Starting phenix.real_space_refine on Thu May 16 18:13:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841_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/8uzj_42841/05_2024/8uzj_42841_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzj_42841/05_2024/8uzj_42841_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 Ca 5 9.91 5 P 5 5.49 5 S 115 5.16 5 Cl 5 4.86 5 C 11285 2.51 5 N 2620 2.21 5 O 3160 1.98 5 H 15835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 33030 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "B" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "C" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "D" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "E" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 27.42, per 1000 atoms: 0.83 Number of scatterers: 33030 At special positions: 0 Unit cell: (100.347, 101.426, 162.929, 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) Ca 5 19.99 Cl 5 17.00 S 115 16.00 P 5 15.00 O 3160 8.00 N 2620 7.00 C 11285 6.00 H 15835 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=2.05 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=2.05 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=2.05 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=2.05 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 604 " - " ASN B 67 " " NAG C 604 " - " ASN C 67 " " NAG D 604 " - " ASN D 67 " " NAG E 604 " - " ASN E 67 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 23 " " NAG H 1 " - " ASN B 110 " " NAG I 1 " - " ASN B 23 " " NAG J 1 " - " ASN C 110 " " NAG K 1 " - " ASN C 23 " " NAG L 1 " - " ASN D 110 " " NAG M 1 " - " ASN D 23 " " NAG N 1 " - " ASN E 110 " " NAG O 1 " - " ASN E 23 " Time building additional restraints: 26.47 Conformation dependent library (CDL) restraints added in 5.7 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 25 sheets defined 39.1% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 229 removed outlier: 3.966A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 257 Processing helix chain 'A' and resid 269 through 295 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 465 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.966A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 257 Processing helix chain 'B' and resid 269 through 295 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 465 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 229 removed outlier: 3.966A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 257 Processing helix chain 'C' and resid 269 through 295 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 465 Processing helix chain 'C' and resid 470 through 477 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.965A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 257 Processing helix chain 'D' and resid 269 through 295 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 465 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 229 removed outlier: 3.965A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 257 Processing helix chain 'E' and resid 269 through 295 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 465 Processing helix chain 'E' and resid 470 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.077A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.375A 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 76 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.303A 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: 6.076A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.375A 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 76 through 79 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.303A 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: 6.077A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.374A 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 76 through 79 Processing sheet with id= O, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.303A 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: 6.077A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.375A 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 76 through 79 Processing sheet with id= T, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.303A 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: 6.077A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.375A 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 76 through 79 Processing sheet with id= Y, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2325 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: 13.13 Time building geometry restraints manager: 27.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15800 1.04 - 1.24: 2169 1.24 - 1.44: 5440 1.44 - 1.64: 9921 1.64 - 1.84: 175 Bond restraints: 33505 Sorted by residual: bond pdb=" C3 EPJ A 604 " pdb=" N1 EPJ A 604 " ideal model delta sigma weight residual 1.718 1.468 0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C3 EPJ D 606 " pdb=" N1 EPJ D 606 " ideal model delta sigma weight residual 1.718 1.468 0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C3 EPJ E 606 " pdb=" N1 EPJ E 606 " ideal model delta sigma weight residual 1.718 1.468 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3 EPJ C 606 " pdb=" N1 EPJ C 606 " ideal model delta sigma weight residual 1.718 1.468 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3 EPJ B 606 " pdb=" N1 EPJ B 606 " ideal model delta sigma weight residual 1.718 1.468 0.250 2.00e-02 2.50e+03 1.56e+02 ... (remaining 33500 not shown) Histogram of bond angle deviations from ideal: 96.08 - 103.69: 423 103.69 - 111.29: 34633 111.29 - 118.90: 10465 118.90 - 126.50: 14229 126.50 - 134.10: 375 Bond angle restraints: 60125 Sorted by residual: angle pdb=" O11 POV C 602 " pdb=" P POV C 602 " pdb=" O12 POV C 602 " ideal model delta sigma weight residual 97.67 109.33 -11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.30 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O11 POV D 602 " pdb=" P POV D 602 " pdb=" O12 POV D 602 " ideal model delta sigma weight residual 97.67 109.30 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O11 POV E 602 " pdb=" P POV E 602 " pdb=" O12 POV E 602 " ideal model delta sigma weight residual 97.67 109.28 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O11 POV A 606 " pdb=" P POV A 606 " pdb=" O12 POV A 606 " ideal model delta sigma weight residual 97.67 109.27 -11.60 3.00e+00 1.11e-01 1.50e+01 ... (remaining 60120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 16105 31.66 - 63.33: 420 63.33 - 94.99: 80 94.99 - 126.66: 35 126.66 - 158.32: 15 Dihedral angle restraints: 16655 sinusoidal: 9480 harmonic: 7175 Sorted by residual: 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 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+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 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 16652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2577 0.092 - 0.183: 213 0.183 - 0.274: 25 0.274 - 0.366: 10 0.366 - 0.457: 5 Chirality restraints: 2830 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.16e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.71e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.70e+01 ... (remaining 2827 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.311 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" C7 NAG A 602 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.451 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 604 " 0.311 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" C7 NAG B 604 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 604 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 604 " -0.451 2.00e-02 2.50e+03 pdb=" O7 NAG B 604 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.311 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" C7 NAG C 604 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.451 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.035 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 447 2.09 - 2.72: 53143 2.72 - 3.34: 94927 3.34 - 3.97: 129967 3.97 - 4.60: 198223 Nonbonded interactions: 476707 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.461 2.100 ... (remaining 476702 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 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478)) } 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: 1.220 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: 0.550 Extract box with map and model: 5.410 Check model and map are aligned: 0.270 Set scattering table: 0.240 Process input model: 118.730 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.300 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 0.250 17665 Z= 0.727 Angle : 1.106 11.662 24115 Z= 0.522 Chirality : 0.060 0.457 2830 Planarity : 0.014 0.262 2845 Dihedral : 17.815 158.319 7280 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.18), residues: 1955 helix: 0.51 (0.17), residues: 790 sheet: -0.37 (0.24), residues: 415 loop : -0.34 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 307 HIS 0.005 0.001 HIS E 104 PHE 0.026 0.003 PHE E 99 TYR 0.020 0.002 TYR B 14 ARG 0.008 0.001 ARG D 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8356 (mtp) cc_final: 0.8076 (mtp) REVERT: B 447 LEU cc_start: 0.7740 (tp) cc_final: 0.7348 (mp) REVERT: C 40 MET cc_start: 0.8376 (mtp) cc_final: 0.7925 (mtp) REVERT: C 253 MET cc_start: 0.7559 (mtt) cc_final: 0.7331 (mtt) REVERT: D 252 PHE cc_start: 0.8150 (t80) cc_final: 0.7821 (t80) REVERT: D 418 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7162 (ttm110) REVERT: E 40 MET cc_start: 0.8286 (mtp) cc_final: 0.7917 (mtp) REVERT: E 174 ASP cc_start: 0.7951 (t0) cc_final: 0.7712 (t70) REVERT: E 240 SER cc_start: 0.8318 (m) cc_final: 0.7763 (p) REVERT: E 322 MET cc_start: 0.7867 (mtp) cc_final: 0.7517 (mtp) REVERT: E 418 ARG cc_start: 0.7544 (ttm170) cc_final: 0.7321 (ttm170) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 2.5322 time to fit residues: 696.5273 Evaluate side-chains 191 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17665 Z= 0.196 Angle : 0.631 5.706 24115 Z= 0.313 Chirality : 0.041 0.149 2830 Planarity : 0.005 0.050 2845 Dihedral : 16.346 150.028 3515 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.56 % Allowed : 4.93 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 1955 helix: 1.45 (0.17), residues: 795 sheet: -0.60 (0.24), residues: 405 loop : 0.11 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 173 HIS 0.004 0.001 HIS E 104 PHE 0.025 0.001 PHE B 99 TYR 0.012 0.001 TYR B 273 ARG 0.002 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 2.355 Fit side-chains revert: symmetry clash REVERT: B 246 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7846 (tt) REVERT: B 249 LEU cc_start: 0.8277 (tp) cc_final: 0.8044 (tp) REVERT: B 447 LEU cc_start: 0.7700 (tp) cc_final: 0.7308 (mp) REVERT: C 40 MET cc_start: 0.8341 (mtp) cc_final: 0.7941 (mtp) REVERT: C 159 MET cc_start: 0.7961 (ttp) cc_final: 0.7705 (ttp) REVERT: C 450 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5708 (mpt) REVERT: D 253 MET cc_start: 0.7503 (mtt) cc_final: 0.7072 (mtt) REVERT: D 418 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7316 (ttm170) REVERT: E 40 MET cc_start: 0.8325 (mtp) cc_final: 0.7760 (mtp) REVERT: E 174 ASP cc_start: 0.7897 (t0) cc_final: 0.7650 (t70) REVERT: E 240 SER cc_start: 0.8041 (m) cc_final: 0.7835 (m) REVERT: E 322 MET cc_start: 0.7957 (mtp) cc_final: 0.7584 (mtp) REVERT: E 450 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5930 (mpt) outliers start: 10 outliers final: 1 residues processed: 223 average time/residue: 2.2866 time to fit residues: 584.1045 Evaluate side-chains 211 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain E residue 450 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17665 Z= 0.370 Angle : 0.682 7.401 24115 Z= 0.347 Chirality : 0.044 0.203 2830 Planarity : 0.006 0.072 2845 Dihedral : 13.997 131.750 3515 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.95 % Allowed : 6.22 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 1955 helix: 1.74 (0.17), residues: 795 sheet: -0.62 (0.23), residues: 405 loop : 0.19 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 173 HIS 0.011 0.002 HIS E 104 PHE 0.030 0.003 PHE B 99 TYR 0.020 0.003 TYR D 14 ARG 0.006 0.001 ARG A 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: B 447 LEU cc_start: 0.7758 (tp) cc_final: 0.7311 (mp) REVERT: C 40 MET cc_start: 0.8456 (mtp) cc_final: 0.7976 (mtp) REVERT: C 159 MET cc_start: 0.8135 (ttp) cc_final: 0.7875 (ttp) REVERT: C 265 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: C 450 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5705 (mpt) REVERT: D 418 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7306 (ttm110) REVERT: E 40 MET cc_start: 0.8368 (mtp) cc_final: 0.7782 (mtp) REVERT: E 174 ASP cc_start: 0.7891 (t0) cc_final: 0.7647 (t70) REVERT: E 240 SER cc_start: 0.7918 (m) cc_final: 0.7709 (m) REVERT: E 260 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7565 (mmp) REVERT: E 322 MET cc_start: 0.7890 (mtp) cc_final: 0.7504 (mtp) outliers start: 17 outliers final: 6 residues processed: 208 average time/residue: 2.4064 time to fit residues: 571.5449 Evaluate side-chains 206 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 260 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17665 Z= 0.162 Angle : 0.534 5.455 24115 Z= 0.270 Chirality : 0.038 0.146 2830 Planarity : 0.004 0.040 2845 Dihedral : 12.337 117.222 3515 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.39 % Allowed : 7.56 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 1955 helix: 2.08 (0.17), residues: 795 sheet: -0.77 (0.24), residues: 395 loop : 0.35 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 173 HIS 0.003 0.001 HIS C 104 PHE 0.014 0.001 PHE B 99 TYR 0.015 0.001 TYR B 273 ARG 0.002 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 2.569 Fit side-chains revert: symmetry clash REVERT: B 447 LEU cc_start: 0.7858 (tp) cc_final: 0.7432 (mp) REVERT: C 40 MET cc_start: 0.8418 (mtp) cc_final: 0.7808 (mtp) REVERT: C 159 MET cc_start: 0.8121 (ttp) cc_final: 0.7854 (ttp) REVERT: D 418 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7264 (ttm110) REVERT: E 40 MET cc_start: 0.8375 (mtp) cc_final: 0.7657 (mtp) REVERT: E 240 SER cc_start: 0.7867 (m) cc_final: 0.7655 (m) REVERT: E 322 MET cc_start: 0.7883 (mtp) cc_final: 0.7539 (mtp) outliers start: 7 outliers final: 2 residues processed: 206 average time/residue: 2.3540 time to fit residues: 558.4130 Evaluate side-chains 200 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17665 Z= 0.155 Angle : 0.508 4.901 24115 Z= 0.257 Chirality : 0.038 0.144 2830 Planarity : 0.004 0.038 2845 Dihedral : 11.403 112.055 3515 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.39 % Allowed : 7.84 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1955 helix: 2.30 (0.17), residues: 795 sheet: -0.90 (0.24), residues: 405 loop : 0.43 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 307 HIS 0.003 0.001 HIS D 104 PHE 0.015 0.001 PHE B 455 TYR 0.012 0.001 TYR B 273 ARG 0.002 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 3.235 Fit side-chains revert: symmetry clash REVERT: A 249 LEU cc_start: 0.7883 (tp) cc_final: 0.7538 (tp) REVERT: B 447 LEU cc_start: 0.7814 (tp) cc_final: 0.7364 (mp) REVERT: C 40 MET cc_start: 0.8389 (mtp) cc_final: 0.7736 (mtp) REVERT: C 159 MET cc_start: 0.8071 (ttp) cc_final: 0.7813 (ttp) REVERT: C 253 MET cc_start: 0.7075 (mtt) cc_final: 0.6742 (mtt) REVERT: C 450 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5951 (mpt) REVERT: D 267 VAL cc_start: 0.8589 (p) cc_final: 0.8385 (t) REVERT: E 40 MET cc_start: 0.8434 (mtp) cc_final: 0.7674 (mtp) REVERT: E 322 MET cc_start: 0.7879 (mtp) cc_final: 0.7590 (mtp) outliers start: 7 outliers final: 2 residues processed: 202 average time/residue: 2.3523 time to fit residues: 544.2101 Evaluate side-chains 198 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 chunk 188 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17665 Z= 0.307 Angle : 0.592 6.151 24115 Z= 0.305 Chirality : 0.040 0.185 2830 Planarity : 0.005 0.054 2845 Dihedral : 11.352 112.378 3515 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.73 % Allowed : 8.01 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1955 helix: 2.29 (0.17), residues: 790 sheet: -0.71 (0.23), residues: 400 loop : 0.30 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 173 HIS 0.009 0.002 HIS E 104 PHE 0.022 0.002 PHE B 99 TYR 0.017 0.002 TYR B 31 ARG 0.005 0.001 ARG A 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 2.908 Fit side-chains REVERT: B 161 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7029 (tt0) REVERT: B 447 LEU cc_start: 0.7858 (tp) cc_final: 0.7418 (mp) REVERT: C 40 MET cc_start: 0.8388 (mtp) cc_final: 0.7791 (mtp) REVERT: C 159 MET cc_start: 0.8129 (ttp) cc_final: 0.7836 (ttp) REVERT: C 253 MET cc_start: 0.7081 (mtt) cc_final: 0.6755 (mtt) REVERT: C 450 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5821 (mpt) REVERT: C 452 PHE cc_start: 0.8016 (m-80) cc_final: 0.7807 (m-80) REVERT: D 267 VAL cc_start: 0.8588 (p) cc_final: 0.8380 (t) REVERT: E 40 MET cc_start: 0.8450 (mtp) cc_final: 0.7819 (mtp) REVERT: E 240 SER cc_start: 0.7820 (m) cc_final: 0.7438 (p) REVERT: E 322 MET cc_start: 0.7893 (mtp) cc_final: 0.7570 (mtp) outliers start: 13 outliers final: 5 residues processed: 197 average time/residue: 2.4185 time to fit residues: 544.4725 Evaluate side-chains 195 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17665 Z= 0.219 Angle : 0.545 6.179 24115 Z= 0.279 Chirality : 0.039 0.155 2830 Planarity : 0.005 0.042 2845 Dihedral : 11.028 112.419 3515 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.62 % Allowed : 8.35 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1955 helix: 2.35 (0.17), residues: 790 sheet: -0.75 (0.23), residues: 400 loop : 0.32 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 173 HIS 0.004 0.001 HIS E 104 PHE 0.017 0.001 PHE B 99 TYR 0.009 0.001 TYR B 273 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 2.550 Fit side-chains revert: symmetry clash REVERT: B 249 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7341 (mp) REVERT: B 447 LEU cc_start: 0.7843 (tp) cc_final: 0.7380 (mp) REVERT: C 40 MET cc_start: 0.8372 (mtp) cc_final: 0.7758 (mtp) REVERT: C 159 MET cc_start: 0.8113 (ttp) cc_final: 0.7815 (ttp) REVERT: C 161 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: C 450 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5813 (mpt) REVERT: E 40 MET cc_start: 0.8452 (mtp) cc_final: 0.8098 (mtp) REVERT: E 240 SER cc_start: 0.7803 (m) cc_final: 0.7430 (p) REVERT: E 322 MET cc_start: 0.7886 (mtp) cc_final: 0.7570 (mtp) outliers start: 11 outliers final: 5 residues processed: 200 average time/residue: 2.3717 time to fit residues: 542.0424 Evaluate side-chains 200 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17665 Z= 0.284 Angle : 0.579 6.452 24115 Z= 0.298 Chirality : 0.040 0.159 2830 Planarity : 0.005 0.064 2845 Dihedral : 10.910 112.497 3515 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.95 % Allowed : 8.18 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1955 helix: 2.30 (0.17), residues: 790 sheet: -0.74 (0.23), residues: 405 loop : 0.30 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 173 HIS 0.007 0.001 HIS E 104 PHE 0.019 0.002 PHE B 99 TYR 0.015 0.002 TYR B 31 ARG 0.012 0.001 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 2.537 Fit side-chains revert: symmetry clash REVERT: B 447 LEU cc_start: 0.7856 (tp) cc_final: 0.7395 (mp) REVERT: C 40 MET cc_start: 0.8362 (mtp) cc_final: 0.7749 (mtp) REVERT: C 159 MET cc_start: 0.8131 (ttp) cc_final: 0.7823 (ttp) REVERT: C 161 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: C 450 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.5769 (mpt) REVERT: C 452 PHE cc_start: 0.7935 (m-80) cc_final: 0.7662 (m-80) REVERT: E 40 MET cc_start: 0.8451 (mtp) cc_final: 0.8092 (mtp) REVERT: E 210 TYR cc_start: 0.8209 (m-80) cc_final: 0.7815 (m-80) REVERT: E 240 SER cc_start: 0.7782 (m) cc_final: 0.7398 (p) outliers start: 17 outliers final: 6 residues processed: 203 average time/residue: 2.4313 time to fit residues: 562.1498 Evaluate side-chains 198 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17665 Z= 0.176 Angle : 0.521 6.302 24115 Z= 0.266 Chirality : 0.038 0.147 2830 Planarity : 0.004 0.035 2845 Dihedral : 10.538 112.349 3515 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.45 % Allowed : 8.46 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 1955 helix: 2.46 (0.17), residues: 790 sheet: -0.90 (0.23), residues: 405 loop : 0.35 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 307 HIS 0.003 0.001 HIS E 104 PHE 0.013 0.001 PHE B 99 TYR 0.008 0.001 TYR B 273 ARG 0.002 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 2.791 Fit side-chains REVERT: B 447 LEU cc_start: 0.7852 (tp) cc_final: 0.7349 (mp) REVERT: C 40 MET cc_start: 0.8349 (mtp) cc_final: 0.7689 (mtp) REVERT: C 159 MET cc_start: 0.8098 (ttp) cc_final: 0.7805 (ttp) REVERT: C 161 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: C 450 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5744 (mpt) REVERT: C 452 PHE cc_start: 0.7957 (m-80) cc_final: 0.7753 (m-80) REVERT: E 40 MET cc_start: 0.8457 (mtp) cc_final: 0.8104 (mtp) REVERT: E 210 TYR cc_start: 0.8212 (m-80) cc_final: 0.7820 (m-80) REVERT: E 240 SER cc_start: 0.7748 (m) cc_final: 0.7387 (p) outliers start: 8 outliers final: 3 residues processed: 193 average time/residue: 2.4022 time to fit residues: 529.6054 Evaluate side-chains 192 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17665 Z= 0.185 Angle : 0.516 6.355 24115 Z= 0.263 Chirality : 0.038 0.145 2830 Planarity : 0.004 0.070 2845 Dihedral : 10.114 112.166 3515 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.39 % Allowed : 8.63 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1955 helix: 2.52 (0.17), residues: 790 sheet: -0.90 (0.24), residues: 405 loop : 0.37 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 173 HIS 0.003 0.001 HIS E 104 PHE 0.013 0.001 PHE B 455 TYR 0.009 0.001 TYR E 31 ARG 0.011 0.000 ARG C 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 2.636 Fit side-chains revert: symmetry clash REVERT: B 447 LEU cc_start: 0.7819 (tp) cc_final: 0.7321 (mp) REVERT: C 40 MET cc_start: 0.8354 (mtp) cc_final: 0.7730 (mtp) REVERT: C 159 MET cc_start: 0.8098 (ttp) cc_final: 0.7811 (ttp) REVERT: C 161 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: C 429 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6392 (mt-10) REVERT: C 450 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5807 (mpt) REVERT: C 452 PHE cc_start: 0.7963 (m-80) cc_final: 0.7763 (m-80) REVERT: E 40 MET cc_start: 0.8477 (mtp) cc_final: 0.8098 (mtp) REVERT: E 210 TYR cc_start: 0.8203 (m-80) cc_final: 0.7817 (m-80) outliers start: 7 outliers final: 1 residues processed: 195 average time/residue: 2.4262 time to fit residues: 539.4841 Evaluate side-chains 188 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 142 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 0.0060 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121623 restraints weight = 51948.681| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.90 r_work: 0.3182 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17665 Z= 0.141 Angle : 0.487 7.020 24115 Z= 0.246 Chirality : 0.037 0.139 2830 Planarity : 0.004 0.036 2845 Dihedral : 9.658 111.944 3515 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.11 % Allowed : 9.08 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.19), residues: 1955 helix: 2.70 (0.17), residues: 780 sheet: -0.93 (0.24), residues: 405 loop : 0.44 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 307 HIS 0.002 0.000 HIS D 104 PHE 0.014 0.001 PHE B 455 TYR 0.008 0.001 TYR A 209 ARG 0.002 0.000 ARG C 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10820.30 seconds wall clock time: 192 minutes 46.69 seconds (11566.69 seconds total)