Starting phenix.real_space_refine on Fri Mar 22 20:05:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v80_43012/03_2024/8v80_43012_trim_updated.pdb" } resolution = 2.34 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= 0.014 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 10 5.49 5 S 120 5.16 5 Cl 5 4.86 5 C 11310 2.51 5 N 2635 2.21 5 O 3160 1.98 5 H 15835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33080 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "B" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "C" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "D" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "E" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 226 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3, 'YLR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 140 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'YLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 28.21, per 1000 atoms: 0.85 Number of scatterers: 33080 At special positions: 0 Unit cell: (100.347, 102.505, 162.929, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 120 16.00 P 10 15.00 O 3160 8.00 N 2635 7.00 C 11310 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 603 " - " ASN B 67 " " NAG C 602 " - " ASN C 67 " " NAG D 602 " - " ASN D 67 " " NAG E 602 " - " ASN E 67 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 23 " " NAG H 1 " - " ASN B 110 " " NAG I 1 " - " ASN B 23 " " NAG J 1 " - " ASN C 110 " " NAG K 1 " - " ASN C 23 " " NAG L 1 " - " ASN D 110 " " NAG M 1 " - " ASN D 23 " " NAG N 1 " - " ASN E 110 " " NAG O 1 " - " ASN E 23 " Time building additional restraints: 27.76 Conformation dependent library (CDL) restraints added in 5.8 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 30 sheets defined 40.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.44 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.793A 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: 3.881A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (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 259 removed outlier: 3.947A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (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 3 through 11 removed outlier: 3.793A 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: 3.880A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (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 259 removed outlier: 3.947A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (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 3 through 11 removed outlier: 3.793A 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: 3.881A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (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 259 removed outlier: 3.947A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (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 3 through 11 removed outlier: 3.793A 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: 3.880A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (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 259 removed outlier: 3.947A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (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 3 through 11 removed outlier: 3.793A 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: 3.881A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (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 259 removed outlier: 3.947A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (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: 6.325A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.291A 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: 4.585A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 185 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.640A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.325A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= I, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= J, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= K, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 173 through 177 removed outlier: 6.640A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.325A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= O, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= P, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= Q, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.639A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.325A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= U, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= V, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= W, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.584A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.640A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.325A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= AA, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= AB, first strand: chain 'E' and resid 76 through 79 Processing sheet with id= AC, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.584A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 173 through 177 removed outlier: 6.640A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2280 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: 12.41 Time building geometry restraints manager: 28.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15800 1.04 - 1.24: 2203 1.24 - 1.44: 5407 1.44 - 1.64: 9930 1.64 - 1.84: 180 Bond restraints: 33520 Sorted by residual: bond pdb=" C3 EPJ B 607 " pdb=" N1 EPJ B 607 " 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 A 605 " pdb=" N1 EPJ A 605 " 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 D 606 " pdb=" N1 EPJ D 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 C 606 " pdb=" N1 EPJ C 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 E 605 " pdb=" N1 EPJ E 605 " ideal model delta sigma weight residual 1.718 1.470 0.248 2.00e-02 2.50e+03 1.54e+02 ... (remaining 33515 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.40: 247 103.40 - 111.07: 33956 111.07 - 118.75: 10950 118.75 - 126.42: 14525 126.42 - 134.10: 412 Bond angle restraints: 60090 Sorted by residual: angle pdb=" O15 YLR B 608 " pdb=" S14 YLR B 608 " pdb=" O16 YLR B 608 " ideal model delta sigma weight residual 101.16 118.14 -16.98 3.00e+00 1.11e-01 3.20e+01 angle pdb=" O15 YLR D 607 " pdb=" S14 YLR D 607 " pdb=" O16 YLR D 607 " ideal model delta sigma weight residual 101.16 118.11 -16.95 3.00e+00 1.11e-01 3.19e+01 angle pdb=" O15 YLR C 607 " pdb=" S14 YLR C 607 " pdb=" O16 YLR C 607 " ideal model delta sigma weight residual 101.16 118.10 -16.94 3.00e+00 1.11e-01 3.19e+01 angle pdb=" O15 YLR A 606 " pdb=" S14 YLR A 606 " pdb=" O16 YLR A 606 " ideal model delta sigma weight residual 101.16 118.08 -16.92 3.00e+00 1.11e-01 3.18e+01 angle pdb=" O15 YLR E 606 " pdb=" S14 YLR E 606 " pdb=" O16 YLR E 606 " ideal model delta sigma weight residual 101.16 118.07 -16.91 3.00e+00 1.11e-01 3.18e+01 ... (remaining 60085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 16021 28.11 - 56.22: 634 56.22 - 84.33: 110 84.33 - 112.44: 55 112.44 - 140.55: 5 Dihedral angle restraints: 16825 sinusoidal: 9650 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 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual 180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+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 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 16822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2583 0.121 - 0.243: 147 0.243 - 0.364: 15 0.364 - 0.486: 0 0.486 - 0.607: 5 Chirality restraints: 2750 Sorted by residual: 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 -2.23 -0.17 2.00e-02 2.50e+03 6.84e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.78e+01 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 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+01 ... (remaining 2747 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.255 2.00e-02 2.50e+03 2.21e-01 6.12e+02 pdb=" C7 NAG J 1 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.006 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.380 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.254 2.00e-02 2.50e+03 2.21e-01 6.11e+02 pdb=" C7 NAG L 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.006 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.380 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.254 2.00e-02 2.50e+03 2.21e-01 6.11e+02 pdb=" C7 NAG N 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.006 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.380 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.181 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 442 2.08 - 2.71: 52744 2.71 - 3.34: 94393 3.34 - 3.97: 129561 3.97 - 4.60: 198686 Nonbonded interactions: 475826 Sorted by model distance: nonbonded pdb="HD21 ASN A 106 " pdb=" HG SER E 149 " model vdw 1.455 2.100 nonbonded pdb=" HG SER B 149 " pdb="HD21 ASN C 106 " model vdw 1.457 2.100 nonbonded pdb=" HG SER C 149 " pdb="HD21 ASN D 106 " model vdw 1.458 2.100 nonbonded pdb=" HG SER D 149 " pdb="HD21 ASN E 106 " model vdw 1.458 2.100 nonbonded pdb=" HG SER A 149 " pdb="HD21 ASN B 106 " model vdw 1.467 2.100 ... (remaining 475821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.420 Extract box with map and model: 5.300 Check model and map are aligned: 0.500 Set scattering table: 0.280 Process input model: 122.380 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.240 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: 0.000 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.014 0.250 17680 Z= 0.781 Angle : 1.162 16.978 24080 Z= 0.550 Chirality : 0.067 0.607 2750 Planarity : 0.011 0.221 2845 Dihedral : 17.791 140.554 7450 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 1955 helix: -0.61 (0.18), residues: 785 sheet: -1.19 (0.19), residues: 440 loop : -0.60 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 307 HIS 0.003 0.001 HIS E 62 PHE 0.019 0.003 PHE B 145 TYR 0.020 0.003 TYR E 14 ARG 0.008 0.001 ARG D 206 *********************** 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 232 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.8401 (t) cc_final: 0.8154 (m) REVERT: A 252 PHE cc_start: 0.7851 (m-80) cc_final: 0.6843 (m-80) REVERT: B 252 PHE cc_start: 0.7926 (m-80) cc_final: 0.6964 (m-80) REVERT: B 436 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6775 (tm-30) REVERT: B 450 MET cc_start: 0.7339 (ttm) cc_final: 0.7079 (ttp) REVERT: C 57 MET cc_start: 0.8430 (mtt) cc_final: 0.8183 (mtt) REVERT: C 68 VAL cc_start: 0.8319 (t) cc_final: 0.8046 (p) REVERT: C 260 MET cc_start: 0.8209 (mmp) cc_final: 0.7971 (mmp) REVERT: D 237 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7598 (mt-10) REVERT: D 252 PHE cc_start: 0.7524 (m-80) cc_final: 0.6525 (m-80) REVERT: D 416 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6758 (tp30) REVERT: D 418 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7423 (mtt180) REVERT: D 436 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6964 (tt0) REVERT: E 40 MET cc_start: 0.8294 (mtp) cc_final: 0.8088 (mtp) REVERT: E 68 VAL cc_start: 0.8504 (t) cc_final: 0.8184 (m) REVERT: E 274 PHE cc_start: 0.8037 (m-10) cc_final: 0.7832 (m-10) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 2.1668 time to fit residues: 577.3045 Evaluate side-chains 187 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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: 0.9980 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 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 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17680 Z= 0.194 Angle : 0.651 6.658 24080 Z= 0.318 Chirality : 0.042 0.186 2750 Planarity : 0.005 0.072 2845 Dihedral : 15.411 123.027 3685 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.73 % Allowed : 4.54 % Favored : 94.73 % 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: -0.35 (0.17), residues: 1955 helix: 0.36 (0.17), residues: 800 sheet: -0.87 (0.21), residues: 440 loop : -0.22 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 307 HIS 0.003 0.001 HIS C 62 PHE 0.015 0.001 PHE B 99 TYR 0.010 0.001 TYR E 14 ARG 0.007 0.000 ARG A 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 220 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7714 (m-80) cc_final: 0.6892 (m-80) REVERT: B 252 PHE cc_start: 0.7736 (m-80) cc_final: 0.6912 (m-80) REVERT: B 450 MET cc_start: 0.7304 (ttm) cc_final: 0.7050 (ttp) REVERT: C 40 MET cc_start: 0.8199 (mtp) cc_final: 0.7869 (mtp) REVERT: C 57 MET cc_start: 0.8289 (mtt) cc_final: 0.8021 (mtm) REVERT: C 416 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6292 (tp30) REVERT: D 40 MET cc_start: 0.8318 (mtp) cc_final: 0.8067 (mtp) REVERT: D 252 PHE cc_start: 0.7399 (m-80) cc_final: 0.6580 (m-80) REVERT: D 416 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6583 (tp30) REVERT: E 274 PHE cc_start: 0.8161 (m-10) cc_final: 0.7952 (m-10) outliers start: 13 outliers final: 7 residues processed: 214 average time/residue: 2.3350 time to fit residues: 568.5861 Evaluate side-chains 203 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 276 SER 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: 4.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17680 Z= 0.247 Angle : 0.635 8.073 24080 Z= 0.312 Chirality : 0.042 0.254 2750 Planarity : 0.005 0.077 2845 Dihedral : 12.869 99.831 3685 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.50 % Allowed : 6.11 % Favored : 93.39 % 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: 0.06 (0.18), residues: 1955 helix: 0.90 (0.17), residues: 800 sheet: -0.85 (0.21), residues: 440 loop : -0.14 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 66 HIS 0.005 0.001 HIS D 296 PHE 0.021 0.002 PHE B 99 TYR 0.014 0.002 TYR E 14 ARG 0.008 0.001 ARG A 446 *********************** 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 214 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7788 (m-80) cc_final: 0.6847 (m-80) REVERT: B 252 PHE cc_start: 0.7926 (m-80) cc_final: 0.6983 (m-80) REVERT: B 450 MET cc_start: 0.7400 (ttm) cc_final: 0.7115 (ttp) REVERT: C 40 MET cc_start: 0.8170 (mtp) cc_final: 0.7955 (mtp) REVERT: C 57 MET cc_start: 0.8270 (mtt) cc_final: 0.8061 (mtm) REVERT: C 416 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6304 (tp30) REVERT: C 418 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7587 (ttp-170) REVERT: D 252 PHE cc_start: 0.7471 (m-80) cc_final: 0.6574 (m-80) REVERT: D 416 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6387 (mm-30) outliers start: 9 outliers final: 7 residues processed: 210 average time/residue: 2.4397 time to fit residues: 581.3356 Evaluate side-chains 206 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 0.1980 chunk 178 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17680 Z= 0.203 Angle : 0.579 7.233 24080 Z= 0.286 Chirality : 0.040 0.235 2750 Planarity : 0.004 0.060 2845 Dihedral : 11.986 87.142 3685 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.84 % Allowed : 6.72 % Favored : 92.44 % 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: 0.28 (0.18), residues: 1955 helix: 1.15 (0.17), residues: 800 sheet: -0.81 (0.21), residues: 440 loop : -0.06 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 173 HIS 0.002 0.001 HIS E 62 PHE 0.018 0.001 PHE B 99 TYR 0.010 0.002 TYR E 14 ARG 0.006 0.000 ARG C 446 *********************** 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 223 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7788 (m-80) cc_final: 0.6854 (m-80) REVERT: B 237 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 252 PHE cc_start: 0.7915 (m-80) cc_final: 0.6966 (m-80) REVERT: B 436 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 40 MET cc_start: 0.8123 (mtp) cc_final: 0.7922 (mtp) REVERT: C 57 MET cc_start: 0.8277 (mtt) cc_final: 0.8069 (mtm) REVERT: C 416 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6227 (tp30) REVERT: C 418 ARG cc_start: 0.7800 (ttm170) cc_final: 0.7592 (ttp-170) REVERT: D 252 PHE cc_start: 0.7528 (m-80) cc_final: 0.6642 (m-80) REVERT: D 416 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6293 (mm-30) outliers start: 15 outliers final: 8 residues processed: 214 average time/residue: 2.3297 time to fit residues: 566.7678 Evaluate side-chains 208 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP 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: 0.9980 chunk 140 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17680 Z= 0.175 Angle : 0.553 6.740 24080 Z= 0.271 Chirality : 0.040 0.223 2750 Planarity : 0.004 0.046 2845 Dihedral : 11.483 87.605 3685 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.73 % Allowed : 7.00 % Favored : 92.27 % 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: 1.38 (0.17), residues: 800 sheet: -0.71 (0.21), residues: 440 loop : 0.06 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 66 HIS 0.002 0.001 HIS E 104 PHE 0.015 0.001 PHE E 99 TYR 0.010 0.001 TYR A 273 ARG 0.006 0.000 ARG A 446 *********************** 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 220 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7761 (m-80) cc_final: 0.6824 (m-80) REVERT: B 237 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 252 PHE cc_start: 0.7849 (m-80) cc_final: 0.6903 (m-80) REVERT: B 436 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 450 MET cc_start: 0.7384 (ttm) cc_final: 0.7129 (ttp) REVERT: C 40 MET cc_start: 0.8095 (mtp) cc_final: 0.7888 (mtp) REVERT: C 57 MET cc_start: 0.8273 (mtt) cc_final: 0.8072 (mtm) REVERT: C 416 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: D 252 PHE cc_start: 0.7525 (m-80) cc_final: 0.6628 (m-80) outliers start: 13 outliers final: 10 residues processed: 214 average time/residue: 2.3883 time to fit residues: 580.2993 Evaluate side-chains 216 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17680 Z= 0.202 Angle : 0.567 7.370 24080 Z= 0.278 Chirality : 0.040 0.229 2750 Planarity : 0.004 0.064 2845 Dihedral : 11.320 88.232 3685 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.78 % Allowed : 7.56 % 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: 0.52 (0.18), residues: 1955 helix: 1.37 (0.17), residues: 825 sheet: -0.74 (0.21), residues: 440 loop : 0.03 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS B 140 PHE 0.016 0.001 PHE B 99 TYR 0.011 0.002 TYR A 273 ARG 0.009 0.001 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 222 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7761 (m-80) cc_final: 0.6801 (m-80) REVERT: B 237 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7340 (mt-10) REVERT: B 252 PHE cc_start: 0.7875 (m-80) cc_final: 0.7362 (m-80) REVERT: B 436 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 450 MET cc_start: 0.7416 (ttm) cc_final: 0.7161 (ttp) REVERT: C 57 MET cc_start: 0.8280 (mtt) cc_final: 0.8062 (mtm) REVERT: C 416 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6232 (tp30) REVERT: D 252 PHE cc_start: 0.7562 (m-80) cc_final: 0.6636 (m-80) REVERT: D 450 MET cc_start: 0.7626 (ttm) cc_final: 0.5937 (mpt) outliers start: 14 outliers final: 10 residues processed: 215 average time/residue: 2.3703 time to fit residues: 579.8252 Evaluate side-chains 212 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17680 Z= 0.190 Angle : 0.560 7.103 24080 Z= 0.275 Chirality : 0.040 0.226 2750 Planarity : 0.004 0.048 2845 Dihedral : 11.214 88.160 3685 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.78 % Allowed : 8.01 % 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: 0.58 (0.18), residues: 1955 helix: 1.44 (0.17), residues: 825 sheet: -0.72 (0.21), residues: 440 loop : 0.05 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 66 HIS 0.002 0.001 HIS D 296 PHE 0.028 0.001 PHE A 99 TYR 0.010 0.001 TYR A 273 ARG 0.006 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 218 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 252 PHE cc_start: 0.7779 (m-80) cc_final: 0.6803 (m-80) REVERT: B 252 PHE cc_start: 0.7869 (m-80) cc_final: 0.7361 (m-80) REVERT: B 436 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7179 (tm-30) REVERT: B 450 MET cc_start: 0.7405 (ttm) cc_final: 0.7154 (ttp) REVERT: C 57 MET cc_start: 0.8273 (mtt) cc_final: 0.8051 (mtm) REVERT: C 416 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6281 (tp30) REVERT: D 252 PHE cc_start: 0.7562 (m-80) cc_final: 0.6623 (m-80) REVERT: D 450 MET cc_start: 0.7608 (ttm) cc_final: 0.5940 (mpt) outliers start: 14 outliers final: 9 residues processed: 212 average time/residue: 2.4210 time to fit residues: 582.4652 Evaluate side-chains 215 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17680 Z= 0.231 Angle : 0.590 7.859 24080 Z= 0.291 Chirality : 0.041 0.249 2750 Planarity : 0.004 0.048 2845 Dihedral : 11.286 89.049 3685 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 0.52 (0.18), residues: 1955 helix: 1.39 (0.17), residues: 825 sheet: -0.78 (0.21), residues: 440 loop : 0.02 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.003 0.001 HIS D 296 PHE 0.027 0.002 PHE B 99 TYR 0.012 0.002 TYR A 14 ARG 0.006 0.001 ARG E 446 *********************** 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 221 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 208 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 252 PHE cc_start: 0.7820 (m-80) cc_final: 0.6808 (m-80) REVERT: B 252 PHE cc_start: 0.7928 (m-80) cc_final: 0.7408 (m-80) REVERT: B 436 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 450 MET cc_start: 0.7460 (ttm) cc_final: 0.7201 (ttp) REVERT: C 57 MET cc_start: 0.8272 (mtt) cc_final: 0.8058 (mtm) REVERT: C 416 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6278 (tp30) REVERT: D 252 PHE cc_start: 0.7583 (m-80) cc_final: 0.6629 (m-80) REVERT: D 450 MET cc_start: 0.7568 (ttm) cc_final: 0.5799 (mpt) outliers start: 13 outliers final: 9 residues processed: 215 average time/residue: 2.4583 time to fit residues: 598.7158 Evaluate side-chains 212 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17680 Z= 0.243 Angle : 0.597 7.669 24080 Z= 0.295 Chirality : 0.041 0.250 2750 Planarity : 0.005 0.115 2845 Dihedral : 11.269 89.600 3685 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.62 % Allowed : 8.07 % Favored : 91.32 % 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: 0.51 (0.18), residues: 1955 helix: 1.39 (0.17), residues: 825 sheet: -0.78 (0.21), residues: 440 loop : 0.01 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 66 HIS 0.003 0.001 HIS E 62 PHE 0.027 0.002 PHE B 99 TYR 0.012 0.002 TYR A 14 ARG 0.019 0.001 ARG A 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 214 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7782 (m-80) cc_final: 0.6758 (m-80) REVERT: B 252 PHE cc_start: 0.7955 (m-80) cc_final: 0.7431 (m-80) REVERT: B 436 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7154 (tm-30) REVERT: B 450 MET cc_start: 0.7469 (ttm) cc_final: 0.7215 (ttp) REVERT: C 57 MET cc_start: 0.8281 (mtt) cc_final: 0.8062 (mtm) REVERT: C 416 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6353 (tp30) REVERT: D 252 PHE cc_start: 0.7585 (m-80) cc_final: 0.6626 (m-80) REVERT: D 450 MET cc_start: 0.7641 (ttm) cc_final: 0.5855 (mpt) REVERT: E 304 MET cc_start: 0.7884 (ttp) cc_final: 0.7361 (ttp) outliers start: 11 outliers final: 10 residues processed: 209 average time/residue: 2.3301 time to fit residues: 554.6149 Evaluate side-chains 210 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 119 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17680 Z= 0.152 Angle : 0.532 5.714 24080 Z= 0.260 Chirality : 0.039 0.206 2750 Planarity : 0.004 0.077 2845 Dihedral : 10.892 88.727 3685 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.67 % Allowed : 8.24 % 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: 0.79 (0.18), residues: 1955 helix: 1.66 (0.17), residues: 820 sheet: -0.71 (0.21), residues: 440 loop : 0.18 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 133 HIS 0.002 0.000 HIS E 104 PHE 0.014 0.001 PHE B 99 TYR 0.009 0.001 TYR A 273 ARG 0.011 0.000 ARG A 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 214 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7755 (m-80) cc_final: 0.6761 (m-80) REVERT: B 252 PHE cc_start: 0.7897 (m-80) cc_final: 0.7378 (m-80) REVERT: B 436 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7127 (tm-30) REVERT: B 450 MET cc_start: 0.7417 (ttm) cc_final: 0.7174 (ttp) REVERT: C 57 MET cc_start: 0.8270 (mtt) cc_final: 0.8046 (mtm) REVERT: D 252 PHE cc_start: 0.7541 (m-80) cc_final: 0.6598 (m-80) REVERT: D 450 MET cc_start: 0.7634 (ttm) cc_final: 0.5951 (mpt) REVERT: E 237 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7783 (mt-10) REVERT: E 304 MET cc_start: 0.7972 (ttp) cc_final: 0.7512 (ttp) REVERT: E 450 MET cc_start: 0.7808 (ttm) cc_final: 0.5973 (mpt) outliers start: 12 outliers final: 8 residues processed: 209 average time/residue: 2.4485 time to fit residues: 588.0671 Evaluate side-chains 211 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER 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: 0.5980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.163057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124183 restraints weight = 51352.494| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.41 r_work: 0.3230 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17680 Z= 0.201 Angle : 0.560 6.923 24080 Z= 0.275 Chirality : 0.040 0.228 2750 Planarity : 0.004 0.087 2845 Dihedral : 10.853 88.436 3685 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.56 % Allowed : 8.40 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 1955 helix: 1.62 (0.17), residues: 825 sheet: -0.71 (0.21), residues: 440 loop : 0.10 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.002 0.001 HIS D 104 PHE 0.022 0.001 PHE B 99 TYR 0.010 0.001 TYR A 273 ARG 0.012 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10650.21 seconds wall clock time: 186 minutes 54.53 seconds (11214.53 seconds total)