Starting phenix.real_space_refine on Sun Apr 14 18:51:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utb_42537/04_2024/8utb_42537_trim_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 8 Type Number sf(0) Gaussians P 5 5.49 5 S 110 5.16 5 Cl 15 4.86 5 C 10675 2.51 5 N 2525 2.21 5 O 2990 1.98 5 F 15 1.80 5 H 15105 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31440 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "B" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "C" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "D" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "E" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 25.87, per 1000 atoms: 0.82 Number of scatterers: 31440 At special positions: 0 Unit cell: (100.347, 102.505, 165.087, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 15 17.00 S 110 16.00 P 5 15.00 F 15 9.00 O 2990 8.00 N 2525 7.00 C 10675 6.00 H 15105 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 603 " - " ASN B 67 " " NAG C 603 " - " ASN C 67 " " NAG D 603 " - " ASN D 67 " " NAG E 603 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 25.70 Conformation dependent library (CDL) restraints added in 6.0 seconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 25 sheets defined 37.1% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 216 through 229 removed outlier: 4.115A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 Processing helix chain 'A' and resid 269 through 295 removed outlier: 3.587A pdb=" N ALA A 275 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 287 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 409 through 458 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 216 through 229 removed outlier: 4.115A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 259 Processing helix chain 'B' and resid 269 through 295 removed outlier: 3.587A pdb=" N ALA B 275 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 287 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 409 through 458 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 216 through 229 removed outlier: 4.115A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 259 Processing helix chain 'C' and resid 269 through 295 removed outlier: 3.587A pdb=" N ALA C 275 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 287 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 409 through 458 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 216 through 229 removed outlier: 4.114A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 259 Processing helix chain 'D' and resid 269 through 295 removed outlier: 3.587A pdb=" N ALA D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 287 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 409 through 458 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 216 through 229 removed outlier: 4.115A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 259 Processing helix chain 'E' and resid 269 through 295 removed outlier: 3.587A pdb=" N ALA E 275 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 287 " --> pdb=" O SER E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 409 through 458 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.360A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 185 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.360A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= H, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.360A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'C' and resid 77 through 79 Processing sheet with id= O, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.360A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= R, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'D' and resid 77 through 79 Processing sheet with id= T, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.361A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= W, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= X, first strand: chain 'E' and resid 77 through 79 Processing sheet with id= Y, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 1785 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: 12.10 Time building geometry restraints manager: 26.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15070 1.03 - 1.23: 663 1.23 - 1.43: 6587 1.43 - 1.64: 9360 1.64 - 1.84: 175 Bond restraints: 31855 Sorted by residual: bond pdb=" C3 EPJ D 604 " pdb=" N1 EPJ D 604 " ideal model delta sigma weight residual 1.718 1.472 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C3 EPJ C 604 " pdb=" N1 EPJ C 604 " ideal model delta sigma weight residual 1.718 1.472 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C3 EPJ B 604 " pdb=" N1 EPJ B 604 " ideal model delta sigma weight residual 1.718 1.472 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C3 EPJ A 603 " pdb=" N1 EPJ A 603 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C3 EPJ E 604 " pdb=" N1 EPJ E 604 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.51e+02 ... (remaining 31850 not shown) Histogram of bond angle deviations from ideal: 79.43 - 90.36: 20 90.36 - 101.29: 71 101.29 - 112.22: 36111 112.22 - 123.15: 17715 123.15 - 134.08: 3248 Bond angle restraints: 57165 Sorted by residual: angle pdb=" CG LEU E 320 " pdb=" CD1 LEU E 320 " pdb="HD12 LEU E 320 " ideal model delta sigma weight residual 109.00 79.43 29.57 3.00e+00 1.11e-01 9.71e+01 angle pdb=" CG LEU B 320 " pdb=" CD1 LEU B 320 " pdb="HD12 LEU B 320 " ideal model delta sigma weight residual 109.00 79.44 29.56 3.00e+00 1.11e-01 9.71e+01 angle pdb=" CG LEU A 320 " pdb=" CD1 LEU A 320 " pdb="HD12 LEU A 320 " ideal model delta sigma weight residual 109.00 79.44 29.56 3.00e+00 1.11e-01 9.71e+01 angle pdb=" CG LEU C 320 " pdb=" CD1 LEU C 320 " pdb="HD12 LEU C 320 " ideal model delta sigma weight residual 109.00 79.47 29.53 3.00e+00 1.11e-01 9.69e+01 angle pdb=" CG LEU D 320 " pdb=" CD1 LEU D 320 " pdb="HD12 LEU D 320 " ideal model delta sigma weight residual 109.00 79.49 29.51 3.00e+00 1.11e-01 9.68e+01 ... (remaining 57160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.85: 15080 29.85 - 59.69: 690 59.69 - 89.54: 100 89.54 - 119.39: 55 119.39 - 149.23: 10 Dihedral angle restraints: 15935 sinusoidal: 9090 harmonic: 6845 Sorted by residual: dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 15932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2142 0.060 - 0.120: 392 0.120 - 0.181: 46 0.181 - 0.241: 16 0.241 - 0.301: 14 Chirality restraints: 2610 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.82e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.79e+02 ... (remaining 2607 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.193 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" C7 NAG J 2 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.278 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.193 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" C7 NAG L 2 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.278 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.193 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" C7 NAG H 2 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.277 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.148 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 3911 2.25 - 2.84: 68010 2.84 - 3.42: 82204 3.42 - 4.01: 117711 4.01 - 4.60: 174476 Nonbonded interactions: 446312 Sorted by model distance: nonbonded pdb=" HE2 HIS A 296 " pdb=" O HOH A 702 " model vdw 1.659 1.850 nonbonded pdb=" HE2 HIS B 296 " pdb=" O HOH B 702 " model vdw 1.659 1.850 nonbonded pdb=" HE2 HIS D 296 " pdb=" O HOH D 702 " model vdw 1.659 1.850 nonbonded pdb=" HE2 HIS E 296 " pdb=" O HOH E 702 " model vdw 1.659 1.850 nonbonded pdb=" HE2 HIS C 296 " pdb=" O HOH C 702 " model vdw 1.660 1.850 ... (remaining 446307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 459)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 459)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 459)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 459)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 459)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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=0.50 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.450 Extract box with map and model: 5.300 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 118.780 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.220 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.012 0.246 16745 Z= 0.760 Angle : 0.914 9.294 22820 Z= 0.433 Chirality : 0.053 0.301 2610 Planarity : 0.015 0.166 2715 Dihedral : 18.532 149.235 7005 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 1860 helix: -1.41 (0.15), residues: 710 sheet: -0.96 (0.22), residues: 435 loop : -1.56 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 307 HIS 0.005 0.002 HIS C 296 PHE 0.018 0.002 PHE B 99 TYR 0.019 0.002 TYR B 31 ARG 0.005 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 317 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: B 133 TRP cc_start: 0.8547 (m100) cc_final: 0.8232 (m100) REVERT: B 273 TYR cc_start: 0.7517 (t80) cc_final: 0.7265 (t80) REVERT: C 293 GLN cc_start: 0.8062 (mt0) cc_final: 0.7840 (mt0) REVERT: D 430 SER cc_start: 0.8097 (m) cc_final: 0.7803 (t) REVERT: E 430 SER cc_start: 0.8130 (m) cc_final: 0.7866 (t) outliers start: 5 outliers final: 0 residues processed: 317 average time/residue: 2.7116 time to fit residues: 955.2493 Evaluate side-chains 276 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.0050 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16745 Z= 0.199 Angle : 0.641 7.071 22820 Z= 0.326 Chirality : 0.041 0.158 2610 Planarity : 0.005 0.064 2715 Dihedral : 15.751 143.358 3400 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.06 % Allowed : 6.28 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 1860 helix: 0.52 (0.18), residues: 715 sheet: -0.67 (0.23), residues: 430 loop : -0.92 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 59 HIS 0.004 0.001 HIS D 296 PHE 0.017 0.001 PHE C 99 TYR 0.016 0.001 TYR D 273 ARG 0.004 0.000 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 277 time to evaluate : 2.696 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7833 (ttm) cc_final: 0.7292 (ttm) REVERT: D 18 GLU cc_start: 0.7924 (tt0) cc_final: 0.7438 (tt0) REVERT: D 260 MET cc_start: 0.6743 (ttp) cc_final: 0.6535 (ttt) REVERT: E 430 SER cc_start: 0.8089 (m) cc_final: 0.7821 (t) outliers start: 18 outliers final: 7 residues processed: 278 average time/residue: 2.5023 time to fit residues: 780.4626 Evaluate side-chains 277 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 270 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain E residue 280 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16745 Z= 0.349 Angle : 0.670 6.781 22820 Z= 0.344 Chirality : 0.043 0.153 2610 Planarity : 0.006 0.051 2715 Dihedral : 13.501 131.742 3400 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.76 % Allowed : 7.10 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 1860 helix: 0.72 (0.18), residues: 715 sheet: -0.59 (0.23), residues: 430 loop : -0.68 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 59 HIS 0.008 0.002 HIS E 104 PHE 0.023 0.002 PHE C 99 TYR 0.020 0.002 TYR A 31 ARG 0.008 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 274 time to evaluate : 2.612 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7903 (ttm) cc_final: 0.7307 (ttm) REVERT: A 445 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: C 260 MET cc_start: 0.6525 (tpp) cc_final: 0.6162 (tpp) REVERT: E 430 SER cc_start: 0.8152 (m) cc_final: 0.7864 (t) outliers start: 13 outliers final: 3 residues processed: 274 average time/residue: 2.6485 time to fit residues: 809.2089 Evaluate side-chains 267 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 263 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16745 Z= 0.251 Angle : 0.593 6.074 22820 Z= 0.308 Chirality : 0.040 0.148 2610 Planarity : 0.005 0.046 2715 Dihedral : 12.675 130.147 3400 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.88 % Allowed : 7.45 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1860 helix: 0.85 (0.18), residues: 715 sheet: -0.58 (0.24), residues: 430 loop : -0.59 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 307 HIS 0.005 0.001 HIS E 104 PHE 0.013 0.001 PHE C 99 TYR 0.014 0.002 TYR D 273 ARG 0.005 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 276 time to evaluate : 2.586 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7901 (ttm) cc_final: 0.7312 (ttm) REVERT: A 445 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: B 249 LEU cc_start: 0.8441 (tt) cc_final: 0.8188 (tp) REVERT: C 260 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.6092 (tpp) REVERT: D 40 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7822 (mtm) REVERT: D 260 MET cc_start: 0.6715 (ttp) cc_final: 0.6422 (ttm) REVERT: E 430 SER cc_start: 0.8123 (m) cc_final: 0.7814 (t) outliers start: 15 outliers final: 5 residues processed: 276 average time/residue: 2.5538 time to fit residues: 790.1366 Evaluate side-chains 276 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 268 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16745 Z= 0.285 Angle : 0.602 5.809 22820 Z= 0.313 Chirality : 0.040 0.149 2610 Planarity : 0.005 0.045 2715 Dihedral : 12.501 130.524 3400 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.70 % Allowed : 7.98 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1860 helix: 0.97 (0.18), residues: 715 sheet: -0.61 (0.23), residues: 430 loop : -0.50 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 307 HIS 0.006 0.001 HIS B 104 PHE 0.017 0.002 PHE C 99 TYR 0.017 0.002 TYR C 31 ARG 0.004 0.001 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 277 time to evaluate : 2.473 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7939 (ttp) cc_final: 0.7422 (ttm) REVERT: A 445 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: C 260 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6053 (tpp) REVERT: D 40 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7825 (mtm) REVERT: D 439 PHE cc_start: 0.8177 (t80) cc_final: 0.7890 (t80) outliers start: 12 outliers final: 3 residues processed: 277 average time/residue: 2.6035 time to fit residues: 806.8375 Evaluate side-chains 274 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 268 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 40 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16745 Z= 0.190 Angle : 0.540 5.056 22820 Z= 0.281 Chirality : 0.039 0.146 2610 Planarity : 0.005 0.043 2715 Dihedral : 11.972 128.802 3400 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.65 % Allowed : 8.39 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1860 helix: 1.10 (0.19), residues: 715 sheet: -0.61 (0.23), residues: 430 loop : -0.39 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 307 HIS 0.003 0.001 HIS E 104 PHE 0.011 0.001 PHE C 252 TYR 0.011 0.001 TYR C 31 ARG 0.006 0.000 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 277 time to evaluate : 2.835 Fit side-chains REVERT: A 304 MET cc_start: 0.7942 (ttp) cc_final: 0.7440 (ttm) REVERT: A 445 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: C 260 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6102 (tpp) REVERT: D 40 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7818 (mtm) REVERT: D 260 MET cc_start: 0.6703 (ttp) cc_final: 0.6439 (ttm) REVERT: D 439 PHE cc_start: 0.8168 (t80) cc_final: 0.7894 (t80) REVERT: E 234 ASP cc_start: 0.7004 (m-30) cc_final: 0.6781 (m-30) outliers start: 11 outliers final: 5 residues processed: 277 average time/residue: 2.6189 time to fit residues: 811.1229 Evaluate side-chains 274 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 266 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain E residue 12 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16745 Z= 0.268 Angle : 0.577 5.408 22820 Z= 0.300 Chirality : 0.040 0.145 2610 Planarity : 0.005 0.041 2715 Dihedral : 11.384 128.673 3400 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.47 % Allowed : 8.86 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1860 helix: 1.15 (0.19), residues: 715 sheet: -0.60 (0.23), residues: 430 loop : -0.36 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 307 HIS 0.005 0.001 HIS B 104 PHE 0.017 0.002 PHE C 99 TYR 0.018 0.002 TYR C 31 ARG 0.005 0.001 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 273 time to evaluate : 2.471 Fit side-chains REVERT: A 304 MET cc_start: 0.8016 (ttp) cc_final: 0.7484 (ttm) REVERT: A 445 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: C 260 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6166 (tpp) REVERT: D 40 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7793 (mtm) REVERT: D 260 MET cc_start: 0.6527 (ttp) cc_final: 0.6304 (ttm) REVERT: D 439 PHE cc_start: 0.8196 (t80) cc_final: 0.7902 (t80) outliers start: 8 outliers final: 3 residues processed: 273 average time/residue: 2.6653 time to fit residues: 824.8096 Evaluate side-chains 283 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 277 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 40 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16745 Z= 0.146 Angle : 0.495 4.189 22820 Z= 0.258 Chirality : 0.038 0.143 2610 Planarity : 0.004 0.041 2715 Dihedral : 10.725 125.933 3400 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.35 % Allowed : 9.27 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1860 helix: 1.31 (0.19), residues: 710 sheet: -0.60 (0.23), residues: 430 loop : -0.16 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 307 HIS 0.002 0.000 HIS C 140 PHE 0.014 0.001 PHE C 134 TYR 0.007 0.001 TYR C 117 ARG 0.008 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 277 time to evaluate : 2.652 Fit side-chains REVERT: A 304 MET cc_start: 0.8004 (ttp) cc_final: 0.7540 (ttm) REVERT: A 445 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: B 250 THR cc_start: 0.8970 (m) cc_final: 0.8737 (m) REVERT: C 260 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6099 (tpt) REVERT: D 38 GLN cc_start: 0.8613 (tt0) cc_final: 0.8198 (mt0) REVERT: D 40 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7767 (mtm) REVERT: D 260 MET cc_start: 0.6534 (ttp) cc_final: 0.6286 (ttm) REVERT: D 439 PHE cc_start: 0.8110 (t80) cc_final: 0.7879 (t80) REVERT: E 40 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7887 (mtm) outliers start: 6 outliers final: 1 residues processed: 277 average time/residue: 2.4987 time to fit residues: 777.8266 Evaluate side-chains 282 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain E residue 40 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16745 Z= 0.261 Angle : 0.560 5.076 22820 Z= 0.291 Chirality : 0.040 0.144 2610 Planarity : 0.005 0.040 2715 Dihedral : 10.703 126.007 3400 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.35 % Allowed : 9.91 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1860 helix: 1.24 (0.19), residues: 720 sheet: -0.56 (0.23), residues: 430 loop : -0.16 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 307 HIS 0.004 0.001 HIS B 104 PHE 0.016 0.002 PHE C 99 TYR 0.018 0.002 TYR C 31 ARG 0.007 0.001 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 278 time to evaluate : 2.433 Fit side-chains REVERT: A 304 MET cc_start: 0.8059 (ttp) cc_final: 0.7660 (ttp) REVERT: A 445 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: C 260 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6143 (tpt) REVERT: D 40 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7778 (mtm) REVERT: D 260 MET cc_start: 0.6562 (ttp) cc_final: 0.6336 (ttm) REVERT: D 439 PHE cc_start: 0.8210 (t80) cc_final: 0.7956 (t80) REVERT: E 40 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7944 (mtm) outliers start: 6 outliers final: 2 residues processed: 278 average time/residue: 2.5499 time to fit residues: 795.1466 Evaluate side-chains 277 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 271 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain E residue 40 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16745 Z= 0.189 Angle : 0.515 4.368 22820 Z= 0.270 Chirality : 0.038 0.140 2610 Planarity : 0.004 0.040 2715 Dihedral : 10.364 124.276 3400 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.29 % Allowed : 10.09 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1860 helix: 1.28 (0.18), residues: 720 sheet: -0.57 (0.23), residues: 430 loop : -0.11 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 307 HIS 0.002 0.001 HIS E 104 PHE 0.018 0.001 PHE C 134 TYR 0.011 0.001 TYR C 31 ARG 0.007 0.000 ARG B 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 2.637 Fit side-chains REVERT: A 304 MET cc_start: 0.8059 (ttp) cc_final: 0.7662 (ttp) REVERT: A 445 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: C 260 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6043 (tpp) REVERT: D 40 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7758 (mtm) REVERT: D 439 PHE cc_start: 0.8174 (t80) cc_final: 0.7932 (t80) REVERT: E 40 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7915 (mtm) outliers start: 5 outliers final: 1 residues processed: 265 average time/residue: 2.6326 time to fit residues: 785.8788 Evaluate side-chains 273 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain E residue 40 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121230 restraints weight = 46834.227| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.89 r_work: 0.3082 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16745 Z= 0.270 Angle : 0.567 5.316 22820 Z= 0.295 Chirality : 0.040 0.145 2610 Planarity : 0.005 0.042 2715 Dihedral : 10.440 124.256 3400 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.29 % Allowed : 10.15 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1860 helix: 1.24 (0.19), residues: 725 sheet: -0.58 (0.23), residues: 430 loop : -0.16 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 307 HIS 0.005 0.001 HIS D 104 PHE 0.017 0.002 PHE C 99 TYR 0.019 0.002 TYR C 31 ARG 0.007 0.001 ARG B 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13261.41 seconds wall clock time: 234 minutes 34.47 seconds (14074.47 seconds total)