Starting phenix.real_space_refine on Fri Mar 22 23:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v82_43015/03_2024/8v82_43015_trim_updated.pdb" } resolution = 2.61 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= 0.010 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 15 5.49 5 S 115 5.16 5 Cl 10 4.86 5 C 11450 2.51 5 N 2645 2.21 5 O 3200 1.98 5 H 15825 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-5265/modules/chem_data/mon_lib" Total number of atoms: 33265 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 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, 6341 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: 6414 Chain: "B" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 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, 6341 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: 6414 Chain: "C" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 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, 6341 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: 6414 Chain: "D" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 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, 6341 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: 6414 Chain: "E" Number of atoms: 6353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 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, 6341 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: 6414 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: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 276 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 172 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 26.32, per 1000 atoms: 0.79 Number of scatterers: 33265 At special positions: 0 Unit cell: (102.505, 101.426, 161.85, 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 10 17.00 S 115 16.00 P 15 15.00 O 3200 8.00 N 2645 7.00 C 11450 6.00 H 15825 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=2.05 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 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 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: 26.29 Conformation dependent library (CDL) restraints added in 6.1 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 39.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.724A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 229 removed outlier: 3.637A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 removed outlier: 4.569A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 253 " --> pdb=" O LEU A 249 " (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 464 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.723A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.637A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 259 removed outlier: 4.568A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (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 464 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.724A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 229 removed outlier: 3.637A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 259 removed outlier: 4.569A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (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 464 Processing helix chain 'C' and resid 470 through 477 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.723A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.637A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 259 removed outlier: 4.569A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET D 253 " --> pdb=" O LEU D 249 " (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 464 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.724A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 229 removed outlier: 3.637A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 259 removed outlier: 4.569A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 253 " --> pdb=" O LEU E 249 " (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 464 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: 5.984A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.170A 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: 4.544A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 177 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.377A 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: 5.983A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.170A 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: 4.544A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 177 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.377A 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: 5.983A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.170A 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: 4.543A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 177 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.377A 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: 5.984A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.171A 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: 4.544A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 177 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.377A 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: 5.984A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.170A 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: 4.544A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 177 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2235 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: 12.88 Time building geometry restraints manager: 27.27 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: 15785 1.05 - 1.25: 2620 1.25 - 1.46: 6618 1.46 - 1.67: 8487 1.67 - 1.87: 180 Bond restraints: 33690 Sorted by residual: bond pdb=" C3 EPJ D 608 " pdb=" N1 EPJ D 608 " 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 608 " pdb=" N1 EPJ C 608 " ideal model delta sigma weight residual 1.718 1.469 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C3 EPJ A 606 " pdb=" N1 EPJ A 606 " ideal model delta sigma weight residual 1.718 1.469 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C3 EPJ B 608 " pdb=" N1 EPJ B 608 " ideal model delta sigma weight residual 1.718 1.469 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C3 EPJ E 607 " pdb=" N1 EPJ E 607 " ideal model delta sigma weight residual 1.718 1.470 0.248 2.00e-02 2.50e+03 1.54e+02 ... (remaining 33685 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.36: 209 103.36 - 111.05: 34039 111.05 - 118.75: 11022 118.75 - 126.44: 14532 126.44 - 134.13: 428 Bond angle restraints: 60230 Sorted by residual: angle pdb=" O11 POV D 605 " pdb=" P POV D 605 " pdb=" O12 POV D 605 " ideal model delta sigma weight residual 97.67 110.41 -12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV A 603 " pdb=" P POV A 603 " pdb=" O12 POV A 603 " ideal model delta sigma weight residual 97.67 110.40 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV A 608 " pdb=" P POV A 608 " pdb=" O12 POV A 608 " ideal model delta sigma weight residual 97.67 110.39 -12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV C 605 " pdb=" P POV C 605 " pdb=" O12 POV C 605 " ideal model delta sigma weight residual 97.67 110.38 -12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 POV B 605 " pdb=" P POV B 605 " pdb=" O12 POV B 605 " ideal model delta sigma weight residual 97.67 110.38 -12.71 3.00e+00 1.11e-01 1.79e+01 ... (remaining 60225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 16222 29.78 - 59.56: 568 59.56 - 89.35: 110 89.35 - 119.13: 35 119.13 - 148.91: 20 Dihedral angle restraints: 16955 sinusoidal: 9780 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 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+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 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+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 -154.78 -25.22 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 16952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2146 0.063 - 0.126: 474 0.126 - 0.189: 100 0.189 - 0.252: 10 0.252 - 0.315: 10 Chirality restraints: 2740 Sorted by residual: chirality pdb=" C6 EPJ C 608 " pdb=" C1 EPJ C 608 " pdb=" C5 EPJ C 608 " pdb=" N1 EPJ C 608 " both_signs ideal model delta sigma weight residual False -2.80 -3.11 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C6 EPJ D 608 " pdb=" C1 EPJ D 608 " pdb=" C5 EPJ D 608 " pdb=" N1 EPJ D 608 " both_signs ideal model delta sigma weight residual False -2.80 -3.11 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C6 EPJ B 608 " pdb=" C1 EPJ B 608 " pdb=" C5 EPJ B 608 " pdb=" N1 EPJ B 608 " both_signs ideal model delta sigma weight residual False -2.80 -3.11 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2737 not shown) Planarity restraints: 4740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " -0.285 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG E 604 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " 0.002 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " -0.284 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG A 602 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.002 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 604 " 0.284 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG D 604 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 604 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG D 604 " -0.418 2.00e-02 2.50e+03 pdb=" O7 NAG D 604 " 0.202 2.00e-02 2.50e+03 ... (remaining 4737 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 2831 2.25 - 2.84: 72469 2.84 - 3.43: 85700 3.43 - 4.01: 125222 4.01 - 4.60: 188655 Nonbonded interactions: 474877 Sorted by model distance: nonbonded pdb=" OE2 GLU B 18 " pdb=" HH TYR B 63 " model vdw 1.667 1.850 nonbonded pdb=" OE2 GLU E 18 " pdb=" HH TYR E 63 " model vdw 1.667 1.850 nonbonded pdb=" OE2 GLU C 18 " pdb=" HH TYR C 63 " model vdw 1.668 1.850 nonbonded pdb=" OE2 GLU A 18 " pdb=" HH TYR A 63 " model vdw 1.668 1.850 nonbonded pdb=" OE2 GLU D 18 " pdb=" HH TYR D 63 " model vdw 1.669 1.850 ... (remaining 474872 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: 0.480 Extract box with map and model: 5.380 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 119.110 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 17865 Z= 0.715 Angle : 1.100 12.742 24265 Z= 0.521 Chirality : 0.058 0.315 2740 Planarity : 0.012 0.245 2870 Dihedral : 19.235 148.910 7590 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -1.47 (0.17), residues: 1955 helix: -0.50 (0.16), residues: 790 sheet: -1.05 (0.21), residues: 460 loop : -1.23 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 307 HIS 0.004 0.001 HIS D 62 PHE 0.012 0.002 PHE E 99 TYR 0.017 0.003 TYR B 273 ARG 0.006 0.001 ARG E 309 *********************** 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 231 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7857 (t0) cc_final: 0.7592 (t0) REVERT: C 278 MET cc_start: 0.7930 (mtp) cc_final: 0.7680 (mtp) REVERT: D 57 MET cc_start: 0.8385 (mtm) cc_final: 0.7946 (mtm) REVERT: E 156 ASP cc_start: 0.7778 (t0) cc_final: 0.7457 (t0) REVERT: E 253 MET cc_start: 0.7881 (mmt) cc_final: 0.7653 (mtp) REVERT: E 278 MET cc_start: 0.7888 (mtp) cc_final: 0.7592 (mtp) REVERT: E 309 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6857 (ttt180) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 3.0317 time to fit residues: 774.0237 Evaluate side-chains 187 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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: 0.5980 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7757 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17865 Z= 0.198 Angle : 0.598 6.285 24265 Z= 0.293 Chirality : 0.040 0.151 2740 Planarity : 0.004 0.032 2870 Dihedral : 18.775 139.665 3825 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.45 % Allowed : 6.44 % Favored : 93.11 % 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: -0.74 (0.17), residues: 1955 helix: 0.27 (0.17), residues: 795 sheet: -0.86 (0.21), residues: 460 loop : -0.93 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 307 HIS 0.003 0.001 HIS A 295 PHE 0.016 0.001 PHE C 274 TYR 0.013 0.001 TYR A 187 ARG 0.004 0.000 ARG B 446 *********************** 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 202 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 2.640 Fit side-chains revert: symmetry clash REVERT: D 57 MET cc_start: 0.8444 (mtm) cc_final: 0.7997 (mtm) REVERT: D 429 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6784 (mt-10) REVERT: E 278 MET cc_start: 0.7898 (mtp) cc_final: 0.7657 (mtp) REVERT: E 303 LYS cc_start: 0.7618 (mmmt) cc_final: 0.7329 (tptp) outliers start: 8 outliers final: 5 residues processed: 195 average time/residue: 3.0964 time to fit residues: 668.5602 Evaluate side-chains 179 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain E residue 456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.7810 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17865 Z= 0.293 Angle : 0.603 5.399 24265 Z= 0.303 Chirality : 0.042 0.151 2740 Planarity : 0.005 0.087 2870 Dihedral : 16.322 124.054 3825 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.34 % Allowed : 7.68 % 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: -0.41 (0.18), residues: 1955 helix: 0.61 (0.17), residues: 795 sheet: -0.66 (0.22), residues: 460 loop : -0.85 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 307 HIS 0.004 0.001 HIS A 295 PHE 0.016 0.002 PHE E 99 TYR 0.015 0.002 TYR B 187 ARG 0.008 0.001 ARG C 309 *********************** 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 188 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 2.700 Fit side-chains revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7884 (t0) cc_final: 0.7570 (t0) REVERT: C 253 MET cc_start: 0.7915 (mmt) cc_final: 0.7523 (mmt) REVERT: D 429 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6878 (mt-10) REVERT: E 156 ASP cc_start: 0.7812 (t0) cc_final: 0.7466 (t0) REVERT: E 278 MET cc_start: 0.8007 (mtp) cc_final: 0.7737 (mtp) outliers start: 6 outliers final: 6 residues processed: 183 average time/residue: 3.1466 time to fit residues: 635.7043 Evaluate side-chains 175 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER 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: 2.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17865 Z= 0.279 Angle : 0.568 6.389 24265 Z= 0.290 Chirality : 0.040 0.149 2740 Planarity : 0.005 0.052 2870 Dihedral : 15.423 111.642 3825 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.67 % Allowed : 7.84 % 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: -0.26 (0.18), residues: 1955 helix: 0.76 (0.17), residues: 790 sheet: -0.66 (0.22), residues: 460 loop : -0.75 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 307 HIS 0.004 0.001 HIS A 295 PHE 0.014 0.002 PHE D 99 TYR 0.014 0.002 TYR B 273 ARG 0.008 0.001 ARG C 309 *********************** 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 191 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 2.771 Fit side-chains revert: symmetry clash REVERT: B 445 ASP cc_start: 0.6373 (OUTLIER) cc_final: 0.6107 (m-30) REVERT: C 156 ASP cc_start: 0.7909 (t0) cc_final: 0.7573 (t0) REVERT: C 253 MET cc_start: 0.7842 (mmt) cc_final: 0.7509 (mmt) REVERT: D 416 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7618 (mm-30) REVERT: D 429 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6910 (mt-10) REVERT: E 156 ASP cc_start: 0.7800 (t0) cc_final: 0.7432 (t0) REVERT: E 278 MET cc_start: 0.8029 (mtp) cc_final: 0.7809 (mtp) REVERT: E 445 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.6167 (m-30) outliers start: 12 outliers final: 9 residues processed: 180 average time/residue: 3.1751 time to fit residues: 631.4467 Evaluate side-chains 185 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER 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: 2.9990 chunk 2 optimal weight: 0.0270 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17865 Z= 0.222 Angle : 0.535 5.544 24265 Z= 0.272 Chirality : 0.039 0.143 2740 Planarity : 0.004 0.039 2870 Dihedral : 14.948 101.780 3825 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.84 % Allowed : 7.79 % Favored : 91.37 % 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: -0.17 (0.18), residues: 1955 helix: 0.89 (0.17), residues: 795 sheet: -0.68 (0.22), residues: 460 loop : -0.72 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 307 HIS 0.003 0.001 HIS A 295 PHE 0.012 0.001 PHE B 99 TYR 0.012 0.002 TYR B 273 ARG 0.003 0.000 ARG C 309 *********************** 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 194 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 2.872 Fit side-chains revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7857 (t0) cc_final: 0.7501 (t0) REVERT: C 253 MET cc_start: 0.7806 (mmt) cc_final: 0.7580 (mmt) REVERT: D 429 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6888 (mt-10) REVERT: E 156 ASP cc_start: 0.7820 (t0) cc_final: 0.7475 (t0) REVERT: E 278 MET cc_start: 0.8029 (mtp) cc_final: 0.7777 (mtp) REVERT: E 445 ASP cc_start: 0.6331 (OUTLIER) cc_final: 0.6099 (m-30) outliers start: 15 outliers final: 9 residues processed: 180 average time/residue: 3.3358 time to fit residues: 660.2673 Evaluate side-chains 181 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 0.0980 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17865 Z= 0.253 Angle : 0.544 5.677 24265 Z= 0.278 Chirality : 0.039 0.145 2740 Planarity : 0.004 0.041 2870 Dihedral : 14.646 96.810 3825 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.15 (0.18), residues: 1955 helix: 0.92 (0.17), residues: 795 sheet: -0.69 (0.22), residues: 460 loop : -0.71 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.003 0.001 HIS E 295 PHE 0.013 0.001 PHE E 99 TYR 0.013 0.002 TYR B 273 ARG 0.004 0.000 ARG E 446 *********************** 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 192 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.6071 (m-30) REVERT: C 156 ASP cc_start: 0.7840 (t0) cc_final: 0.7502 (t0) REVERT: C 253 MET cc_start: 0.7735 (mmt) cc_final: 0.7468 (mmt) REVERT: D 57 MET cc_start: 0.8360 (mtt) cc_final: 0.8147 (mtm) REVERT: D 429 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6876 (mt-10) REVERT: E 156 ASP cc_start: 0.7797 (t0) cc_final: 0.7431 (t0) REVERT: E 278 MET cc_start: 0.8041 (mtp) cc_final: 0.7840 (mtp) REVERT: E 445 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.6142 (m-30) outliers start: 13 outliers final: 8 residues processed: 180 average time/residue: 3.2347 time to fit residues: 642.3052 Evaluate side-chains 187 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 177 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17865 Z= 0.191 Angle : 0.513 6.080 24265 Z= 0.260 Chirality : 0.038 0.142 2740 Planarity : 0.004 0.038 2870 Dihedral : 14.096 87.631 3825 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.62 % Allowed : 8.29 % 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: -0.02 (0.18), residues: 1955 helix: 1.07 (0.17), residues: 795 sheet: -0.74 (0.21), residues: 460 loop : -0.61 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 307 HIS 0.002 0.001 HIS E 295 PHE 0.009 0.001 PHE D 99 TYR 0.011 0.001 TYR B 273 ARG 0.004 0.000 ARG E 446 *********************** 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 196 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 253 MET cc_start: 0.7744 (mmt) cc_final: 0.7476 (mmt) REVERT: D 429 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6861 (mt-10) REVERT: E 278 MET cc_start: 0.8044 (mtp) cc_final: 0.7763 (mtp) outliers start: 11 outliers final: 8 residues processed: 186 average time/residue: 3.0885 time to fit residues: 634.6999 Evaluate side-chains 184 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER 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: 3.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 119 optimal weight: 0.1980 chunk 128 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.7806 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17865 Z= 0.236 Angle : 0.531 6.597 24265 Z= 0.271 Chirality : 0.039 0.144 2740 Planarity : 0.004 0.036 2870 Dihedral : 13.833 85.367 3825 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.56 % Allowed : 8.63 % 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: -0.03 (0.18), residues: 1955 helix: 1.06 (0.17), residues: 795 sheet: -0.71 (0.21), residues: 460 loop : -0.62 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 307 HIS 0.003 0.001 HIS E 295 PHE 0.016 0.001 PHE C 274 TYR 0.012 0.002 TYR B 273 ARG 0.004 0.000 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 189 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7841 (t0) cc_final: 0.7480 (t0) REVERT: D 429 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6870 (mt-10) REVERT: E 278 MET cc_start: 0.8055 (mtp) cc_final: 0.7835 (mtp) outliers start: 10 outliers final: 9 residues processed: 181 average time/residue: 3.2122 time to fit residues: 649.7880 Evaluate side-chains 183 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17865 Z= 0.195 Angle : 0.514 6.835 24265 Z= 0.261 Chirality : 0.038 0.141 2740 Planarity : 0.004 0.038 2870 Dihedral : 13.448 84.682 3825 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.67 % Allowed : 8.46 % 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: 0.05 (0.18), residues: 1955 helix: 1.14 (0.17), residues: 795 sheet: -0.72 (0.21), residues: 460 loop : -0.56 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS E 295 PHE 0.012 0.001 PHE C 274 TYR 0.011 0.001 TYR B 273 ARG 0.004 0.000 ARG E 446 *********************** 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 193 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7808 (t0) cc_final: 0.7468 (t0) REVERT: C 278 MET cc_start: 0.7968 (mtt) cc_final: 0.7747 (mtp) REVERT: D 429 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6852 (mt-10) REVERT: E 278 MET cc_start: 0.8048 (mtp) cc_final: 0.7750 (mtp) REVERT: E 445 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6280 (m-30) outliers start: 12 outliers final: 10 residues processed: 183 average time/residue: 3.0461 time to fit residues: 617.2710 Evaluate side-chains 189 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER 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: 4.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.3524 ------------------------------------------------------------------------------- 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: 0.7801 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17865 Z= 0.226 Angle : 0.528 6.427 24265 Z= 0.269 Chirality : 0.039 0.144 2740 Planarity : 0.004 0.037 2870 Dihedral : 13.074 85.059 3825 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.67 % Allowed : 8.63 % Favored : 90.70 % 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: 0.04 (0.18), residues: 1955 helix: 1.14 (0.17), residues: 795 sheet: -0.70 (0.21), residues: 460 loop : -0.60 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 307 HIS 0.003 0.001 HIS E 295 PHE 0.014 0.001 PHE C 274 TYR 0.012 0.002 TYR B 273 ARG 0.004 0.000 ARG E 446 ********************** 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 192 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 2.817 Fit side-chains revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7842 (t0) cc_final: 0.7481 (t0) REVERT: C 278 MET cc_start: 0.7854 (mtt) cc_final: 0.7648 (mtp) REVERT: D 429 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6855 (mt-10) REVERT: E 278 MET cc_start: 0.8056 (mtp) cc_final: 0.7824 (mtp) REVERT: E 445 ASP cc_start: 0.6540 (OUTLIER) cc_final: 0.6309 (m-30) outliers start: 12 outliers final: 10 residues processed: 182 average time/residue: 3.0933 time to fit residues: 622.9383 Evaluate side-chains 188 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 466 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125735 restraints weight = 62101.970| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.42 r_work: 0.3314 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17865 Z= 0.189 Angle : 0.508 6.279 24265 Z= 0.258 Chirality : 0.038 0.141 2740 Planarity : 0.004 0.037 2870 Dihedral : 12.661 84.083 3825 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.62 % Allowed : 8.68 % Favored : 90.70 % 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: 0.16 (0.18), residues: 1955 helix: 1.32 (0.17), residues: 780 sheet: -0.71 (0.21), residues: 460 loop : -0.56 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS E 295 PHE 0.016 0.001 PHE C 274 TYR 0.011 0.001 TYR B 273 ARG 0.003 0.000 ARG E 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11139.12 seconds wall clock time: 195 minutes 25.17 seconds (11725.17 seconds total)