Starting phenix.real_space_refine on Fri Mar 22 19:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v86_43025/03_2024/8v86_43025_trim_updated.pdb" } resolution = 2.47 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= 0.011 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: 7 Type Number sf(0) Gaussians Br 5 7.06 5 P 10 5.49 5 S 120 5.16 5 C 11255 2.51 5 N 2625 2.21 5 O 3170 1.98 5 H 15835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "E GLU 9": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33020 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: 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: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 27.89, per 1000 atoms: 0.84 Number of scatterers: 33020 At special positions: 0 Unit cell: (102.505, 100.347, 166.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 5 34.99 S 120 16.00 P 10 15.00 O 3170 8.00 N 2625 7.00 C 11255 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=2.04 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 503 " - " ASN A 67 " " NAG B 505 " - " ASN B 67 " " NAG C 505 " - " ASN C 67 " " NAG D 505 " - " ASN D 67 " " NAG E 505 " - " 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: 25.86 Conformation dependent library (CDL) restraints added in 6.2 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: 50 helices and 25 sheets defined 39.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.78 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 215 through 230 removed outlier: 4.181A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.824A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) 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 10 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 230 removed outlier: 4.181A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 257 removed outlier: 3.824A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) 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 10 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 230 removed outlier: 4.181A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 257 removed outlier: 3.824A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) 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 10 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 230 removed outlier: 4.181A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 238 through 257 removed outlier: 3.824A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) 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 10 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 230 removed outlier: 4.181A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 238 through 257 removed outlier: 3.825A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) 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: 6.326A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.495A 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: 4.843A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.251A 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: 6.326A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.494A 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: 4.843A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.252A 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: 6.326A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.494A 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: 4.843A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.251A 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: 6.326A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.495A 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: 4.843A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.251A 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: 6.327A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.495A 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: 4.843A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2295 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: 12.18 Time building geometry restraints manager: 26.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15800 1.05 - 1.26: 2605 1.26 - 1.47: 7194 1.47 - 1.69: 7661 1.69 - 1.90: 180 Bond restraints: 33440 Sorted by residual: bond pdb=" C4 YLI E 501 " pdb=" C9 YLI E 501 " ideal model delta sigma weight residual 0.000 1.519 -1.519 2.00e-02 2.50e+03 5.77e+03 bond pdb=" C4 YLI C 501 " pdb=" C9 YLI C 501 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C4 YLI B 501 " pdb=" C9 YLI B 501 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C4 YLI D 501 " pdb=" C9 YLI D 501 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C4 YLI A 504 " pdb=" C9 YLI A 504 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.14: 817 106.14 - 113.19: 38740 113.19 - 120.24: 10622 120.24 - 127.30: 9536 127.30 - 134.35: 250 Bond angle restraints: 59965 Sorted by residual: angle pdb=" O15 YLI A 504 " pdb=" S14 YLI A 504 " pdb=" O16 YLI A 504 " ideal model delta sigma weight residual 101.63 118.81 -17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" O15 YLI C 501 " pdb=" S14 YLI C 501 " pdb=" O16 YLI C 501 " ideal model delta sigma weight residual 101.63 118.78 -17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O15 YLI B 501 " pdb=" S14 YLI B 501 " pdb=" O16 YLI B 501 " ideal model delta sigma weight residual 101.63 118.77 -17.14 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O15 YLI D 501 " pdb=" S14 YLI D 501 " pdb=" O16 YLI D 501 " ideal model delta sigma weight residual 101.63 118.75 -17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O15 YLI E 501 " pdb=" S14 YLI E 501 " pdb=" O16 YLI E 501 " ideal model delta sigma weight residual 101.63 118.74 -17.11 3.00e+00 1.11e-01 3.25e+01 ... (remaining 59960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 16132 31.48 - 62.96: 498 62.96 - 94.44: 105 94.44 - 125.92: 35 125.92 - 157.40: 10 Dihedral angle restraints: 16780 sinusoidal: 9605 harmonic: 7175 Sorted by residual: dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 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 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+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 -153.65 -26.35 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 16777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 2695 0.155 - 0.309: 25 0.309 - 0.464: 5 0.464 - 0.618: 0 0.618 - 0.773: 5 Chirality restraints: 2730 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 -2.29 -0.11 2.00e-02 2.50e+03 3.18e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.13e+01 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 -2.29 -0.11 2.00e-02 2.50e+03 3.05e+01 ... (remaining 2727 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.266 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C7 NAG J 2 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.388 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " 0.266 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C7 NAG L 2 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " -0.388 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.266 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C7 NAG F 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.014 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.388 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.193 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.11: 653 2.11 - 2.76: 59594 2.76 - 3.40: 96241 3.40 - 4.05: 137563 4.05 - 4.70: 214191 Nonbonded interactions: 508242 Sorted by model distance: nonbonded pdb="HD21 LEU E 214 " pdb="HD11 ILE E 259 " model vdw 1.458 2.440 nonbonded pdb="HD21 LEU B 214 " pdb="HD11 ILE B 259 " model vdw 1.459 2.440 nonbonded pdb="HD21 LEU C 214 " pdb="HD11 ILE C 259 " model vdw 1.459 2.440 nonbonded pdb="HD21 LEU D 214 " pdb="HD11 ILE D 259 " model vdw 1.459 2.440 nonbonded pdb="HD21 LEU A 214 " pdb="HD11 ILE A 259 " model vdw 1.460 2.440 ... (remaining 508237 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: 0.950 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: 0.470 Extract box with map and model: 5.350 Check model and map are aligned: 0.470 Set scattering table: 0.320 Process input model: 124.610 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.280 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.031 1.519 17600 Z= 1.790 Angle : 0.947 17.179 23955 Z= 0.459 Chirality : 0.060 0.773 2730 Planarity : 0.012 0.229 2845 Dihedral : 18.451 157.396 7405 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.05 (0.17), residues: 1955 helix: -0.73 (0.16), residues: 790 sheet: -0.64 (0.23), residues: 420 loop : -0.39 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 54 HIS 0.003 0.001 HIS B 296 PHE 0.019 0.002 PHE B 99 TYR 0.018 0.002 TYR C 117 ARG 0.004 0.001 ARG E 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 : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 322 MET cc_start: 0.8770 (mtp) cc_final: 0.8535 (mtp) REVERT: C 46 ASN cc_start: 0.8060 (m110) cc_final: 0.7587 (m110) REVERT: C 97 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6874 (mt-10) REVERT: C 234 ASP cc_start: 0.7982 (m-30) cc_final: 0.7567 (m-30) REVERT: D 322 MET cc_start: 0.8624 (mtp) cc_final: 0.8258 (mtp) REVERT: E 46 ASN cc_start: 0.8173 (m110) cc_final: 0.7717 (m110) outliers start: 0 outliers final: 1 residues processed: 243 average time/residue: 2.6909 time to fit residues: 729.8235 Evaluate side-chains 207 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS E 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 17600 Z= 0.275 Angle : 0.790 11.209 23955 Z= 0.376 Chirality : 0.043 0.289 2730 Planarity : 0.005 0.033 2845 Dihedral : 20.819 156.461 3642 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.95 % Allowed : 6.27 % Favored : 92.77 % 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: -0.34 (0.17), residues: 1955 helix: 0.08 (0.16), residues: 790 sheet: -0.12 (0.23), residues: 405 loop : -0.41 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.002 0.001 HIS C 297 PHE 0.021 0.001 PHE D 99 TYR 0.011 0.001 TYR B 117 ARG 0.002 0.000 ARG B 309 *********************** 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 223 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7252 (mt-10) REVERT: C 46 ASN cc_start: 0.8054 (m110) cc_final: 0.7598 (m110) REVERT: C 97 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6852 (mt-10) REVERT: C 234 ASP cc_start: 0.7982 (m-30) cc_final: 0.7560 (m-30) REVERT: D 191 LYS cc_start: 0.7921 (tptt) cc_final: 0.7622 (mmpt) REVERT: D 322 MET cc_start: 0.8669 (mtp) cc_final: 0.8310 (mtp) REVERT: D 415 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: E 46 ASN cc_start: 0.8188 (m110) cc_final: 0.7753 (m110) REVERT: E 464 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8656 (mp) outliers start: 17 outliers final: 9 residues processed: 212 average time/residue: 2.7820 time to fit residues: 658.4076 Evaluate side-chains 216 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 458 ILE Chi-restraints excluded: chain E residue 464 LEU 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: 6.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 17600 Z= 0.323 Angle : 0.753 10.807 23955 Z= 0.364 Chirality : 0.042 0.146 2730 Planarity : 0.004 0.033 2845 Dihedral : 20.140 155.806 3640 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.01 % Allowed : 6.67 % Favored : 92.32 % 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: 0.07 (0.18), residues: 1955 helix: 0.57 (0.17), residues: 790 sheet: 0.04 (0.23), residues: 405 loop : -0.34 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 54 HIS 0.003 0.001 HIS B 295 PHE 0.023 0.002 PHE D 99 TYR 0.010 0.001 TYR A 117 ARG 0.005 0.001 ARG D 78 *********************** 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 224 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 46 ASN cc_start: 0.8066 (m110) cc_final: 0.7623 (m110) REVERT: C 97 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6857 (mt-10) REVERT: C 234 ASP cc_start: 0.7992 (m-30) cc_final: 0.7567 (m-30) REVERT: D 191 LYS cc_start: 0.7912 (tptt) cc_final: 0.7619 (mmpt) REVERT: D 322 MET cc_start: 0.8693 (mtp) cc_final: 0.8388 (mtp) REVERT: D 415 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6159 (mp0) REVERT: E 46 ASN cc_start: 0.8181 (m110) cc_final: 0.7764 (m110) outliers start: 18 outliers final: 13 residues processed: 214 average time/residue: 2.8155 time to fit residues: 671.0680 Evaluate side-chains 211 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.0870 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 0.0000 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17600 Z= 0.224 Angle : 0.689 10.338 23955 Z= 0.333 Chirality : 0.042 0.182 2730 Planarity : 0.004 0.034 2845 Dihedral : 19.599 154.817 3640 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.78 % Allowed : 7.23 % Favored : 91.99 % 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: 0.32 (0.18), residues: 1955 helix: 0.82 (0.17), residues: 790 sheet: 0.15 (0.24), residues: 405 loop : -0.25 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 133 HIS 0.001 0.000 HIS E 296 PHE 0.019 0.001 PHE B 99 TYR 0.009 0.001 TYR C 194 ARG 0.005 0.000 ARG D 185 *********************** 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 213 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 2.469 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7228 (mt-10) REVERT: C 46 ASN cc_start: 0.8088 (m110) cc_final: 0.7621 (m110) REVERT: C 234 ASP cc_start: 0.7989 (m-30) cc_final: 0.7559 (m-30) REVERT: D 191 LYS cc_start: 0.7937 (tptt) cc_final: 0.7638 (mmpt) REVERT: D 322 MET cc_start: 0.8684 (mtp) cc_final: 0.8349 (mtp) REVERT: D 415 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: E 46 ASN cc_start: 0.8176 (m110) cc_final: 0.7746 (m110) outliers start: 14 outliers final: 12 residues processed: 206 average time/residue: 2.8418 time to fit residues: 652.3294 Evaluate side-chains 209 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E 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: 1.9990 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 0.0040 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17600 Z= 0.239 Angle : 0.677 8.820 23955 Z= 0.330 Chirality : 0.041 0.150 2730 Planarity : 0.004 0.033 2845 Dihedral : 19.484 154.597 3640 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.90 % Allowed : 7.45 % Favored : 91.65 % 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: 0.36 (0.18), residues: 1955 helix: 0.86 (0.17), residues: 790 sheet: 0.18 (0.24), residues: 405 loop : -0.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 59 HIS 0.002 0.001 HIS E 295 PHE 0.021 0.001 PHE D 99 TYR 0.009 0.001 TYR C 194 ARG 0.003 0.000 ARG D 185 *********************** 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 213 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 2.594 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7227 (mt-10) REVERT: C 46 ASN cc_start: 0.8093 (m110) cc_final: 0.7631 (m110) REVERT: C 234 ASP cc_start: 0.7992 (m-30) cc_final: 0.7563 (m-30) REVERT: D 191 LYS cc_start: 0.7937 (tptt) cc_final: 0.7641 (mmpt) REVERT: D 322 MET cc_start: 0.8685 (mtp) cc_final: 0.8344 (mtp) REVERT: D 415 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: E 46 ASN cc_start: 0.8183 (m110) cc_final: 0.7756 (m110) outliers start: 16 outliers final: 12 residues processed: 205 average time/residue: 2.7928 time to fit residues: 639.0397 Evaluate side-chains 207 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E 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: 3.9990 chunk 169 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17600 Z= 0.239 Angle : 0.677 8.820 23955 Z= 0.330 Chirality : 0.041 0.150 2730 Planarity : 0.004 0.033 2845 Dihedral : 19.484 154.597 3640 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.73 % Allowed : 7.84 % Favored : 91.43 % 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: 0.36 (0.18), residues: 1955 helix: 0.86 (0.17), residues: 790 sheet: 0.18 (0.24), residues: 405 loop : -0.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 59 HIS 0.002 0.001 HIS E 295 PHE 0.021 0.001 PHE D 99 TYR 0.009 0.001 TYR C 194 ARG 0.003 0.000 ARG D 185 *********************** 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 207 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 2.824 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7227 (mt-10) REVERT: C 46 ASN cc_start: 0.8093 (m110) cc_final: 0.7631 (m110) REVERT: C 234 ASP cc_start: 0.7992 (m-30) cc_final: 0.7563 (m-30) REVERT: D 191 LYS cc_start: 0.7937 (tptt) cc_final: 0.7641 (mmpt) REVERT: D 322 MET cc_start: 0.8686 (mtp) cc_final: 0.8344 (mtp) REVERT: D 415 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: E 46 ASN cc_start: 0.8183 (m110) cc_final: 0.7756 (m110) outliers start: 13 outliers final: 12 residues processed: 200 average time/residue: 2.8309 time to fit residues: 630.7050 Evaluate side-chains 207 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E 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: 1.9990 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 0.0670 chunk 117 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17600 Z= 0.235 Angle : 0.669 8.769 23955 Z= 0.325 Chirality : 0.042 0.162 2730 Planarity : 0.004 0.033 2845 Dihedral : 19.206 153.752 3640 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.90 % Allowed : 7.62 % Favored : 91.48 % 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: 0.46 (0.18), residues: 1955 helix: 0.97 (0.17), residues: 790 sheet: 0.22 (0.24), residues: 405 loop : -0.20 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 54 HIS 0.002 0.001 HIS E 295 PHE 0.022 0.001 PHE D 99 TYR 0.009 0.001 TYR C 194 ARG 0.004 0.000 ARG D 185 *********************** 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 208 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 3.070 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7226 (mt-10) REVERT: C 46 ASN cc_start: 0.8096 (m110) cc_final: 0.7661 (m110) REVERT: C 234 ASP cc_start: 0.7996 (m-30) cc_final: 0.7562 (m-30) REVERT: D 191 LYS cc_start: 0.7935 (tptt) cc_final: 0.7642 (mmpt) REVERT: D 322 MET cc_start: 0.8687 (mtp) cc_final: 0.8333 (mtp) REVERT: D 415 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: E 46 ASN cc_start: 0.8187 (m110) cc_final: 0.7763 (m110) outliers start: 16 outliers final: 13 residues processed: 199 average time/residue: 2.8324 time to fit residues: 627.2704 Evaluate side-chains 205 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E 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: 4.9990 chunk 75 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 128 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17600 Z= 0.234 Angle : 0.653 8.078 23955 Z= 0.318 Chirality : 0.041 0.161 2730 Planarity : 0.004 0.033 2845 Dihedral : 18.685 152.287 3640 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.95 % Allowed : 7.34 % Favored : 91.71 % 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: 0.53 (0.18), residues: 1955 helix: 1.10 (0.17), residues: 790 sheet: -0.04 (0.23), residues: 430 loop : -0.05 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.004 0.001 HIS C 295 PHE 0.026 0.002 PHE E 99 TYR 0.012 0.002 TYR D 117 ARG 0.015 0.001 ARG D 185 *********************** 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 : 2.710 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7173 (mt-10) REVERT: C 46 ASN cc_start: 0.8076 (m110) cc_final: 0.7618 (m110) REVERT: C 234 ASP cc_start: 0.8000 (m-30) cc_final: 0.7567 (m-30) REVERT: D 191 LYS cc_start: 0.7934 (tptt) cc_final: 0.7642 (mmpt) REVERT: D 322 MET cc_start: 0.8694 (mtp) cc_final: 0.8330 (mtp) REVERT: D 415 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: E 46 ASN cc_start: 0.8228 (m110) cc_final: 0.7806 (m110) outliers start: 17 outliers final: 15 residues processed: 202 average time/residue: 2.8596 time to fit residues: 642.4778 Evaluate side-chains 208 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E 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: 3.9990 chunk 164 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17600 Z= 0.219 Angle : 0.646 8.080 23955 Z= 0.314 Chirality : 0.041 0.157 2730 Planarity : 0.004 0.035 2845 Dihedral : 18.360 151.123 3640 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.01 % Allowed : 7.51 % Favored : 91.48 % 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: 0.63 (0.18), residues: 1955 helix: 1.20 (0.17), residues: 790 sheet: -0.01 (0.23), residues: 430 loop : -0.01 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.003 0.001 HIS C 295 PHE 0.023 0.001 PHE D 99 TYR 0.011 0.001 TYR D 117 ARG 0.010 0.000 ARG D 185 *********************** 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 214 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 2.768 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7168 (mt-10) REVERT: C 46 ASN cc_start: 0.8077 (m110) cc_final: 0.7620 (m110) REVERT: C 234 ASP cc_start: 0.8003 (m-30) cc_final: 0.7567 (m-30) REVERT: C 258 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6861 (mm-30) REVERT: D 191 LYS cc_start: 0.7933 (tptt) cc_final: 0.7640 (mmpt) REVERT: D 322 MET cc_start: 0.8689 (mtp) cc_final: 0.8321 (mtp) REVERT: D 415 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6177 (mp0) REVERT: E 46 ASN cc_start: 0.8228 (m110) cc_final: 0.7809 (m110) outliers start: 18 outliers final: 15 residues processed: 205 average time/residue: 2.8073 time to fit residues: 641.1758 Evaluate side-chains 210 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 0.0570 chunk 122 optimal weight: 0.6980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17600 Z= 0.207 Angle : 0.638 8.058 23955 Z= 0.310 Chirality : 0.041 0.158 2730 Planarity : 0.004 0.036 2845 Dihedral : 18.064 150.148 3640 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.01 % Allowed : 7.79 % Favored : 91.20 % 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: 0.69 (0.18), residues: 1955 helix: 1.26 (0.17), residues: 790 sheet: 0.01 (0.23), residues: 430 loop : 0.02 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.002 0.001 HIS E 295 PHE 0.023 0.001 PHE D 99 TYR 0.012 0.001 TYR D 117 ARG 0.007 0.000 ARG D 185 ********************** 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 212 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 2.723 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7165 (mt-10) REVERT: C 46 ASN cc_start: 0.8076 (m110) cc_final: 0.7621 (m110) REVERT: C 234 ASP cc_start: 0.8003 (m-30) cc_final: 0.7568 (m-30) REVERT: D 191 LYS cc_start: 0.7974 (tptt) cc_final: 0.7657 (mmpt) REVERT: D 322 MET cc_start: 0.8685 (mtp) cc_final: 0.8316 (mtp) REVERT: D 415 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: E 46 ASN cc_start: 0.8227 (m110) cc_final: 0.7811 (m110) outliers start: 18 outliers final: 15 residues processed: 203 average time/residue: 2.8389 time to fit residues: 641.9625 Evaluate side-chains 209 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.092256 restraints weight = 49610.743| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.77 r_work: 0.2804 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17600 Z= 0.196 Angle : 0.634 7.653 23955 Z= 0.307 Chirality : 0.041 0.156 2730 Planarity : 0.004 0.040 2845 Dihedral : 17.986 149.884 3640 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.95 % Allowed : 7.79 % 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: 0.72 (0.18), residues: 1955 helix: 1.29 (0.17), residues: 790 sheet: 0.02 (0.23), residues: 430 loop : 0.03 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.002 0.001 HIS E 295 PHE 0.023 0.001 PHE D 99 TYR 0.012 0.001 TYR D 117 ARG 0.004 0.000 ARG D 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11438.06 seconds wall clock time: 200 minutes 32.73 seconds (12032.73 seconds total)