Starting phenix.real_space_refine on Wed Nov 20 02:27:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/11_2024/8k1s_36800.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/11_2024/8k1s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/11_2024/8k1s_36800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/11_2024/8k1s_36800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/11_2024/8k1s_36800.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1s_36800/11_2024/8k1s_36800.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 S 76 5.16 5 C 13712 2.51 5 N 3398 2.21 5 O 3794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21000 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "B" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "C" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "D" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "E" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "F" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "I" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.04, per 1000 atoms: 0.67 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: 5.06 Conformation dependent library (CDL) restraints added in 2.9 seconds 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4958 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 68.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.689A pdb=" N GLU A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.546A pdb=" N GLY A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 123 through 139 removed outlier: 3.547A pdb=" N GLY B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 59 through 67 Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 123 through 140 removed outlier: 3.547A pdb=" N GLY C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 59 through 67 Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.546A pdb=" N GLY D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 removed outlier: 3.556A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 67 Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU E 94 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 123 through 140 removed outlier: 3.546A pdb=" N GLY E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 131 " --> pdb=" O ASP E 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.557A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.689A pdb=" N GLU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 123 through 139 removed outlier: 3.546A pdb=" N GLY F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 29 removed outlier: 3.558A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 67 Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.689A pdb=" N GLU G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 123 through 140 removed outlier: 3.547A pdb=" N GLY G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS G 131 " --> pdb=" O ASP G 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN G 134 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 29 removed outlier: 3.558A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 67 Processing helix chain 'H' and resid 68 through 71 Processing helix chain 'H' and resid 81 through 95 removed outlier: 3.690A pdb=" N GLU H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 123 through 139 removed outlier: 3.547A pdb=" N GLY H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 35 removed outlier: 3.678A pdb=" N ALA I 21 " --> pdb=" O PRO I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 73 through 102 Processing helix chain 'I' and resid 128 through 157 removed outlier: 3.569A pdb=" N VAL I 132 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 157 through 174 Processing helix chain 'I' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL I 189 " --> pdb=" O MET I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 205 Processing helix chain 'I' and resid 208 through 219 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 251 removed outlier: 3.504A pdb=" N LEU I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 275 Processing helix chain 'I' and resid 285 through 289 Processing helix chain 'I' and resid 290 through 303 removed outlier: 3.578A pdb=" N LEU I 299 " --> pdb=" O VAL I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 331 Processing helix chain 'I' and resid 344 through 373 Processing helix chain 'I' and resid 376 through 389 Processing helix chain 'I' and resid 402 through 419 Processing helix chain 'I' and resid 419 through 427 removed outlier: 3.746A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 35 removed outlier: 3.677A pdb=" N ALA J 21 " --> pdb=" O PRO J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 73 through 102 Processing helix chain 'J' and resid 128 through 157 removed outlier: 3.567A pdb=" N VAL J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 157 through 174 Processing helix chain 'J' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL J 189 " --> pdb=" O MET J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 205 Processing helix chain 'J' and resid 208 through 219 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 225 through 251 removed outlier: 3.503A pdb=" N LEU J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 275 Processing helix chain 'J' and resid 285 through 289 Processing helix chain 'J' and resid 290 through 303 removed outlier: 3.578A pdb=" N LEU J 299 " --> pdb=" O VAL J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 331 Processing helix chain 'J' and resid 344 through 373 Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 402 through 419 Processing helix chain 'J' and resid 419 through 427 removed outlier: 3.745A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 35 removed outlier: 3.677A pdb=" N ALA K 21 " --> pdb=" O PRO K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 73 through 102 Processing helix chain 'K' and resid 128 through 157 removed outlier: 3.569A pdb=" N VAL K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix Processing helix chain 'K' and resid 157 through 174 Processing helix chain 'K' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL K 189 " --> pdb=" O MET K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 205 Processing helix chain 'K' and resid 208 through 219 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 225 through 251 removed outlier: 3.504A pdb=" N LEU K 236 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 275 Processing helix chain 'K' and resid 285 through 289 Processing helix chain 'K' and resid 290 through 303 removed outlier: 3.577A pdb=" N LEU K 299 " --> pdb=" O VAL K 295 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 331 Processing helix chain 'K' and resid 344 through 373 Processing helix chain 'K' and resid 376 through 389 Processing helix chain 'K' and resid 402 through 419 Processing helix chain 'K' and resid 419 through 427 removed outlier: 3.745A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 35 removed outlier: 3.677A pdb=" N ALA L 21 " --> pdb=" O PRO L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 73 through 102 Processing helix chain 'L' and resid 128 through 157 removed outlier: 3.569A pdb=" N VAL L 132 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix Processing helix chain 'L' and resid 157 through 174 Processing helix chain 'L' and resid 185 through 189 removed outlier: 3.976A pdb=" N VAL L 189 " --> pdb=" O MET L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 205 Processing helix chain 'L' and resid 208 through 219 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 225 through 251 removed outlier: 3.504A pdb=" N LEU L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 275 Processing helix chain 'L' and resid 285 through 289 Processing helix chain 'L' and resid 290 through 303 removed outlier: 3.578A pdb=" N LEU L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 344 through 373 Processing helix chain 'L' and resid 376 through 389 Processing helix chain 'L' and resid 402 through 419 Processing helix chain 'L' and resid 419 through 427 removed outlier: 3.744A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.302A pdb=" N VAL A 32 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL A 53 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA A 34 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.304A pdb=" N VAL B 32 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 53 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA B 34 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL C 32 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL C 53 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 34 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 6.304A pdb=" N VAL D 32 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL D 53 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA D 34 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL E 32 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL E 53 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL F 32 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL F 53 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA F 34 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL G 32 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL G 53 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA G 34 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 54 removed outlier: 6.303A pdb=" N VAL H 32 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL H 53 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA H 34 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.739A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1358 hydrogen bonds defined for protein. 3978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.97 Time building geometry restraints manager: 5.66 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: 0.00 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 48.630 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.500 ------------------------------------------------------------------------------- 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= 0.237 Angle : 0.610 15.459 29133 Z= 0.326 Chirality : 0.043 0.287 3543 Planarity : 0.003 0.037 3542 Dihedral : 10.425 143.931 7529 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 4.10 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2663 helix: 1.47 (0.12), residues: 1647 sheet: 0.88 (0.30), residues: 296 loop : -0.93 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 158 HIS 0.003 0.001 HIS E 110 PHE 0.024 0.001 PHE J 202 TYR 0.003 0.001 TYR F 73 ARG 0.002 0.000 ARG I 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 639 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7263 (mp0) REVERT: A 111 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7530 (mmpt) REVERT: B 23 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7738 (mtmm) REVERT: B 126 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7416 (ttpp) REVERT: B 134 GLN cc_start: 0.7508 (tp40) cc_final: 0.7225 (mt0) REVERT: C 35 VAL cc_start: 0.8311 (p) cc_final: 0.8104 (m) REVERT: C 111 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7454 (mmpt) REVERT: E 111 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7592 (mmpt) REVERT: F 23 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7787 (mtpt) REVERT: F 59 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6279 (mt-10) REVERT: F 126 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7356 (ttpp) REVERT: F 127 ASP cc_start: 0.7602 (m-30) cc_final: 0.7354 (m-30) REVERT: G 16 ARG cc_start: 0.8351 (mtm180) cc_final: 0.8070 (mtm-85) REVERT: G 35 VAL cc_start: 0.8303 (p) cc_final: 0.8069 (t) REVERT: G 111 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7381 (mmpt) REVERT: I 158 TRP cc_start: 0.6190 (m100) cc_final: 0.5471 (t60) REVERT: I 331 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7236 (mtm-85) REVERT: I 360 PHE cc_start: 0.6889 (t80) cc_final: 0.6603 (m-10) REVERT: I 394 THR cc_start: 0.8226 (t) cc_final: 0.7854 (t) REVERT: J 81 MET cc_start: 0.7231 (ttm) cc_final: 0.7019 (ttt) REVERT: J 196 LEU cc_start: 0.8001 (mt) cc_final: 0.7445 (tp) REVERT: J 394 THR cc_start: 0.7429 (t) cc_final: 0.6965 (t) REVERT: K 81 MET cc_start: 0.7254 (ttm) cc_final: 0.6979 (ttt) REVERT: K 196 LEU cc_start: 0.8054 (mt) cc_final: 0.7491 (tp) REVERT: K 394 THR cc_start: 0.7357 (t) cc_final: 0.6902 (t) REVERT: L 158 TRP cc_start: 0.6127 (m100) cc_final: 0.5509 (t60) REVERT: L 331 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7175 (mtm-85) REVERT: L 333 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7714 (mmpt) REVERT: L 394 THR cc_start: 0.8366 (t) cc_final: 0.8042 (t) outliers start: 17 outliers final: 2 residues processed: 648 average time/residue: 1.2676 time to fit residues: 938.4745 Evaluate side-chains 441 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 435 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 111 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 206 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 83 GLN C 38 ASN C 61 ASN C 70 ASN C 110 HIS D 51 HIS E 105 GLN F 61 ASN F 83 GLN F 106 ASN F 110 HIS G 38 ASN G 61 ASN G 70 ASN G 110 HIS H 38 ASN I 174 ASN I 434 ASN J 239 ASN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2789 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= 0.209 Angle : 0.632 7.363 29133 Z= 0.310 Chirality : 0.043 0.160 3543 Planarity : 0.004 0.038 3542 Dihedral : 9.742 131.854 2927 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.48 % Allowed : 14.18 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2663 helix: 2.25 (0.12), residues: 1702 sheet: 0.80 (0.29), residues: 288 loop : -0.74 (0.26), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 181 HIS 0.003 0.001 HIS A 110 PHE 0.035 0.002 PHE J 202 TYR 0.013 0.001 TYR I 270 ARG 0.006 0.001 ARG J 340 *********************** 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 536 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 458 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7082 (mp0) REVERT: B 23 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7654 (mtpt) REVERT: B 108 TYR cc_start: 0.6979 (m-10) cc_final: 0.6453 (m-80) REVERT: B 127 ASP cc_start: 0.8157 (m-30) cc_final: 0.7830 (m-30) REVERT: C 16 ARG cc_start: 0.8412 (mtm180) cc_final: 0.8071 (mtm-85) REVERT: C 111 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7375 (mmpt) REVERT: C 135 SER cc_start: 0.7589 (m) cc_final: 0.6958 (p) REVERT: D 51 HIS cc_start: 0.6714 (m-70) cc_final: 0.6447 (m170) REVERT: D 126 LYS cc_start: 0.7417 (ttpt) cc_final: 0.6886 (mmtp) REVERT: E 127 ASP cc_start: 0.7931 (m-30) cc_final: 0.7471 (m-30) REVERT: F 60 GLU cc_start: 0.7567 (tp30) cc_final: 0.7298 (tp30) REVERT: F 108 TYR cc_start: 0.6988 (m-80) cc_final: 0.6471 (m-80) REVERT: F 127 ASP cc_start: 0.8000 (m-30) cc_final: 0.7642 (m-30) REVERT: G 111 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7473 (mmtt) REVERT: G 128 MET cc_start: 0.8037 (mmm) cc_final: 0.7794 (mmp) REVERT: G 135 SER cc_start: 0.7593 (m) cc_final: 0.6995 (p) REVERT: H 126 LYS cc_start: 0.7400 (ttpt) cc_final: 0.6840 (mmtp) REVERT: I 146 LEU cc_start: 0.7845 (tt) cc_final: 0.7614 (tt) REVERT: I 150 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7449 (pt) REVERT: I 243 MET cc_start: 0.7763 (ttt) cc_final: 0.7492 (ttp) REVERT: I 331 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7277 (mtm-85) REVERT: I 333 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7998 (mmpt) REVERT: I 394 THR cc_start: 0.8450 (t) cc_final: 0.8181 (t) REVERT: J 196 LEU cc_start: 0.8098 (mt) cc_final: 0.7420 (tp) REVERT: J 340 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.7134 (mtt-85) REVERT: K 196 LEU cc_start: 0.8127 (mt) cc_final: 0.7417 (tp) REVERT: L 150 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7198 (pt) REVERT: L 243 MET cc_start: 0.7792 (ttt) cc_final: 0.7471 (ttp) REVERT: L 331 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7251 (mtm-85) REVERT: L 333 LYS cc_start: 0.8106 (mmtm) cc_final: 0.7827 (mmpt) REVERT: L 394 THR cc_start: 0.8547 (t) cc_final: 0.8305 (t) outliers start: 78 outliers final: 23 residues processed: 509 average time/residue: 1.4121 time to fit residues: 824.2656 Evaluate side-chains 434 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 406 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL 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 F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 65 VAL 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 24 PHE Chi-restraints excluded: chain K residue 150 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21428 Z= 0.226 Angle : 0.618 6.744 29133 Z= 0.301 Chirality : 0.043 0.168 3543 Planarity : 0.004 0.036 3542 Dihedral : 9.570 129.430 2915 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.79 % Allowed : 16.05 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2663 helix: 2.42 (0.12), residues: 1686 sheet: 0.66 (0.29), residues: 288 loop : -0.93 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 181 HIS 0.003 0.001 HIS H 110 PHE 0.034 0.001 PHE K 202 TYR 0.010 0.001 TYR B 107 ARG 0.005 0.001 ARG L 436 *********************** 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 513 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 428 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7122 (mp0) REVERT: A 127 ASP cc_start: 0.7972 (m-30) cc_final: 0.7545 (m-30) REVERT: B 23 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7603 (mtpt) REVERT: B 108 TYR cc_start: 0.6994 (m-80) cc_final: 0.6493 (m-80) REVERT: B 127 ASP cc_start: 0.8009 (m-30) cc_final: 0.7655 (m-30) REVERT: B 128 MET cc_start: 0.8674 (mmm) cc_final: 0.8399 (mmp) REVERT: C 60 GLU cc_start: 0.7401 (tp30) cc_final: 0.7106 (tp30) REVERT: C 111 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7390 (mmpt) REVERT: C 128 MET cc_start: 0.8126 (mmm) cc_final: 0.7916 (mmp) REVERT: D 56 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7540 (t0) REVERT: D 83 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: D 126 LYS cc_start: 0.7298 (ttpt) cc_final: 0.6795 (mmtp) REVERT: E 127 ASP cc_start: 0.8013 (m-30) cc_final: 0.7463 (m-30) REVERT: F 60 GLU cc_start: 0.7469 (tp30) cc_final: 0.7159 (tp30) REVERT: F 108 TYR cc_start: 0.6990 (m-80) cc_final: 0.6500 (m-80) REVERT: F 127 ASP cc_start: 0.8024 (m-30) cc_final: 0.7624 (m-30) REVERT: G 60 GLU cc_start: 0.7370 (tp30) cc_final: 0.7087 (tp30) REVERT: G 111 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7752 (mtpt) REVERT: G 135 SER cc_start: 0.7582 (m) cc_final: 0.7126 (p) REVERT: H 59 GLU cc_start: 0.7994 (mp0) cc_final: 0.7416 (mp0) REVERT: H 83 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: H 126 LYS cc_start: 0.7386 (ttpt) cc_final: 0.6858 (mmtp) REVERT: I 150 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7417 (pt) REVERT: I 243 MET cc_start: 0.7824 (ttt) cc_final: 0.7549 (ttp) REVERT: I 267 TRP cc_start: 0.7467 (m100) cc_final: 0.7026 (m100) REVERT: I 331 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7251 (mtm-85) REVERT: I 333 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7929 (mmpt) REVERT: I 394 THR cc_start: 0.8487 (t) cc_final: 0.8233 (t) REVERT: J 143 ILE cc_start: 0.8127 (mt) cc_final: 0.7912 (mm) REVERT: J 196 LEU cc_start: 0.8068 (mt) cc_final: 0.7412 (tp) REVERT: K 81 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6435 (ttm) REVERT: K 143 ILE cc_start: 0.8190 (mt) cc_final: 0.7985 (mm) REVERT: K 196 LEU cc_start: 0.8066 (mt) cc_final: 0.7388 (tp) REVERT: K 395 MET cc_start: 0.8220 (mtp) cc_final: 0.7841 (mtp) REVERT: L 243 MET cc_start: 0.7784 (ttt) cc_final: 0.7492 (ttp) REVERT: L 267 TRP cc_start: 0.7480 (m100) cc_final: 0.6909 (m100) REVERT: L 331 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7308 (mtm-85) REVERT: L 333 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7841 (mmtt) REVERT: L 340 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6735 (ttp-110) outliers start: 85 outliers final: 34 residues processed: 479 average time/residue: 1.3744 time to fit residues: 745.8494 Evaluate side-chains 428 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain J residue 24 PHE 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 24 PHE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21428 Z= 0.275 Angle : 0.645 8.377 29133 Z= 0.314 Chirality : 0.044 0.171 3543 Planarity : 0.004 0.036 3542 Dihedral : 9.695 130.576 2915 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.64 % Allowed : 16.58 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2663 helix: 2.38 (0.12), residues: 1698 sheet: 0.52 (0.29), residues: 288 loop : -0.98 (0.26), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 181 HIS 0.004 0.001 HIS H 110 PHE 0.034 0.002 PHE K 202 TYR 0.011 0.001 TYR G 45 ARG 0.006 0.001 ARG I 151 *********************** 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 504 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 400 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7219 (mp0) REVERT: A 127 ASP cc_start: 0.8022 (m-30) cc_final: 0.7480 (m-30) REVERT: B 23 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7589 (mtpt) REVERT: B 108 TYR cc_start: 0.7045 (m-10) cc_final: 0.6597 (m-80) REVERT: B 114 GLU cc_start: 0.7621 (tt0) cc_final: 0.7317 (mt-10) REVERT: B 127 ASP cc_start: 0.7998 (m-30) cc_final: 0.7670 (m-30) REVERT: B 128 MET cc_start: 0.8743 (mmm) cc_final: 0.8484 (mmp) REVERT: C 111 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7769 (mtpt) REVERT: D 56 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7567 (t0) REVERT: D 83 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: D 126 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6839 (mmtp) REVERT: E 127 ASP cc_start: 0.7926 (m-30) cc_final: 0.7421 (m-30) REVERT: F 108 TYR cc_start: 0.7054 (m-10) cc_final: 0.6619 (m-80) REVERT: G 111 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7406 (mmpt) REVERT: H 83 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: H 126 LYS cc_start: 0.7392 (ttpt) cc_final: 0.6853 (mmtp) REVERT: I 150 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7356 (pt) REVERT: I 243 MET cc_start: 0.7882 (ttt) cc_final: 0.7608 (ttp) REVERT: I 331 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7321 (mtm-85) REVERT: I 333 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7933 (mmpt) REVERT: I 340 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6498 (mtp-110) REVERT: K 81 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6427 (ttm) REVERT: L 243 MET cc_start: 0.7796 (ttt) cc_final: 0.7500 (ttp) REVERT: L 331 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7172 (mtm-85) REVERT: L 333 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7761 (mmpt) REVERT: L 340 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6491 (mtp-110) outliers start: 104 outliers final: 44 residues processed: 474 average time/residue: 0.8996 time to fit residues: 481.3747 Evaluate side-chains 434 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 380 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 229 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 C 105 GLN E 105 GLN F 51 HIS ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21428 Z= 0.238 Angle : 0.630 8.167 29133 Z= 0.304 Chirality : 0.044 0.168 3543 Planarity : 0.004 0.035 3542 Dihedral : 9.621 127.956 2915 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.10 % Allowed : 17.70 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2663 helix: 2.46 (0.12), residues: 1701 sheet: 0.43 (0.30), residues: 288 loop : -0.96 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 181 HIS 0.003 0.001 HIS H 110 PHE 0.040 0.001 PHE L 94 TYR 0.016 0.001 TYR L 188 ARG 0.006 0.001 ARG K 340 *********************** 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 490 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 398 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7221 (mp0) REVERT: A 127 ASP cc_start: 0.7913 (m-30) cc_final: 0.7372 (m-30) REVERT: B 23 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7625 (mtmp) REVERT: B 108 TYR cc_start: 0.7047 (m-10) cc_final: 0.6620 (m-80) REVERT: B 114 GLU cc_start: 0.7594 (tt0) cc_final: 0.7280 (mt-10) REVERT: C 60 GLU cc_start: 0.7641 (tp30) cc_final: 0.7404 (tp30) REVERT: C 111 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7755 (mtpt) REVERT: D 56 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7515 (t0) REVERT: D 126 LYS cc_start: 0.7346 (ttpt) cc_final: 0.6839 (mmtp) REVERT: E 72 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: E 127 ASP cc_start: 0.7930 (m-30) cc_final: 0.7405 (m-30) REVERT: F 108 TYR cc_start: 0.7104 (m-10) cc_final: 0.6605 (m-80) REVERT: G 60 GLU cc_start: 0.7669 (tp30) cc_final: 0.7418 (tp30) REVERT: G 111 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7748 (mtpt) REVERT: H 126 LYS cc_start: 0.7333 (ttpt) cc_final: 0.6855 (mttp) REVERT: I 150 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7369 (pt) REVERT: I 243 MET cc_start: 0.7825 (ttt) cc_final: 0.7577 (ttp) REVERT: I 331 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7289 (mtm-85) REVERT: I 333 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7916 (mmpt) REVERT: I 340 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6536 (mtp-110) REVERT: L 243 MET cc_start: 0.7794 (ttt) cc_final: 0.7538 (ttp) REVERT: L 331 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7184 (mtm-85) REVERT: L 333 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7765 (mmpt) REVERT: L 340 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6569 (mtp-110) outliers start: 92 outliers final: 46 residues processed: 459 average time/residue: 1.3909 time to fit residues: 721.6040 Evaluate side-chains 435 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 381 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 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 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 72 GLU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE 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 213 PHE Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 422 THR Chi-restraints excluded: chain K residue 24 PHE 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 213 PHE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 0.0570 chunk 134 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 105 GLN E 105 GLN G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21428 Z= 0.179 Angle : 0.612 9.075 29133 Z= 0.293 Chirality : 0.043 0.225 3543 Planarity : 0.003 0.035 3542 Dihedral : 9.391 122.644 2915 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.57 % Allowed : 19.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.17), residues: 2663 helix: 2.58 (0.12), residues: 1699 sheet: 0.34 (0.30), residues: 288 loop : -0.85 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 181 HIS 0.003 0.001 HIS D 110 PHE 0.037 0.001 PHE I 94 TYR 0.016 0.001 TYR L 188 ARG 0.011 0.001 ARG E 69 *********************** 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 475 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7057 (mp0) REVERT: A 127 ASP cc_start: 0.7915 (m-30) cc_final: 0.7426 (m-30) REVERT: B 23 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7573 (mtmp) REVERT: B 60 GLU cc_start: 0.7486 (tp30) cc_final: 0.7039 (tp30) REVERT: B 108 TYR cc_start: 0.7014 (m-10) cc_final: 0.6553 (m-80) REVERT: B 114 GLU cc_start: 0.7546 (tt0) cc_final: 0.7317 (mt-10) REVERT: C 60 GLU cc_start: 0.7501 (tp30) cc_final: 0.7146 (tp30) REVERT: C 64 LEU cc_start: 0.8307 (mm) cc_final: 0.8075 (mm) REVERT: C 111 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7721 (mtpt) REVERT: C 139 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5691 (mt-10) REVERT: D 56 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7481 (t0) REVERT: D 59 GLU cc_start: 0.8128 (mp0) cc_final: 0.7531 (mp0) REVERT: D 126 LYS cc_start: 0.7289 (ttpt) cc_final: 0.6835 (mttp) REVERT: E 72 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: E 127 ASP cc_start: 0.7887 (m-30) cc_final: 0.7367 (m-30) REVERT: F 108 TYR cc_start: 0.7039 (m-10) cc_final: 0.6607 (m-80) REVERT: G 60 GLU cc_start: 0.7599 (tp30) cc_final: 0.7387 (tp30) REVERT: G 111 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7699 (mtpt) REVERT: G 139 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.5772 (mt-10) REVERT: H 126 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6825 (mmtp) REVERT: I 277 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8540 (ptm-80) REVERT: I 331 ARG cc_start: 0.7600 (mtp85) cc_final: 0.7282 (mtm-85) REVERT: I 333 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7860 (mmpt) REVERT: I 340 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6779 (mtm-85) REVERT: K 213 PHE cc_start: 0.7833 (t80) cc_final: 0.7571 (t80) REVERT: K 243 MET cc_start: 0.7642 (ttp) cc_final: 0.7382 (ttt) REVERT: L 243 MET cc_start: 0.7736 (ttt) cc_final: 0.7491 (ttp) REVERT: L 277 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8610 (ptm-80) REVERT: L 331 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7282 (mtm-85) REVERT: L 333 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7801 (mmtt) REVERT: L 340 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6683 (mtm-85) outliers start: 80 outliers final: 33 residues processed: 450 average time/residue: 1.3868 time to fit residues: 704.6028 Evaluate side-chains 428 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 384 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL 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 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 72 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 333 LYS Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 24 PHE 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 422 THR Chi-restraints excluded: chain K residue 24 PHE 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 278 THR Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 155 optimal weight: 0.0980 chunk 117 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 105 GLN E 105 GLN G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21428 Z= 0.227 Angle : 0.635 9.267 29133 Z= 0.305 Chirality : 0.044 0.226 3543 Planarity : 0.004 0.035 3542 Dihedral : 9.466 122.718 2915 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.39 % Allowed : 20.20 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2663 helix: 2.57 (0.12), residues: 1702 sheet: 0.30 (0.30), residues: 288 loop : -0.88 (0.27), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 267 HIS 0.003 0.001 HIS H 110 PHE 0.030 0.001 PHE K 202 TYR 0.014 0.001 TYR I 270 ARG 0.012 0.001 ARG E 69 *********************** 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 471 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 395 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7131 (mp0) REVERT: A 127 ASP cc_start: 0.7900 (m-30) cc_final: 0.7374 (m-30) REVERT: B 23 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7580 (mtmp) REVERT: B 70 ASN cc_start: 0.7477 (p0) cc_final: 0.7224 (p0) REVERT: B 108 TYR cc_start: 0.7002 (m-10) cc_final: 0.6601 (m-80) REVERT: B 114 GLU cc_start: 0.7533 (tt0) cc_final: 0.7249 (mt-10) REVERT: C 83 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7419 (mm110) REVERT: C 111 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7739 (mtpt) REVERT: C 139 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5703 (mt-10) REVERT: D 56 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7521 (t0) REVERT: D 59 GLU cc_start: 0.8094 (mp0) cc_final: 0.7468 (mp0) REVERT: D 126 LYS cc_start: 0.7346 (ttpt) cc_final: 0.6835 (mmtp) REVERT: E 72 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: E 127 ASP cc_start: 0.7945 (m-30) cc_final: 0.7430 (m-30) REVERT: F 39 GLU cc_start: 0.6971 (pt0) cc_final: 0.6738 (pm20) REVERT: F 108 TYR cc_start: 0.7042 (m-10) cc_final: 0.6576 (m-80) REVERT: G 111 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7767 (mtpt) REVERT: G 139 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5752 (mt-10) REVERT: H 56 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7860 (t0) REVERT: H 126 LYS cc_start: 0.7313 (ttpt) cc_final: 0.6831 (mmtp) REVERT: I 277 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8616 (ptm-80) REVERT: I 331 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7299 (mtm-85) REVERT: I 333 LYS cc_start: 0.8175 (mmpt) cc_final: 0.7872 (mmpt) REVERT: I 340 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6636 (mtp-110) REVERT: J 267 TRP cc_start: 0.7742 (m-10) cc_final: 0.7499 (m-10) REVERT: K 213 PHE cc_start: 0.7822 (t80) cc_final: 0.7561 (t80) REVERT: L 243 MET cc_start: 0.7816 (ttt) cc_final: 0.7556 (ttp) REVERT: L 277 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8657 (ptm-80) REVERT: L 331 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7287 (mtm-85) REVERT: L 333 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7835 (mmtt) REVERT: L 340 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6678 (mtp-110) outliers start: 76 outliers final: 40 residues processed: 452 average time/residue: 1.3597 time to fit residues: 695.7881 Evaluate side-chains 427 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 376 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 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 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 72 GLU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 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 278 THR Chi-restraints excluded: chain I residue 321 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 J residue 422 THR 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 422 THR Chi-restraints excluded: chain L residue 151 ARG Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 231 optimal weight: 0.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 105 GLN E 105 GLN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21428 Z= 0.198 Angle : 0.632 10.297 29133 Z= 0.302 Chirality : 0.044 0.279 3543 Planarity : 0.004 0.035 3542 Dihedral : 9.348 120.600 2915 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.08 % Allowed : 21.00 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2663 helix: 2.58 (0.12), residues: 1703 sheet: 0.28 (0.30), residues: 285 loop : -0.91 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 267 HIS 0.003 0.001 HIS F 110 PHE 0.030 0.001 PHE L 136 TYR 0.014 0.001 TYR L 270 ARG 0.009 0.001 ARG E 69 *********************** 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 466 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 397 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7010 (mp0) REVERT: A 127 ASP cc_start: 0.7864 (m-30) cc_final: 0.7332 (m-30) REVERT: B 16 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8373 (mtm180) REVERT: B 23 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7561 (mtmp) REVERT: B 70 ASN cc_start: 0.7544 (p0) cc_final: 0.7334 (p0) REVERT: B 108 TYR cc_start: 0.7038 (m-10) cc_final: 0.6621 (m-80) REVERT: B 114 GLU cc_start: 0.7518 (tt0) cc_final: 0.7299 (mt-10) REVERT: C 111 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7720 (mtpt) REVERT: C 139 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5738 (mt-10) REVERT: D 56 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7493 (t0) REVERT: D 59 GLU cc_start: 0.8076 (mp0) cc_final: 0.7485 (mp0) REVERT: D 126 LYS cc_start: 0.7323 (ttpt) cc_final: 0.6893 (mttp) REVERT: E 72 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: E 127 ASP cc_start: 0.7934 (m-30) cc_final: 0.7413 (m-30) REVERT: F 39 GLU cc_start: 0.7030 (pt0) cc_final: 0.6764 (pm20) REVERT: F 62 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: F 108 TYR cc_start: 0.6982 (m-10) cc_final: 0.6548 (m-80) REVERT: G 111 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7411 (mmpt) REVERT: G 139 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5788 (mt-10) REVERT: H 59 GLU cc_start: 0.7968 (mp0) cc_final: 0.7323 (mp0) REVERT: H 126 LYS cc_start: 0.7330 (ttpt) cc_final: 0.6874 (mmtp) REVERT: I 277 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8559 (ptm-80) REVERT: I 331 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7290 (mtm-85) REVERT: I 333 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7828 (mmpt) REVERT: I 340 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6849 (mtm-85) REVERT: J 243 MET cc_start: 0.7614 (ttp) cc_final: 0.7339 (ttt) REVERT: K 213 PHE cc_start: 0.7757 (t80) cc_final: 0.7538 (t80) REVERT: K 243 MET cc_start: 0.7622 (ttp) cc_final: 0.7379 (ttt) REVERT: L 277 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8634 (ptm-80) REVERT: L 331 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7279 (mtm-85) REVERT: L 333 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7826 (mmtt) REVERT: L 340 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6816 (mtm-85) outliers start: 69 outliers final: 36 residues processed: 441 average time/residue: 1.4108 time to fit residues: 701.4121 Evaluate side-chains 438 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 391 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 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 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 72 GLU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 131 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 278 THR Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 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 422 THR 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 L residue 277 ARG Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 G 83 GLN G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21428 Z= 0.365 Angle : 0.729 13.859 29133 Z= 0.354 Chirality : 0.047 0.283 3543 Planarity : 0.004 0.037 3542 Dihedral : 9.925 134.067 2915 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.25 % Allowed : 21.18 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2663 helix: 2.19 (0.12), residues: 1710 sheet: 0.11 (0.30), residues: 288 loop : -1.02 (0.27), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP K 267 HIS 0.004 0.001 HIS C 109 PHE 0.065 0.002 PHE L 94 TYR 0.016 0.002 TYR I 270 ARG 0.015 0.001 ARG E 69 *********************** 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 467 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 394 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7081 (mp0) REVERT: A 127 ASP cc_start: 0.7956 (m-30) cc_final: 0.7436 (m-30) REVERT: B 23 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7709 (mtmm) REVERT: B 59 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6881 (mt-10) REVERT: B 70 ASN cc_start: 0.7563 (p0) cc_final: 0.7348 (p0) REVERT: B 108 TYR cc_start: 0.7058 (m-10) cc_final: 0.6550 (m-80) REVERT: B 114 GLU cc_start: 0.7552 (tt0) cc_final: 0.7258 (mt-10) REVERT: C 111 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7856 (mtpt) REVERT: C 139 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5548 (mt-10) REVERT: D 56 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7627 (t0) REVERT: D 59 GLU cc_start: 0.8142 (mp0) cc_final: 0.7505 (mp0) REVERT: D 126 LYS cc_start: 0.7406 (ttpt) cc_final: 0.6836 (mmtp) REVERT: E 72 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: E 127 ASP cc_start: 0.8051 (m-30) cc_final: 0.7541 (m-30) REVERT: F 62 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: F 70 ASN cc_start: 0.7582 (p0) cc_final: 0.7307 (p0) REVERT: F 108 TYR cc_start: 0.7063 (m-10) cc_final: 0.6516 (m-80) REVERT: F 134 GLN cc_start: 0.7351 (tp40) cc_final: 0.7128 (mt0) REVERT: G 111 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7842 (mtpt) REVERT: G 139 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5659 (mt-10) REVERT: H 56 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (t0) REVERT: H 126 LYS cc_start: 0.7426 (ttpt) cc_final: 0.6887 (mttp) REVERT: I 94 PHE cc_start: 0.6616 (t80) cc_final: 0.6222 (t80) REVERT: I 331 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7487 (mtm-85) REVERT: I 340 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6740 (mtp-110) REVERT: K 213 PHE cc_start: 0.7869 (t80) cc_final: 0.7645 (t80) REVERT: L 98 ILE cc_start: 0.8354 (mm) cc_final: 0.8150 (mp) REVERT: L 331 ARG cc_start: 0.7688 (mtp85) cc_final: 0.7416 (mtp180) REVERT: L 333 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7829 (mmtt) REVERT: L 340 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6718 (mtp-110) outliers start: 73 outliers final: 41 residues processed: 450 average time/residue: 1.4189 time to fit residues: 725.2880 Evaluate side-chains 436 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 385 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 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 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 72 GLU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 131 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 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 278 THR Chi-restraints excluded: chain I residue 321 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 J residue 422 THR Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 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 422 THR Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN E 105 GLN G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN K 434 ASN L 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 21428 Z= 0.248 Angle : 0.685 11.852 29133 Z= 0.330 Chirality : 0.045 0.302 3543 Planarity : 0.004 0.100 3542 Dihedral : 9.704 128.341 2915 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.67 % Allowed : 22.02 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.17), residues: 2663 helix: 2.29 (0.12), residues: 1706 sheet: 0.02 (0.30), residues: 288 loop : -1.03 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP K 267 HIS 0.004 0.001 HIS C 30 PHE 0.076 0.002 PHE I 94 TYR 0.018 0.001 TYR I 270 ARG 0.016 0.001 ARG A 69 ********************** 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 451 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 391 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7108 (mp0) REVERT: A 127 ASP cc_start: 0.7908 (m-30) cc_final: 0.7384 (m-30) REVERT: B 23 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7690 (mtmm) REVERT: B 59 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6892 (mt-10) REVERT: B 108 TYR cc_start: 0.7058 (m-10) cc_final: 0.6544 (m-80) REVERT: B 114 GLU cc_start: 0.7497 (tt0) cc_final: 0.7221 (mt-10) REVERT: C 111 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7777 (mtpt) REVERT: C 127 ASP cc_start: 0.7567 (m-30) cc_final: 0.7244 (m-30) REVERT: C 139 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5658 (mt-10) REVERT: D 56 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7541 (t0) REVERT: D 59 GLU cc_start: 0.8084 (mp0) cc_final: 0.7463 (mp0) REVERT: D 126 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6807 (mmtp) REVERT: E 72 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: E 127 ASP cc_start: 0.7978 (m-30) cc_final: 0.7466 (m-30) REVERT: F 62 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: F 70 ASN cc_start: 0.7547 (p0) cc_final: 0.7307 (p0) REVERT: F 108 TYR cc_start: 0.7014 (m-10) cc_final: 0.6523 (m-80) REVERT: G 111 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7782 (mtpt) REVERT: G 139 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5682 (mt-10) REVERT: H 126 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6794 (mmtp) REVERT: I 277 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8689 (ptm-80) REVERT: I 331 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7402 (mtm-85) REVERT: L 331 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7396 (mtp180) REVERT: L 333 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7835 (mmtt) REVERT: L 340 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6744 (mtp-110) outliers start: 60 outliers final: 38 residues processed: 435 average time/residue: 1.4055 time to fit residues: 689.7503 Evaluate side-chains 423 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 376 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 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 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 72 GLU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 131 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 278 THR Chi-restraints excluded: chain I residue 321 VAL 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 J residue 422 THR 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 L residue 277 ARG Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 209 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN E 105 GLN F 51 HIS G 105 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN L 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.198253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146415 restraints weight = 23767.068| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.28 r_work: 0.3701 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21428 Z= 0.262 Angle : 0.696 10.804 29133 Z= 0.335 Chirality : 0.045 0.294 3543 Planarity : 0.004 0.096 3542 Dihedral : 9.716 128.022 2915 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.90 % Allowed : 22.16 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.17), residues: 2663 helix: 2.25 (0.12), residues: 1714 sheet: 0.06 (0.30), residues: 285 loop : -0.98 (0.27), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP J 267 HIS 0.004 0.001 HIS C 30 PHE 0.057 0.002 PHE L 94 TYR 0.016 0.001 TYR I 270 ARG 0.016 0.001 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10391.64 seconds wall clock time: 275 minutes 19.84 seconds (16519.84 seconds total)