent geometry : angle 0.60951 (29133) hydrogen bonds : bond 0.24391 ( 1358) hydrogen bonds : angle 7.02181 ( 3978) *********************** 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 : 0.792 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: 0.6107 time to fit residues: 450.8037 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 : 0.796 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 83 GLN C 38 ASN C 61 ASN C 70 ASN C 110 HIS D 51 HIS ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN F 106 ASN 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** ** J 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 GLN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.206527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166724 restraints weight = 23920.153| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.49 r_work: 0.3796 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21428 Z= 0.186 Angle : 0.662 7.131 29133 Z= 0.327 Chirality : 0.045 0.157 3543 Planarity : 0.004 0.037 3542 Dihedral : 9.872 128.800 2927 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.92 % Allowed : 13.82 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.16), residues: 2663 helix: 2.11 (0.12), residues: 1686 sheet: 0.72 (0.29), residues: 288 loop : -0.92 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 340 TYR 0.013 0.001 TYR I 270 PHE 0.037 0.002 PHE J 202 TRP 0.015 0.001 TRP L 181 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00431 (21428) covalent geometry : angle 0.66215 (29133) hydrogen bonds : bond 0.04524 ( 1358) hydrogen bonds : angle 4.62004 ( 3978) *********************** 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 547 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 459 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7109 (mp0) REVERT: A 111 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7795 (mmpt) REVERT: A 127 ASP cc_start: 0.8370 (m-30) cc_final: 0.7868 (m-30) REVERT: B 23 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8077 (mtpt) REVERT: B 108 TYR cc_start: 0.7597 (m-10) cc_final: 0.7042 (m-80) REVERT: B 127 ASP cc_start: 0.8396 (m-30) cc_final: 0.8036 (m-30) REVERT: C 111 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7809 (mmpt) REVERT: C 127 ASP cc_start: 0.8082 (m-30) cc_final: 0.7840 (m-30) REVERT: C 135 SER cc_start: 0.7818 (m) cc_final: 0.7539 (m) REVERT: D 64 LEU cc_start: 0.7888 (mm) cc_final: 0.7455 (mm) REVERT: D 83 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: D 126 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7068 (mmtp) REVERT: E 111 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7771 (mmpt) REVERT: E 127 ASP cc_start: 0.8440 (m-30) cc_final: 0.7936 (m-30) REVERT: F 23 LYS cc_start: 0.8268 (mtpp) cc_final: 0.8045 (mtpt) REVERT: F 60 GLU cc_start: 0.7791 (tp30) cc_final: 0.7463 (tp30) REVERT: F 108 TYR cc_start: 0.7478 (m-10) cc_final: 0.6940 (m-10) REVERT: F 127 ASP cc_start: 0.8301 (m-30) cc_final: 0.7970 (m-30) REVERT: G 111 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7782 (mmpt) REVERT: G 114 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7421 (mt-10) REVERT: G 135 SER cc_start: 0.7804 (m) cc_final: 0.7541 (m) REVERT: H 126 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7029 (mmtp) REVERT: I 91 PHE cc_start: 0.7325 (t80) cc_final: 0.7060 (t80) REVERT: I 146 LEU cc_start: 0.7827 (tt) cc_final: 0.7476 (tt) REVERT: I 150 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6165 (pt) REVERT: I 151 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6684 (tpt-90) REVERT: I 196 LEU cc_start: 0.7954 (mt) cc_final: 0.7669 (mt) REVERT: I 243 MET cc_start: 0.7772 (ttt) cc_final: 0.7359 (ttp) REVERT: I 267 TRP cc_start: 0.7371 (m100) cc_final: 0.6969 (m100) REVERT: I 331 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7186 (mtm-85) REVERT: I 333 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7764 (mmpt) REVERT: I 355 SER cc_start: 0.8488 (t) cc_final: 0.8109 (m) REVERT: J 196 LEU cc_start: 0.7819 (mt) cc_final: 0.7199 (tp) REVERT: J 331 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7579 (mtp85) REVERT: J 334 LYS cc_start: 0.7747 (pttt) cc_final: 0.7414 (mptt) REVERT: J 340 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7719 (mtp85) REVERT: K 331 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7677 (mtp85) REVERT: L 58 THR cc_start: 0.6384 (m) cc_final: 0.6175 (p) REVERT: L 91 PHE cc_start: 0.7263 (t80) cc_final: 0.7006 (t80) REVERT: L 146 LEU cc_start: 0.7326 (mp) cc_final: 0.6844 (tt) REVERT: L 150 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6110 (pt) REVERT: L 243 MET cc_start: 0.7760 (ttt) cc_final: 0.7387 (ttp) REVERT: L 267 TRP cc_start: 0.7478 (m100) cc_final: 0.7123 (m100) REVERT: L 331 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7141 (mtm-85) REVERT: L 333 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7621 (mmtt) REVERT: L 355 SER cc_start: 0.8487 (t) cc_final: 0.8086 (m) outliers start: 88 outliers final: 31 residues processed: 513 average time/residue: 0.6691 time to fit residues: 387.1252 Evaluate side-chains 449 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 410 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 105 GLN 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 111 LYS 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 150 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 150 ILE 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 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 223 THR 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 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 E 134 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.207318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.167691 restraints weight = 24188.473| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.44 r_work: 0.3823 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21428 Z= 0.130 Angle : 0.601 6.790 29133 Z= 0.291 Chirality : 0.043 0.164 3543 Planarity : 0.004 0.036 3542 Dihedral : 9.491 125.972 2927 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.57 % Allowed : 16.36 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.17), residues: 2663 helix: 2.49 (0.12), residues: 1686 sheet: 0.62 (0.29), residues: 285 loop : -0.93 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 27 TYR 0.009 0.001 TYR G 45 PHE 0.032 0.001 PHE K 202 TRP 0.020 0.001 TRP L 181 HIS 0.003 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00287 (21428) covalent geometry : angle 0.60057 (29133) hydrogen bonds : bond 0.03792 ( 1358) hydrogen bonds : angle 4.25837 ( 3978) *********************** 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 507 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 427 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7102 (mp0) REVERT: A 111 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7858 (mmpt) REVERT: A 127 ASP cc_start: 0.8249 (m-30) cc_final: 0.7779 (m-30) REVERT: B 23 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7992 (mtpt) REVERT: B 93 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8018 (mmtm) REVERT: B 108 TYR cc_start: 0.7475 (m-80) cc_final: 0.6952 (m-80) REVERT: B 127 ASP cc_start: 0.8256 (m-30) cc_final: 0.7933 (m-30) REVERT: C 16 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8334 (mtp180) REVERT: C 27 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7401 (mtm110) REVERT: C 60 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: C 111 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7826 (mmpt) REVERT: D 23 LYS cc_start: 0.8009 (mttp) cc_final: 0.7796 (mttm) REVERT: D 56 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7682 (t0) REVERT: D 126 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7076 (mmtp) REVERT: E 111 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7810 (mmpt) REVERT: E 127 ASP cc_start: 0.8290 (m-30) cc_final: 0.7822 (m-30) REVERT: F 23 LYS cc_start: 0.8250 (mtpp) cc_final: 0.8029 (mtpt) REVERT: F 60 GLU cc_start: 0.7678 (tp30) cc_final: 0.7299 (tp30) REVERT: F 108 TYR cc_start: 0.7429 (m-80) cc_final: 0.6916 (m-80) REVERT: F 127 ASP cc_start: 0.8274 (m-30) cc_final: 0.7913 (m-30) REVERT: G 16 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8309 (mtp180) REVERT: G 60 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: G 111 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7761 (mmpt) REVERT: G 135 SER cc_start: 0.7799 (m) cc_final: 0.7354 (p) REVERT: H 56 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7668 (t0) REVERT: H 59 GLU cc_start: 0.7961 (mp0) cc_final: 0.7374 (mp0) REVERT: H 126 LYS cc_start: 0.7562 (ttpt) cc_final: 0.7000 (mmtp) REVERT: I 94 PHE cc_start: 0.7745 (t80) cc_final: 0.7523 (t80) REVERT: I 100 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.5490 (ttt) REVERT: I 196 LEU cc_start: 0.8044 (mt) cc_final: 0.7787 (mt) REVERT: I 243 MET cc_start: 0.7705 (ttt) cc_final: 0.7399 (ttp) REVERT: I 267 TRP cc_start: 0.7343 (m100) cc_final: 0.6991 (m100) REVERT: I 331 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7248 (mtm-85) REVERT: I 355 SER cc_start: 0.8503 (t) cc_final: 0.8209 (m) REVERT: J 134 PHE cc_start: 0.6443 (t80) cc_final: 0.6236 (t80) REVERT: J 143 ILE cc_start: 0.8181 (mt) cc_final: 0.7940 (mm) REVERT: J 331 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7619 (mtt-85) REVERT: J 334 LYS cc_start: 0.7792 (pttt) cc_final: 0.7447 (mptt) REVERT: K 143 ILE cc_start: 0.8174 (mt) cc_final: 0.7937 (mm) REVERT: K 196 LEU cc_start: 0.7831 (mt) cc_final: 0.7076 (tp) REVERT: K 243 MET cc_start: 0.7470 (ttp) cc_final: 0.7224 (ttt) REVERT: K 331 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7487 (mtp85) REVERT: K 395 MET cc_start: 0.8122 (mtp) cc_final: 0.7764 (mtp) REVERT: L 81 MET cc_start: 0.5428 (ttp) cc_final: 0.5219 (ttp) REVERT: L 94 PHE cc_start: 0.7811 (t80) cc_final: 0.7523 (t80) REVERT: L 146 LEU cc_start: 0.7296 (mp) cc_final: 0.6922 (tt) REVERT: L 181 TRP cc_start: 0.6825 (m-10) cc_final: 0.6588 (m-10) REVERT: L 243 MET cc_start: 0.7752 (ttt) cc_final: 0.7465 (ttp) REVERT: L 267 TRP cc_start: 0.7494 (m100) cc_final: 0.7181 (m100) REVERT: L 331 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7161 (mtm-85) REVERT: L 333 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7649 (mmtt) REVERT: L 355 SER cc_start: 0.8490 (t) cc_final: 0.8197 (m) outliers start: 80 outliers final: 29 residues processed: 477 average time/residue: 0.6312 time to fit residues: 339.6702 Evaluate side-chains 431 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 392 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 93 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 60 GLU 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 F residue 130 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 60 GLU 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 106 ASN Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 189 VAL 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 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 L residue 189 VAL Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 262 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 30 optimal weight: 0.0070 chunk 16 optimal weight: 0.0980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 51 HIS B 106 ASN E 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** L 434 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.208405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168820 restraints weight = 24222.555| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.47 r_work: 0.3835 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21428 Z= 0.116 Angle : 0.587 7.583 29133 Z= 0.282 Chirality : 0.042 0.184 3543 Planarity : 0.003 0.036 3542 Dihedral : 9.196 123.498 2923 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.66 % Allowed : 16.85 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.17), residues: 2663 helix: 2.68 (0.12), residues: 1690 sheet: 0.56 (0.29), residues: 285 loop : -0.88 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 27 TYR 0.011 0.001 TYR I 270 PHE 0.030 0.001 PHE I 202 TRP 0.020 0.001 TRP L 181 HIS 0.003 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00251 (21428) covalent geometry : angle 0.58720 (29133) hydrogen bonds : bond 0.03395 ( 1358) hydrogen bonds : angle 4.08418 ( 3978) *********************** 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 512 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 430 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7095 (mp0) REVERT: A 111 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7851 (mmpt) REVERT: A 127 ASP cc_start: 0.8230 (m-30) cc_final: 0.7744 (m-30) REVERT: B 23 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8056 (mtpt) REVERT: B 60 GLU cc_start: 0.7530 (tp30) cc_final: 0.7111 (tp30) REVERT: B 108 TYR cc_start: 0.7450 (m-10) cc_final: 0.6981 (m-80) REVERT: B 127 ASP cc_start: 0.8254 (m-30) cc_final: 0.7913 (m-30) REVERT: C 16 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8287 (mtp180) REVERT: C 27 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7453 (ttp80) REVERT: C 60 GLU cc_start: 0.7728 (tp30) cc_final: 0.7240 (tp30) REVERT: C 111 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8127 (mtpt) REVERT: C 127 ASP cc_start: 0.8039 (m-30) cc_final: 0.7785 (m-30) REVERT: D 23 LYS cc_start: 0.7958 (mttp) cc_final: 0.7728 (mttm) REVERT: D 59 GLU cc_start: 0.7914 (mp0) cc_final: 0.7536 (mp0) REVERT: D 126 LYS cc_start: 0.7539 (ttpt) cc_final: 0.7051 (mmtp) REVERT: E 111 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7808 (mmpt) REVERT: E 127 ASP cc_start: 0.8300 (m-30) cc_final: 0.7818 (m-30) REVERT: F 23 LYS cc_start: 0.8257 (mtpp) cc_final: 0.8026 (mtpt) REVERT: F 60 GLU cc_start: 0.7654 (tp30) cc_final: 0.7310 (tp30) REVERT: F 108 TYR cc_start: 0.7416 (m-10) cc_final: 0.6962 (m-80) REVERT: F 127 ASP cc_start: 0.8198 (m-30) cc_final: 0.7854 (m-30) REVERT: G 16 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8291 (mtp180) REVERT: G 27 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7419 (ttp80) REVERT: G 111 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7764 (mmpt) REVERT: G 114 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7322 (mt-10) REVERT: G 135 SER cc_start: 0.7759 (m) cc_final: 0.7431 (p) REVERT: H 59 GLU cc_start: 0.7976 (mp0) cc_final: 0.7436 (mp0) REVERT: H 126 LYS cc_start: 0.7546 (ttpt) cc_final: 0.6992 (mmtp) REVERT: I 94 PHE cc_start: 0.7693 (t80) cc_final: 0.7486 (t80) REVERT: I 191 ASP cc_start: 0.7378 (m-30) cc_final: 0.7017 (m-30) REVERT: I 196 LEU cc_start: 0.8103 (mt) cc_final: 0.7843 (mt) REVERT: I 243 MET cc_start: 0.7667 (ttt) cc_final: 0.7352 (ttp) REVERT: I 267 TRP cc_start: 0.7413 (m100) cc_final: 0.7061 (m100) REVERT: I 331 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7224 (mtm-85) REVERT: I 340 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6521 (mtp-110) REVERT: I 355 SER cc_start: 0.8485 (t) cc_final: 0.8164 (m) REVERT: J 243 MET cc_start: 0.7446 (ttp) cc_final: 0.7193 (ttt) REVERT: J 267 TRP cc_start: 0.7489 (m100) cc_final: 0.7241 (m-10) REVERT: J 323 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7656 (mp) REVERT: J 331 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7612 (mtp85) REVERT: J 334 LYS cc_start: 0.7833 (pttt) cc_final: 0.7463 (mptt) REVERT: K 196 LEU cc_start: 0.7761 (mt) cc_final: 0.7052 (tp) REVERT: K 331 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7498 (mtp85) REVERT: L 94 PHE cc_start: 0.7683 (t80) cc_final: 0.7457 (t80) REVERT: L 146 LEU cc_start: 0.7359 (mp) cc_final: 0.6911 (tt) REVERT: L 188 TYR cc_start: 0.6761 (m-80) cc_final: 0.6542 (m-10) REVERT: L 243 MET cc_start: 0.7690 (ttt) cc_final: 0.7387 (ttp) REVERT: L 277 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8687 (ptm-80) REVERT: L 331 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7034 (mtm-85) REVERT: L 333 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7499 (mmpt) REVERT: L 340 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6538 (mtp-110) REVERT: L 355 SER cc_start: 0.8490 (t) cc_final: 0.8169 (m) outliers start: 82 outliers final: 23 residues processed: 483 average time/residue: 0.6096 time to fit residues: 332.3600 Evaluate side-chains 435 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 404 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 I residue 277 ARG 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 J residue 323 LEU Chi-restraints excluded: chain K residue 65 VAL 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 277 ARG Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 193 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 243 optimal weight: 0.6980 chunk 200 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 174 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN E 105 GLN I 85 GLN I 174 ASN J 253 ASN K 253 ASN L 85 GLN L 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.202353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151106 restraints weight = 23960.679| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.31 r_work: 0.3747 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21428 Z= 0.118 Angle : 0.589 7.705 29133 Z= 0.282 Chirality : 0.042 0.193 3543 Planarity : 0.004 0.072 3542 Dihedral : 9.099 117.251 2923 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.57 % Allowed : 18.77 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.17), residues: 2663 helix: 2.71 (0.12), residues: 1702 sheet: 0.50 (0.29), residues: 285 loop : -0.78 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 27 TYR 0.013 0.001 TYR I 270 PHE 0.031 0.001 PHE L 202 TRP 0.017 0.001 TRP I 181 HIS 0.004 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00259 (21428) covalent geometry : angle 0.58932 (29133) hydrogen bonds : bond 0.03343 ( 1358) hydrogen bonds : angle 4.05446 ( 3978) *********************** 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 493 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 413 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7908 (mt-10) cc_final: 0.6814 (mp0) REVERT: A 72 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: A 111 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7563 (mmpt) REVERT: A 127 ASP cc_start: 0.8389 (m-30) cc_final: 0.7832 (m-30) REVERT: B 16 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8555 (mtm180) REVERT: B 23 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7939 (mtmp) REVERT: B 60 GLU cc_start: 0.7536 (tp30) cc_final: 0.6969 (tp30) REVERT: B 108 TYR cc_start: 0.7576 (m-10) cc_final: 0.6959 (m-80) REVERT: C 16 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8223 (mtp180) REVERT: C 27 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7282 (ttp80) REVERT: C 60 GLU cc_start: 0.7693 (tp30) cc_final: 0.6978 (tp30) REVERT: C 64 LEU cc_start: 0.7972 (mm) cc_final: 0.7656 (mm) REVERT: C 111 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8042 (mtpt) REVERT: C 127 ASP cc_start: 0.8198 (m-30) cc_final: 0.7842 (m-30) REVERT: D 23 LYS cc_start: 0.7862 (mttp) cc_final: 0.7623 (mttm) REVERT: D 59 GLU cc_start: 0.7739 (mp0) cc_final: 0.7027 (mp0) REVERT: D 126 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6627 (mmtp) REVERT: E 111 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7504 (mmpt) REVERT: E 127 ASP cc_start: 0.8472 (m-30) cc_final: 0.7920 (m-30) REVERT: F 23 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7908 (mtmp) REVERT: F 60 GLU cc_start: 0.7587 (tp30) cc_final: 0.7133 (tp30) REVERT: F 108 TYR cc_start: 0.7561 (m-10) cc_final: 0.7032 (m-80) REVERT: G 16 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8201 (mtp180) REVERT: G 27 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7191 (ttp80) REVERT: G 60 GLU cc_start: 0.7811 (tp30) cc_final: 0.7536 (tp30) REVERT: G 111 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7484 (mmpt) REVERT: G 114 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7412 (mt-10) REVERT: G 127 ASP cc_start: 0.8182 (m-30) cc_final: 0.7828 (m-30) REVERT: G 135 SER cc_start: 0.7499 (m) cc_final: 0.7070 (p) REVERT: H 59 GLU cc_start: 0.7735 (mp0) cc_final: 0.7023 (mp0) REVERT: H 126 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6573 (mmtp) REVERT: I 94 PHE cc_start: 0.7682 (t80) cc_final: 0.7449 (t80) REVERT: I 196 LEU cc_start: 0.7809 (mt) cc_final: 0.7563 (mt) REVERT: I 243 MET cc_start: 0.7414 (ttt) cc_final: 0.7057 (ttp) REVERT: I 267 TRP cc_start: 0.7265 (m100) cc_final: 0.6881 (m100) REVERT: I 277 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8492 (ptm-80) REVERT: I 331 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7003 (mtm-85) REVERT: I 340 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6658 (mtp-110) REVERT: I 355 SER cc_start: 0.8362 (t) cc_final: 0.7992 (m) REVERT: J 267 TRP cc_start: 0.7285 (m100) cc_final: 0.6997 (m-10) REVERT: J 323 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7509 (mp) REVERT: J 331 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7449 (mtp85) REVERT: J 334 LYS cc_start: 0.7918 (pttt) cc_final: 0.7312 (mptt) REVERT: K 196 LEU cc_start: 0.7687 (mt) cc_final: 0.6875 (tp) REVERT: K 267 TRP cc_start: 0.7310 (m100) cc_final: 0.6729 (m-10) REVERT: K 323 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7538 (mp) REVERT: K 331 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7353 (mtp85) REVERT: K 400 GLU cc_start: 0.7245 (mp0) cc_final: 0.6882 (mp0) REVERT: L 94 PHE cc_start: 0.7669 (t80) cc_final: 0.7400 (t80) REVERT: L 146 LEU cc_start: 0.7253 (mp) cc_final: 0.6880 (tt) REVERT: L 181 TRP cc_start: 0.7020 (m-90) cc_final: 0.6814 (m-90) REVERT: L 243 MET cc_start: 0.7451 (ttt) cc_final: 0.7093 (ttp) REVERT: L 277 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8535 (ptm-80) REVERT: L 331 ARG cc_start: 0.7738 (mtp85) cc_final: 0.6807 (mtm-85) REVERT: L 333 LYS cc_start: 0.7806 (mmtm) cc_final: 0.7221 (mmpt) REVERT: L 340 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6738 (mtm-85) REVERT: L 355 SER cc_start: 0.8398 (t) cc_final: 0.8028 (m) outliers start: 80 outliers final: 27 residues processed: 465 average time/residue: 0.6882 time to fit residues: 359.7819 Evaluate side-chains 434 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 396 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 72 GLU 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 G residue 131 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR 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 J residue 323 LEU Chi-restraints excluded: chain K residue 65 VAL 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 323 LEU Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 340 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 0.0870 chunk 155 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 37 optimal weight: 0.0070 chunk 219 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN E 105 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 ASN K 253 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 174 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 = 0.4302 r_free = 0.4302 target = 0.201826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151440 restraints weight = 23743.378| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.24 r_work: 0.3735 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3970 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= 0.129 Angle : 0.598 8.092 29133 Z= 0.287 Chirality : 0.043 0.184 3543 Planarity : 0.004 0.063 3542 Dihedral : 9.194 119.040 2923 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.57 % Allowed : 19.26 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.17), residues: 2663 helix: 2.68 (0.12), residues: 1703 sheet: 0.40 (0.30), residues: 285 loop : -0.72 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 340 TYR 0.017 0.001 TYR L 188 PHE 0.030 0.001 PHE L 202 TRP 0.019 0.001 TRP I 181 HIS 0.003 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00294 (21428) covalent geometry : angle 0.59830 (29133) hydrogen bonds : bond 0.03405 ( 1358) hydrogen bonds : angle 4.06620 ( 3978) *********************** 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 492 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 412 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7954 (mt-10) cc_final: 0.6840 (mp0) REVERT: A 111 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7577 (mmpt) REVERT: A 127 ASP cc_start: 0.8452 (m-30) cc_final: 0.7912 (m-30) REVERT: B 23 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7923 (mtmp) REVERT: B 39 GLU cc_start: 0.7165 (pt0) cc_final: 0.6836 (mp0) REVERT: B 60 GLU cc_start: 0.7580 (tp30) cc_final: 0.7014 (tp30) REVERT: B 70 ASN cc_start: 0.7455 (p0) cc_final: 0.7247 (p0) REVERT: B 108 TYR cc_start: 0.7570 (m-10) cc_final: 0.6967 (m-80) REVERT: B 114 GLU cc_start: 0.8310 (tt0) cc_final: 0.8069 (mt-10) REVERT: B 128 MET cc_start: 0.8879 (tpt) cc_final: 0.8542 (mmp) REVERT: C 16 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8106 (mtp180) REVERT: C 27 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7281 (ttp80) REVERT: C 60 GLU cc_start: 0.7731 (tp30) cc_final: 0.7070 (tp30) REVERT: C 64 LEU cc_start: 0.7999 (mm) cc_final: 0.7743 (mm) REVERT: C 83 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7707 (mm110) REVERT: C 111 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8085 (mtpt) REVERT: C 127 ASP cc_start: 0.8249 (m-30) cc_final: 0.7889 (m-30) REVERT: C 139 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5785 (mt-10) REVERT: D 23 LYS cc_start: 0.7799 (mttp) cc_final: 0.7558 (mttm) REVERT: D 59 GLU cc_start: 0.7786 (mp0) cc_final: 0.7145 (mp0) REVERT: D 126 LYS cc_start: 0.7291 (ttpt) cc_final: 0.6667 (mmtp) REVERT: E 111 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7544 (mmpt) REVERT: E 127 ASP cc_start: 0.8484 (m-30) cc_final: 0.7962 (m-30) REVERT: F 23 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7947 (mtpt) REVERT: F 59 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6481 (mm-30) REVERT: F 60 GLU cc_start: 0.7563 (tp30) cc_final: 0.7114 (tp30) REVERT: F 62 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: F 70 ASN cc_start: 0.7508 (p0) cc_final: 0.7297 (p0) REVERT: F 108 TYR cc_start: 0.7507 (m-10) cc_final: 0.6956 (m-80) REVERT: F 114 GLU cc_start: 0.8305 (tt0) cc_final: 0.8091 (mt-10) REVERT: F 128 MET cc_start: 0.8783 (tpt) cc_final: 0.8517 (mmp) REVERT: G 16 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8070 (mtp180) REVERT: G 27 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7122 (ttp80) REVERT: G 83 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7649 (mm110) REVERT: G 111 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8001 (mtpt) REVERT: G 127 ASP cc_start: 0.8175 (m-30) cc_final: 0.7873 (m-30) REVERT: G 135 SER cc_start: 0.7566 (m) cc_final: 0.7049 (p) REVERT: G 139 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5814 (mt-10) REVERT: H 59 GLU cc_start: 0.7731 (mp0) cc_final: 0.7154 (mp0) REVERT: H 126 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6617 (mmtp) REVERT: I 94 PHE cc_start: 0.7650 (t80) cc_final: 0.7390 (t80) REVERT: I 196 LEU cc_start: 0.7796 (mt) cc_final: 0.7550 (mt) REVERT: I 243 MET cc_start: 0.7473 (ttt) cc_final: 0.7090 (ttp) REVERT: I 267 TRP cc_start: 0.7230 (m100) cc_final: 0.6867 (m100) REVERT: I 277 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8501 (ptm-80) REVERT: I 331 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7027 (mtm-85) REVERT: I 340 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6749 (mtp-110) REVERT: I 355 SER cc_start: 0.8363 (t) cc_final: 0.8068 (m) REVERT: J 243 MET cc_start: 0.7141 (ttp) cc_final: 0.6921 (ttt) REVERT: J 331 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7566 (mtp85) REVERT: J 334 LYS cc_start: 0.7968 (pttt) cc_final: 0.7365 (mptt) REVERT: K 196 LEU cc_start: 0.7769 (mt) cc_final: 0.6951 (tp) REVERT: K 267 TRP cc_start: 0.7353 (m100) cc_final: 0.6735 (m-10) REVERT: K 331 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7354 (mtp85) REVERT: L 94 PHE cc_start: 0.7620 (t80) cc_final: 0.7306 (t80) REVERT: L 146 LEU cc_start: 0.7324 (mp) cc_final: 0.6926 (tt) REVERT: L 243 MET cc_start: 0.7462 (ttt) cc_final: 0.7173 (ttp) REVERT: L 277 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8615 (ptm-80) REVERT: L 331 ARG cc_start: 0.7688 (mtp85) cc_final: 0.6859 (mtm-85) REVERT: L 333 LYS cc_start: 0.7843 (mmtm) cc_final: 0.7336 (mmtt) REVERT: L 340 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6872 (mtp-110) REVERT: L 355 SER cc_start: 0.8427 (t) cc_final: 0.8069 (m) outliers start: 80 outliers final: 30 residues processed: 465 average time/residue: 0.6902 time to fit residues: 360.0419 Evaluate side-chains 437 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 396 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 35 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 131 LYS 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 106 ASN Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 283 SER 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 36 MET Chi-restraints excluded: chain K residue 65 VAL 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 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 277 ARG 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 86 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN E 105 GLN F 110 HIS ** I 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN ** L 174 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 = 0.4283 r_free = 0.4283 target = 0.200349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148470 restraints weight = 24014.298| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.31 r_work: 0.3710 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21428 Z= 0.153 Angle : 0.633 9.536 29133 Z= 0.305 Chirality : 0.044 0.249 3543 Planarity : 0.004 0.058 3542 Dihedral : 9.399 123.219 2923 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.39 % Allowed : 19.93 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.17), residues: 2663 helix: 2.54 (0.12), residues: 1706 sheet: 0.30 (0.30), residues: 285 loop : -0.89 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 69 TYR 0.019 0.001 TYR L 188 PHE 0.031 0.001 PHE K 202 TRP 0.032 0.001 TRP J 267 HIS 0.004 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00360 (21428) covalent geometry : angle 0.63250 (29133) hydrogen bonds : bond 0.03591 ( 1358) hydrogen bonds : angle 4.14347 ( 3978) *********************** 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 486 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 410 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7983 (mt-10) cc_final: 0.6796 (mp0) REVERT: A 72 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: A 111 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7563 (mmpt) REVERT: A 127 ASP cc_start: 0.8493 (m-30) cc_final: 0.7931 (m-30) REVERT: B 23 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7912 (mtmp) REVERT: B 39 GLU cc_start: 0.7443 (pt0) cc_final: 0.6740 (pm20) REVERT: B 108 TYR cc_start: 0.7621 (m-10) cc_final: 0.6958 (m-80) REVERT: B 114 GLU cc_start: 0.8316 (tt0) cc_final: 0.7875 (mt-10) REVERT: C 16 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.8127 (mtp180) REVERT: C 60 GLU cc_start: 0.7809 (tp30) cc_final: 0.7141 (tp30) REVERT: C 64 LEU cc_start: 0.8046 (mm) cc_final: 0.7812 (mm) REVERT: C 83 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7705 (mm110) REVERT: C 111 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8085 (mtpt) REVERT: C 127 ASP cc_start: 0.8232 (m-30) cc_final: 0.7977 (m-30) REVERT: C 139 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5742 (mt-10) REVERT: D 23 LYS cc_start: 0.7752 (mttp) cc_final: 0.7534 (mttm) REVERT: D 59 GLU cc_start: 0.7857 (mp0) cc_final: 0.7054 (mp0) REVERT: D 126 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6655 (mmtp) REVERT: E 111 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7562 (mmpt) REVERT: E 127 ASP cc_start: 0.8554 (m-30) cc_final: 0.8015 (m-30) REVERT: F 23 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7932 (mtmp) REVERT: F 60 GLU cc_start: 0.7538 (tp30) cc_final: 0.7128 (tp30) REVERT: F 62 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: F 108 TYR cc_start: 0.7543 (m-10) cc_final: 0.6964 (m-80) REVERT: F 114 GLU cc_start: 0.8283 (tt0) cc_final: 0.8030 (mt-10) REVERT: G 16 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8087 (mtp180) REVERT: G 27 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7087 (ttp80) REVERT: G 60 GLU cc_start: 0.7742 (tp30) cc_final: 0.7507 (tp30) REVERT: G 111 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8007 (mtpt) REVERT: G 127 ASP cc_start: 0.8244 (m-30) cc_final: 0.8000 (m-30) REVERT: G 135 SER cc_start: 0.7609 (m) cc_final: 0.7086 (p) REVERT: G 139 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5695 (mt-10) REVERT: H 56 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7813 (t0) REVERT: H 126 LYS cc_start: 0.7288 (ttpt) cc_final: 0.6570 (mmtp) REVERT: I 94 PHE cc_start: 0.7619 (t80) cc_final: 0.7354 (t80) REVERT: I 243 MET cc_start: 0.7472 (ttt) cc_final: 0.7087 (ttp) REVERT: I 267 TRP cc_start: 0.7261 (m100) cc_final: 0.6915 (m100) REVERT: I 277 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8639 (ptm-80) REVERT: I 331 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7012 (mtm-85) REVERT: I 340 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6792 (mtp-110) REVERT: I 355 SER cc_start: 0.8404 (t) cc_final: 0.8132 (m) REVERT: J 213 PHE cc_start: 0.7273 (t80) cc_final: 0.7049 (t80) REVERT: J 331 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7511 (mtp85) REVERT: J 334 LYS cc_start: 0.7956 (pttt) cc_final: 0.7294 (mptt) REVERT: J 400 GLU cc_start: 0.7417 (mp0) cc_final: 0.7127 (mp0) REVERT: K 81 MET cc_start: 0.6318 (ttm) cc_final: 0.6113 (ttp) REVERT: K 213 PHE cc_start: 0.7220 (t80) cc_final: 0.6974 (t80) REVERT: K 331 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7464 (mtp85) REVERT: K 400 GLU cc_start: 0.7321 (mp0) cc_final: 0.6978 (mp0) REVERT: L 94 PHE cc_start: 0.7645 (t80) cc_final: 0.7345 (t80) REVERT: L 146 LEU cc_start: 0.7328 (mp) cc_final: 0.6947 (tt) REVERT: L 243 MET cc_start: 0.7475 (ttt) cc_final: 0.7125 (ttp) REVERT: L 277 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8656 (ptm-80) REVERT: L 331 ARG cc_start: 0.7775 (mtp85) cc_final: 0.6915 (mtm-85) REVERT: L 333 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7390 (mmtt) REVERT: L 340 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6976 (mtp-110) REVERT: L 355 SER cc_start: 0.8386 (t) cc_final: 0.8116 (m) outliers start: 76 outliers final: 34 residues processed: 454 average time/residue: 0.6895 time to fit residues: 351.3195 Evaluate side-chains 445 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 60 GLU Chi-restraints excluded: chain A residue 72 GLU 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 111 LYS 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 35 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 131 LYS 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 56 ASN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 422 THR 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 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG 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 174 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 19 optimal weight: 0.0570 chunk 209 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN J 253 ASN K 253 ASN L 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.201386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150384 restraints weight = 23906.982| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.29 r_work: 0.3742 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21428 Z= 0.117 Angle : 0.606 8.861 29133 Z= 0.289 Chirality : 0.043 0.293 3543 Planarity : 0.004 0.050 3542 Dihedral : 9.147 117.752 2923 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.85 % Allowed : 20.60 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.17), residues: 2663 helix: 2.68 (0.12), residues: 1703 sheet: 0.21 (0.29), residues: 285 loop : -0.80 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 69 TYR 0.021 0.001 TYR L 188 PHE 0.030 0.001 PHE L 136 TRP 0.043 0.001 TRP J 267 HIS 0.005 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00260 (21428) covalent geometry : angle 0.60590 (29133) hydrogen bonds : bond 0.03218 ( 1358) hydrogen bonds : angle 4.04964 ( 3978) *********************** 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 471 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 407 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8000 (mt-10) cc_final: 0.6879 (mp0) REVERT: A 72 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: A 111 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7690 (mmpt) REVERT: A 127 ASP cc_start: 0.8504 (m-30) cc_final: 0.7957 (m-30) REVERT: B 23 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7973 (mtmp) REVERT: B 39 GLU cc_start: 0.7471 (pt0) cc_final: 0.6793 (pm20) REVERT: B 40 GLU cc_start: 0.8199 (mp0) cc_final: 0.7929 (mp0) REVERT: B 60 GLU cc_start: 0.7546 (tp30) cc_final: 0.7005 (tp30) REVERT: B 108 TYR cc_start: 0.7605 (m-10) cc_final: 0.7019 (m-80) REVERT: B 114 GLU cc_start: 0.8312 (tt0) cc_final: 0.8106 (mt-10) REVERT: C 16 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8099 (mtp180) REVERT: C 60 GLU cc_start: 0.7824 (tp30) cc_final: 0.7283 (tp30) REVERT: C 83 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7739 (mm110) REVERT: C 111 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8076 (mtpt) REVERT: C 127 ASP cc_start: 0.8249 (m-30) cc_final: 0.7893 (m-30) REVERT: C 139 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5889 (mt-10) REVERT: D 23 LYS cc_start: 0.7805 (mttp) cc_final: 0.7593 (mttm) REVERT: D 59 GLU cc_start: 0.7844 (mp0) cc_final: 0.7206 (mp0) REVERT: D 126 LYS cc_start: 0.7308 (ttpt) cc_final: 0.6771 (mmtp) REVERT: E 111 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7633 (mmpt) REVERT: E 127 ASP cc_start: 0.8540 (m-30) cc_final: 0.7982 (m-30) REVERT: F 16 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8552 (mtm180) REVERT: F 23 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7953 (mtmp) REVERT: F 60 GLU cc_start: 0.7604 (tp30) cc_final: 0.7232 (tp30) REVERT: F 62 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: F 108 TYR cc_start: 0.7589 (m-10) cc_final: 0.7013 (m-80) REVERT: F 114 GLU cc_start: 0.8253 (tt0) cc_final: 0.7987 (mt-10) REVERT: G 16 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8044 (mtp180) REVERT: G 83 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7739 (mm110) REVERT: G 111 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8046 (mtpt) REVERT: G 127 ASP cc_start: 0.8250 (m-30) cc_final: 0.7903 (m-30) REVERT: G 135 SER cc_start: 0.7662 (m) cc_final: 0.7242 (p) REVERT: G 139 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5943 (mt-10) REVERT: H 59 GLU cc_start: 0.7863 (mp0) cc_final: 0.7257 (mp0) REVERT: H 126 LYS cc_start: 0.7306 (ttpt) cc_final: 0.6740 (mmtp) REVERT: I 94 PHE cc_start: 0.7517 (t80) cc_final: 0.7234 (t80) REVERT: I 243 MET cc_start: 0.7424 (ttt) cc_final: 0.7086 (ttp) REVERT: I 277 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8296 (ptm-80) REVERT: I 331 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7083 (mtm-85) REVERT: I 340 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6902 (mtm-85) REVERT: I 355 SER cc_start: 0.8481 (t) cc_final: 0.8205 (m) REVERT: J 243 MET cc_start: 0.7225 (ttp) cc_final: 0.7021 (ttt) REVERT: J 331 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7570 (mtp85) REVERT: J 400 GLU cc_start: 0.7520 (mp0) cc_final: 0.7226 (mp0) REVERT: K 147 ILE cc_start: 0.6730 (mt) cc_final: 0.6510 (mt) REVERT: K 213 PHE cc_start: 0.7286 (t80) cc_final: 0.7069 (t80) REVERT: K 267 TRP cc_start: 0.7403 (m100) cc_final: 0.6824 (m-10) REVERT: K 331 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7372 (mtp85) REVERT: K 400 GLU cc_start: 0.7492 (mp0) cc_final: 0.7110 (mp0) REVERT: L 94 PHE cc_start: 0.7547 (t80) cc_final: 0.7211 (t80) REVERT: L 146 LEU cc_start: 0.7308 (mp) cc_final: 0.6906 (tt) REVERT: L 243 MET cc_start: 0.7391 (ttt) cc_final: 0.7079 (ttp) REVERT: L 277 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8499 (ptm-80) REVERT: L 331 ARG cc_start: 0.7803 (mtp85) cc_final: 0.6970 (mtm-85) REVERT: L 333 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7424 (mmtt) REVERT: L 340 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7199 (mtm-85) REVERT: L 355 SER cc_start: 0.8535 (t) cc_final: 0.8215 (m) outliers start: 64 outliers final: 29 residues processed: 443 average time/residue: 0.6826 time to fit residues: 339.7082 Evaluate side-chains 430 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 60 GLU Chi-restraints excluded: chain A residue 72 GLU 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 C residue 131 LYS 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 F residue 62 GLU 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 263 VAL Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain J residue 36 MET 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 74 VAL 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 80 ILE Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 340 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 20 optimal weight: 0.0270 chunk 263 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 226 optimal weight: 50.0000 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- 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 I 174 ASN J 434 ASN ** L 174 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 = 0.4286 r_free = 0.4286 target = 0.200574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148761 restraints weight = 23795.204| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.30 r_work: 0.3714 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21428 Z= 0.150 Angle : 0.639 9.900 29133 Z= 0.307 Chirality : 0.044 0.271 3543 Planarity : 0.004 0.073 3542 Dihedral : 9.369 122.361 2923 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.72 % Allowed : 21.44 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.17), residues: 2663 helix: 2.57 (0.12), residues: 1706 sheet: 0.19 (0.30), residues: 285 loop : -0.86 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 69 TYR 0.018 0.001 TYR L 270 PHE 0.030 0.001 PHE K 202 TRP 0.047 0.002 TRP J 267 HIS 0.005 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00352 (21428) covalent geometry : angle 0.63860 (29133) hydrogen bonds : bond 0.03538 ( 1358) hydrogen bonds : angle 4.13181 ( 3978) *********************** 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 458 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 397 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7959 (mt-10) cc_final: 0.6794 (mp0) REVERT: A 72 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: A 111 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7553 (mmpt) REVERT: A 127 ASP cc_start: 0.8470 (m-30) cc_final: 0.7894 (m-30) REVERT: B 23 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7918 (mtmp) REVERT: B 39 GLU cc_start: 0.7438 (pt0) cc_final: 0.6721 (pm20) REVERT: B 40 GLU cc_start: 0.8211 (mp0) cc_final: 0.7917 (mp0) REVERT: B 108 TYR cc_start: 0.7638 (m-10) cc_final: 0.7051 (m-80) REVERT: B 114 GLU cc_start: 0.8283 (tt0) cc_final: 0.7876 (mt-10) REVERT: C 16 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8112 (mtp180) REVERT: C 60 GLU cc_start: 0.7763 (tp30) cc_final: 0.7212 (tp30) REVERT: C 111 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8045 (mtpt) REVERT: C 127 ASP cc_start: 0.8275 (m-30) cc_final: 0.8006 (m-30) REVERT: C 139 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5813 (mt-10) REVERT: D 23 LYS cc_start: 0.7747 (mttp) cc_final: 0.7535 (mttm) REVERT: D 59 GLU cc_start: 0.7800 (mp0) cc_final: 0.7174 (mp0) REVERT: D 126 LYS cc_start: 0.7282 (ttpt) cc_final: 0.6696 (mmtp) REVERT: E 111 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7521 (mmpt) REVERT: E 127 ASP cc_start: 0.8521 (m-30) cc_final: 0.7974 (m-30) REVERT: F 23 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7922 (mtmp) REVERT: F 39 GLU cc_start: 0.7631 (pt0) cc_final: 0.6864 (pm20) REVERT: F 40 GLU cc_start: 0.8113 (mp0) cc_final: 0.7859 (mp0) REVERT: F 60 GLU cc_start: 0.7509 (tp30) cc_final: 0.6987 (tp30) REVERT: F 62 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: F 108 TYR cc_start: 0.7569 (m-10) cc_final: 0.6951 (m-80) REVERT: F 114 GLU cc_start: 0.8277 (tt0) cc_final: 0.7905 (mt-10) REVERT: G 16 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8064 (mtp180) REVERT: G 83 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7719 (mm110) REVERT: G 111 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7518 (mmpt) REVERT: G 127 ASP cc_start: 0.8269 (m-30) cc_final: 0.7975 (m-30) REVERT: G 135 SER cc_start: 0.7642 (m) cc_final: 0.7149 (p) REVERT: G 139 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5802 (mt-10) REVERT: H 126 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6659 (mmtp) REVERT: I 94 PHE cc_start: 0.7560 (t80) cc_final: 0.7255 (t80) REVERT: I 243 MET cc_start: 0.7424 (ttt) cc_final: 0.7067 (ttp) REVERT: I 277 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8589 (ptm-80) REVERT: I 331 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7061 (mtm-85) REVERT: I 340 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6892 (mtp-110) REVERT: I 355 SER cc_start: 0.8438 (t) cc_final: 0.8175 (m) REVERT: J 213 PHE cc_start: 0.7303 (t80) cc_final: 0.7054 (t80) REVERT: J 331 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7413 (mtp85) REVERT: J 400 GLU cc_start: 0.7484 (mp0) cc_final: 0.7166 (mp0) REVERT: K 147 ILE cc_start: 0.6720 (mt) cc_final: 0.6491 (mt) REVERT: K 213 PHE cc_start: 0.7280 (t80) cc_final: 0.7023 (t80) REVERT: K 331 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7446 (mtp85) REVERT: K 400 GLU cc_start: 0.7392 (mp0) cc_final: 0.6956 (mp0) REVERT: L 94 PHE cc_start: 0.7605 (t80) cc_final: 0.7271 (t80) REVERT: L 146 LEU cc_start: 0.7283 (mp) cc_final: 0.6894 (tt) REVERT: L 243 MET cc_start: 0.7418 (ttt) cc_final: 0.7127 (ttp) REVERT: L 277 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8650 (ptm-80) REVERT: L 331 ARG cc_start: 0.7765 (mtp85) cc_final: 0.6904 (mtm-85) REVERT: L 333 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7372 (mmtt) REVERT: L 340 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7121 (mtp-110) REVERT: L 355 SER cc_start: 0.8410 (t) cc_final: 0.8140 (m) outliers start: 61 outliers final: 32 residues processed: 433 average time/residue: 0.7050 time to fit residues: 342.6167 Evaluate side-chains 439 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 395 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 60 GLU Chi-restraints excluded: chain A residue 72 GLU 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 111 LYS 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 F residue 62 GLU 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 106 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 36 MET 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 74 VAL 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 L residue 277 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 226 optimal weight: 50.0000 chunk 171 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 83 GLN C 105 GLN E 105 GLN I 174 ASN L 174 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.196105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144220 restraints weight = 23932.546| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.27 r_work: 0.3673 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21428 Z= 0.233 Angle : 0.722 10.850 29133 Z= 0.352 Chirality : 0.047 0.304 3543 Planarity : 0.004 0.071 3542 Dihedral : 10.004 136.396 2923 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.54 % Allowed : 21.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.17), residues: 2663 helix: 2.19 (0.12), residues: 1713 sheet: 0.09 (0.29), residues: 285 loop : -1.13 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 69 TYR 0.015 0.002 TYR I 188 PHE 0.035 0.002 PHE J 202 TRP 0.058 0.003 TRP J 267 HIS 0.006 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00566 (21428) covalent geometry : angle 0.72174 (29133) hydrogen bonds : bond 0.04189 ( 1358) hydrogen bonds : angle 4.36298 ( 3978) ********************** 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 460 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 403 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.8135 (t) cc_final: 0.7924 (m) REVERT: A 24 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: A 31 GLU cc_start: 0.7982 (mt-10) cc_final: 0.6821 (mp0) REVERT: A 111 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7583 (mmpt) REVERT: A 127 ASP cc_start: 0.8568 (m-30) cc_final: 0.7999 (m-30) REVERT: B 23 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7967 (mtmp) REVERT: B 39 GLU cc_start: 0.7550 (pt0) cc_final: 0.6789 (pm20) REVERT: B 59 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 108 TYR cc_start: 0.7613 (m-10) cc_final: 0.7006 (m-80) REVERT: B 114 GLU cc_start: 0.8297 (tt0) cc_final: 0.7873 (mt-10) REVERT: B 127 ASP cc_start: 0.8247 (m-30) cc_final: 0.7921 (m-30) REVERT: B 134 GLN cc_start: 0.7322 (tp40) cc_final: 0.6721 (mt0) REVERT: C 16 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8189 (mtp180) REVERT: C 27 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7266 (ttp80) REVERT: C 60 GLU cc_start: 0.7786 (tp30) cc_final: 0.7381 (tp30) REVERT: C 127 ASP cc_start: 0.8301 (m-30) cc_final: 0.8090 (m-30) REVERT: C 139 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5533 (mt-10) REVERT: D 23 LYS cc_start: 0.7757 (mttp) cc_final: 0.7546 (mttm) REVERT: D 41 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7918 (mmtt) REVERT: D 126 LYS cc_start: 0.7394 (ttpt) cc_final: 0.6663 (mmtp) REVERT: E 111 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7601 (mmpt) REVERT: E 127 ASP cc_start: 0.8616 (m-30) cc_final: 0.8062 (m-30) REVERT: F 23 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7938 (mtmp) REVERT: F 39 GLU cc_start: 0.7788 (pt0) cc_final: 0.6912 (pm20) REVERT: F 62 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: F 108 TYR cc_start: 0.7570 (m-10) cc_final: 0.6964 (m-80) REVERT: F 114 GLU cc_start: 0.8270 (tt0) cc_final: 0.7861 (mt-10) REVERT: F 134 GLN cc_start: 0.7289 (tp40) cc_final: 0.6705 (mt0) REVERT: G 16 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8140 (mtp180) REVERT: G 27 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7144 (ttp80) REVERT: G 60 GLU cc_start: 0.7868 (tp30) cc_final: 0.7616 (tp30) REVERT: G 111 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8170 (mtpt) REVERT: G 139 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5555 (mt-10) REVERT: H 41 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7926 (mmtt) REVERT: H 126 LYS cc_start: 0.7354 (ttpt) cc_final: 0.6639 (mttp) REVERT: I 94 PHE cc_start: 0.7577 (t80) cc_final: 0.7308 (t80) REVERT: I 331 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7075 (mtp180) REVERT: I 340 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7007 (mtp-110) REVERT: I 355 SER cc_start: 0.8402 (t) cc_final: 0.8193 (m) REVERT: J 213 PHE cc_start: 0.7488 (t80) cc_final: 0.7191 (t80) REVERT: J 331 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7542 (mtp85) REVERT: J 400 GLU cc_start: 0.7489 (mp0) cc_final: 0.7086 (mp0) REVERT: K 147 ILE cc_start: 0.6831 (mt) cc_final: 0.6601 (mt) REVERT: K 196 LEU cc_start: 0.7804 (mt) cc_final: 0.7449 (mt) REVERT: K 213 PHE cc_start: 0.7460 (t80) cc_final: 0.7159 (t80) REVERT: K 331 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7336 (mtp85) REVERT: K 400 GLU cc_start: 0.7427 (mp0) cc_final: 0.7016 (mp0) REVERT: L 94 PHE cc_start: 0.7659 (t80) cc_final: 0.7364 (t80) REVERT: L 146 LEU cc_start: 0.7461 (mp) cc_final: 0.7136 (tt) REVERT: L 293 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8250 (p) REVERT: L 331 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7027 (mtp180) REVERT: L 333 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7428 (mmtt) REVERT: L 340 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7093 (mtp-110) REVERT: L 355 SER cc_start: 0.8412 (t) cc_final: 0.8207 (m) outliers start: 57 outliers final: 31 residues processed: 444 average time/residue: 0.7271 time to fit residues: 361.0022 Evaluate side-chains 432 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 391 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 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 F residue 62 GLU 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 106 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 422 THR 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 74 VAL 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 L residue 196 LEU Chi-restraints excluded: chain L residue 293 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 159 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 35 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 J 434 ASN K 434 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.199261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147965 restraints weight = 23827.296| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.27 r_work: 0.3710 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21428 Z= 0.147 Angle : 0.655 10.558 29133 Z= 0.315 Chirality : 0.044 0.301 3543 Planarity : 0.004 0.062 3542 Dihedral : 9.593 125.986 2919 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.32 % Allowed : 22.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.17), residues: 2663 helix: 2.39 (0.12), residues: 1706 sheet: 0.05 (0.30), residues: 285 loop : -1.11 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 69 TYR 0.017 0.001 TYR E 45 PHE 0.030 0.001 PHE K 202 TRP 0.052 0.002 TRP J 267 HIS 0.005 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00342 (21428) covalent geometry : angle 0.65470 (29133) hydrogen bonds : bond 0.03584 ( 1358) hydrogen bonds : angle 4.22002 ( 3978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9139.97 seconds wall clock time: 156 minutes 23.75 seconds (9383.75 seconds total)