Starting phenix.real_space_refine on Fri Mar 15 22:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip6_35633/03_2024/8ip6_35633.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip6_35633/03_2024/8ip6_35633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip6_35633/03_2024/8ip6_35633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip6_35633/03_2024/8ip6_35633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip6_35633/03_2024/8ip6_35633.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip6_35633/03_2024/8ip6_35633.pdb" } resolution = 2.9 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= 0.047 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 Cl 1 4.86 5 C 8315 2.51 5 N 2175 2.21 5 O 2365 1.98 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: 12921 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2613 Chain: "B" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2613 Chain: "C" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2613 Chain: "D" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2613 Chain: "E" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2613 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.80, per 1000 atoms: 0.99 Number of scatterers: 12921 At special positions: 0 Unit cell: (112.554, 111.54, 141.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 65 16.00 O 2365 8.00 N 2175 7.00 C 8315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 4.8 seconds 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 71.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.761A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 219 removed outlier: 3.693A pdb=" N ARG A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.528A pdb=" N ILE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.668A pdb=" N LEU A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.803A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.103A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 360 removed outlier: 4.184A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 401 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.761A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 183 through 219 removed outlier: 3.693A pdb=" N ARG B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Proline residue: B 209 - end of helix Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.528A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.668A pdb=" N LEU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.802A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 4.101A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 360 removed outlier: 4.184A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 401 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.761A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 172 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 183 through 219 removed outlier: 3.693A pdb=" N ARG C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.528A pdb=" N ILE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.668A pdb=" N LEU C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.803A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 4.102A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 360 removed outlier: 4.184A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 401 Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.761A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 183 through 219 removed outlier: 3.693A pdb=" N ARG D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 209 - end of helix Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.528A pdb=" N ILE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.668A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.803A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 4.102A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 360 removed outlier: 4.184A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 401 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.762A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 172 Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 219 removed outlier: 3.693A pdb=" N ARG E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.528A pdb=" N ILE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.668A pdb=" N LEU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.802A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 4.101A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 360 removed outlier: 4.184A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY E 356 " --> pdb=" O PHE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 401 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 4.220A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103 removed outlier: 4.219A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103 removed outlier: 4.219A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103 removed outlier: 4.220A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103 removed outlier: 4.220A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2905 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: 3.98 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4235 1.34 - 1.46: 1965 1.46 - 1.57: 6835 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 13155 Sorted by residual: bond pdb=" CA VAL A 82 " pdb=" CB VAL A 82 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.69e-01 bond pdb=" CA VAL D 82 " pdb=" CB VAL D 82 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.54e-01 bond pdb=" CA VAL E 82 " pdb=" CB VAL E 82 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.48e-01 bond pdb=" CA VAL C 82 " pdb=" CB VAL C 82 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.48e-01 bond pdb=" CA VAL B 82 " pdb=" CB VAL B 82 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.31e-01 ... (remaining 13150 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.11: 275 107.11 - 113.83: 7596 113.83 - 120.55: 5324 120.55 - 127.28: 4470 127.28 - 134.00: 120 Bond angle restraints: 17785 Sorted by residual: angle pdb=" C LEU D 351 " pdb=" N PHE D 352 " pdb=" CA PHE D 352 " ideal model delta sigma weight residual 121.14 118.24 2.90 1.75e+00 3.27e-01 2.75e+00 angle pdb=" C LEU E 351 " pdb=" N PHE E 352 " pdb=" CA PHE E 352 " ideal model delta sigma weight residual 121.14 118.24 2.90 1.75e+00 3.27e-01 2.75e+00 angle pdb=" C LEU B 351 " pdb=" N PHE B 352 " pdb=" CA PHE B 352 " ideal model delta sigma weight residual 121.14 118.24 2.90 1.75e+00 3.27e-01 2.75e+00 angle pdb=" C LEU C 351 " pdb=" N PHE C 352 " pdb=" CA PHE C 352 " ideal model delta sigma weight residual 121.14 118.27 2.87 1.75e+00 3.27e-01 2.70e+00 angle pdb=" C LEU A 351 " pdb=" N PHE A 352 " pdb=" CA PHE A 352 " ideal model delta sigma weight residual 121.14 118.27 2.87 1.75e+00 3.27e-01 2.69e+00 ... (remaining 17780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 7290 17.49 - 34.99: 585 34.99 - 52.48: 100 52.48 - 69.98: 10 69.98 - 87.47: 10 Dihedral angle restraints: 7995 sinusoidal: 3295 harmonic: 4700 Sorted by residual: dihedral pdb=" CB GLU E 147 " pdb=" CG GLU E 147 " pdb=" CD GLU E 147 " pdb=" OE1 GLU E 147 " ideal model delta sinusoidal sigma weight residual 0.00 85.72 -85.72 1 3.00e+01 1.11e-03 9.87e+00 dihedral pdb=" CB GLU B 147 " pdb=" CG GLU B 147 " pdb=" CD GLU B 147 " pdb=" OE1 GLU B 147 " ideal model delta sinusoidal sigma weight residual 0.00 85.69 -85.69 1 3.00e+01 1.11e-03 9.87e+00 dihedral pdb=" CB GLU C 147 " pdb=" CG GLU C 147 " pdb=" CD GLU C 147 " pdb=" OE1 GLU C 147 " ideal model delta sinusoidal sigma weight residual 0.00 85.63 -85.63 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 7992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1383 0.026 - 0.052: 357 0.052 - 0.078: 195 0.078 - 0.104: 92 0.104 - 0.130: 33 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA LEU B 167 " pdb=" N LEU B 167 " pdb=" C LEU B 167 " pdb=" CB LEU B 167 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA LEU E 167 " pdb=" N LEU E 167 " pdb=" C LEU E 167 " pdb=" CB LEU E 167 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA LEU C 167 " pdb=" N LEU C 167 " pdb=" C LEU C 167 " pdb=" CB LEU C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2057 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 163 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C LEU C 163 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU C 163 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE C 164 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 163 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C LEU A 163 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU A 163 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 164 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 163 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C LEU E 163 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU E 163 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE E 164 " 0.010 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3744 2.83 - 3.35: 12582 3.35 - 3.86: 20753 3.86 - 4.38: 22868 4.38 - 4.90: 41705 Nonbonded interactions: 101652 Sorted by model distance: nonbonded pdb=" OE1 GLU D 185 " pdb=" OG SER D 271 " model vdw 2.309 2.440 nonbonded pdb=" OE1 GLU C 185 " pdb=" OG SER C 271 " model vdw 2.310 2.440 nonbonded pdb=" OE1 GLU B 185 " pdb=" OG SER B 271 " model vdw 2.310 2.440 nonbonded pdb=" OE1 GLU E 185 " pdb=" OG SER E 271 " model vdw 2.310 2.440 nonbonded pdb=" OE1 GLU A 185 " pdb=" OG SER A 271 " model vdw 2.310 2.440 ... (remaining 101647 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 82 through 128 or resid 130 through 401)) selection = (chain 'B' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'C' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'D' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'E' and (resid 82 through 128 or resid 130 through 401)) } 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: 0.880 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: 0.010 Extract box with map and model: 4.740 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 45.600 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.003 0.020 13155 Z= 0.161 Angle : 0.427 4.812 17785 Z= 0.233 Chirality : 0.036 0.130 2060 Planarity : 0.003 0.028 2250 Dihedral : 13.001 87.474 4935 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.51 (0.22), residues: 1595 helix: 4.02 (0.15), residues: 1040 sheet: 3.02 (0.33), residues: 145 loop : -0.04 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 162 HIS 0.002 0.000 HIS B 371 PHE 0.014 0.001 PHE D 86 TYR 0.014 0.001 TYR C 299 ARG 0.001 0.000 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.656 Fit side-chains REVERT: A 139 TYR cc_start: 0.9253 (p90) cc_final: 0.8948 (p90) REVERT: A 257 GLU cc_start: 0.7899 (tt0) cc_final: 0.7659 (tp30) REVERT: A 382 PHE cc_start: 0.8671 (m-80) cc_final: 0.8433 (m-80) REVERT: A 383 MET cc_start: 0.5563 (mmp) cc_final: 0.5255 (mpp) REVERT: B 383 MET cc_start: 0.5257 (mmp) cc_final: 0.4976 (mtm) REVERT: B 391 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7684 (tpt170) REVERT: C 383 MET cc_start: 0.5609 (mmp) cc_final: 0.5337 (tpp) REVERT: D 108 TYR cc_start: 0.8900 (m-10) cc_final: 0.8610 (m-80) REVERT: D 139 TYR cc_start: 0.9319 (p90) cc_final: 0.9104 (p90) REVERT: D 190 GLU cc_start: 0.8106 (tt0) cc_final: 0.7856 (tt0) REVERT: D 257 GLU cc_start: 0.7945 (tt0) cc_final: 0.7643 (tp30) REVERT: D 383 MET cc_start: 0.5076 (mmp) cc_final: 0.4771 (tpp) REVERT: D 391 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7516 (tpt170) REVERT: E 190 GLU cc_start: 0.8239 (tt0) cc_final: 0.7715 (tt0) REVERT: E 383 MET cc_start: 0.5298 (mmp) cc_final: 0.5051 (mpp) REVERT: E 391 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7647 (tpt170) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 1.3558 time to fit residues: 394.0834 Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 194 GLN B 223 HIS C 194 GLN D 194 GLN E 194 GLN E 223 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 13155 Z= 0.461 Angle : 0.642 7.919 17785 Z= 0.325 Chirality : 0.042 0.153 2060 Planarity : 0.004 0.038 2250 Dihedral : 3.856 14.519 1740 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.83 % Allowed : 9.15 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.94 (0.21), residues: 1595 helix: 3.30 (0.15), residues: 1105 sheet: 2.84 (0.33), residues: 145 loop : -0.04 (0.38), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 196 HIS 0.004 0.001 HIS E 122 PHE 0.025 0.002 PHE E 86 TYR 0.025 0.002 TYR D 299 ARG 0.005 0.001 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.582 Fit side-chains REVERT: A 139 TYR cc_start: 0.9284 (p90) cc_final: 0.8991 (p90) REVERT: A 257 GLU cc_start: 0.7980 (tt0) cc_final: 0.7760 (tp30) REVERT: A 361 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8092 (ppp) REVERT: A 382 PHE cc_start: 0.8796 (m-80) cc_final: 0.8362 (m-80) REVERT: A 383 MET cc_start: 0.5709 (mmp) cc_final: 0.5416 (mpp) REVERT: B 266 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8064 (tp30) REVERT: B 383 MET cc_start: 0.5057 (mmp) cc_final: 0.4777 (mtm) REVERT: B 391 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7717 (tpt170) REVERT: C 383 MET cc_start: 0.5574 (mmp) cc_final: 0.5308 (tpp) REVERT: C 391 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7255 (tpt170) REVERT: D 108 TYR cc_start: 0.8936 (m-10) cc_final: 0.8693 (m-80) REVERT: D 139 TYR cc_start: 0.9309 (p90) cc_final: 0.9085 (p90) REVERT: D 257 GLU cc_start: 0.7934 (tt0) cc_final: 0.7645 (tp30) REVERT: D 383 MET cc_start: 0.5002 (mmp) cc_final: 0.4668 (tpp) REVERT: D 391 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7492 (tpt170) REVERT: E 190 GLU cc_start: 0.8219 (tt0) cc_final: 0.7865 (tt0) REVERT: E 292 MET cc_start: 0.8917 (mmt) cc_final: 0.8602 (mmt) REVERT: E 383 MET cc_start: 0.5533 (mmp) cc_final: 0.4890 (mpt) REVERT: E 391 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7679 (tpt170) outliers start: 26 outliers final: 8 residues processed: 187 average time/residue: 1.3374 time to fit residues: 270.8698 Evaluate side-chains 169 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 194 GLN C 194 GLN D 194 GLN E 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13155 Z= 0.206 Angle : 0.514 9.266 17785 Z= 0.261 Chirality : 0.037 0.132 2060 Planarity : 0.003 0.031 2250 Dihedral : 3.610 14.763 1740 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.27 % Allowed : 10.21 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.24 (0.22), residues: 1595 helix: 3.52 (0.15), residues: 1105 sheet: 2.90 (0.34), residues: 145 loop : 0.13 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 162 HIS 0.001 0.000 HIS E 288 PHE 0.020 0.001 PHE E 352 TYR 0.025 0.002 TYR B 154 ARG 0.005 0.000 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.709 Fit side-chains REVERT: A 139 TYR cc_start: 0.9261 (p90) cc_final: 0.8985 (p90) REVERT: A 257 GLU cc_start: 0.7972 (tt0) cc_final: 0.7733 (tp30) REVERT: A 361 MET cc_start: 0.8617 (ptp) cc_final: 0.8132 (ppp) REVERT: A 383 MET cc_start: 0.5641 (mmp) cc_final: 0.5321 (mpp) REVERT: B 190 GLU cc_start: 0.8149 (tt0) cc_final: 0.7799 (tt0) REVERT: B 261 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 383 MET cc_start: 0.5120 (mmp) cc_final: 0.4816 (mtm) REVERT: C 383 MET cc_start: 0.5585 (mmp) cc_final: 0.5307 (tpp) REVERT: C 391 ARG cc_start: 0.7469 (mtt180) cc_final: 0.7208 (tpt170) REVERT: D 108 TYR cc_start: 0.8932 (m-10) cc_final: 0.8685 (m-80) REVERT: D 139 TYR cc_start: 0.9306 (p90) cc_final: 0.9084 (p90) REVERT: D 257 GLU cc_start: 0.7927 (tt0) cc_final: 0.7715 (tp30) REVERT: D 359 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.6990 (t80) REVERT: D 383 MET cc_start: 0.4955 (mmp) cc_final: 0.4637 (tpp) REVERT: D 391 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7411 (tpt170) REVERT: E 266 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8036 (tp30) REVERT: E 391 ARG cc_start: 0.7895 (mtt180) cc_final: 0.7626 (tpt170) outliers start: 18 outliers final: 8 residues processed: 189 average time/residue: 1.3126 time to fit residues: 269.5222 Evaluate side-chains 173 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 359 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13155 Z= 0.198 Angle : 0.509 9.941 17785 Z= 0.257 Chirality : 0.037 0.131 2060 Planarity : 0.003 0.032 2250 Dihedral : 3.563 13.917 1740 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.92 % Allowed : 12.32 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.28 (0.22), residues: 1595 helix: 3.53 (0.15), residues: 1105 sheet: 2.96 (0.34), residues: 145 loop : 0.22 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 162 HIS 0.001 0.000 HIS A 288 PHE 0.016 0.001 PHE C 352 TYR 0.023 0.002 TYR B 154 ARG 0.005 0.000 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.706 Fit side-chains REVERT: A 139 TYR cc_start: 0.9266 (p90) cc_final: 0.8960 (p90) REVERT: A 257 GLU cc_start: 0.7976 (tt0) cc_final: 0.7722 (tp30) REVERT: A 361 MET cc_start: 0.8636 (ptp) cc_final: 0.8140 (ppp) REVERT: A 383 MET cc_start: 0.5578 (mmp) cc_final: 0.5265 (mpp) REVERT: B 190 GLU cc_start: 0.8144 (tt0) cc_final: 0.7725 (tt0) REVERT: B 257 GLU cc_start: 0.7445 (tp30) cc_final: 0.7194 (tp30) REVERT: B 261 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: B 383 MET cc_start: 0.4800 (mmp) cc_final: 0.4521 (mtm) REVERT: C 383 MET cc_start: 0.5452 (mmp) cc_final: 0.5192 (tpp) REVERT: C 391 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7167 (tpt170) REVERT: D 108 TYR cc_start: 0.8944 (m-10) cc_final: 0.8681 (m-80) REVERT: D 139 TYR cc_start: 0.9321 (p90) cc_final: 0.9108 (p90) REVERT: D 257 GLU cc_start: 0.7922 (tt0) cc_final: 0.7702 (tp30) REVERT: D 359 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7253 (t80) REVERT: D 383 MET cc_start: 0.4923 (mmp) cc_final: 0.4621 (mpp) REVERT: D 391 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7492 (tpt170) REVERT: E 391 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7661 (tpt170) outliers start: 13 outliers final: 6 residues processed: 178 average time/residue: 1.4144 time to fit residues: 272.8908 Evaluate side-chains 172 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 359 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 138 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13155 Z= 0.383 Angle : 0.597 10.314 17785 Z= 0.302 Chirality : 0.040 0.142 2060 Planarity : 0.004 0.031 2250 Dihedral : 3.807 14.597 1740 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.13 % Allowed : 12.82 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.99 (0.21), residues: 1595 helix: 3.31 (0.15), residues: 1105 sheet: 2.74 (0.34), residues: 145 loop : 0.16 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 196 HIS 0.003 0.001 HIS C 232 PHE 0.018 0.002 PHE E 86 TYR 0.027 0.003 TYR C 154 ARG 0.005 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.567 Fit side-chains REVERT: A 139 TYR cc_start: 0.9284 (p90) cc_final: 0.9025 (p90) REVERT: A 257 GLU cc_start: 0.8019 (tt0) cc_final: 0.7805 (tp30) REVERT: A 382 PHE cc_start: 0.8691 (m-80) cc_final: 0.8399 (m-80) REVERT: A 383 MET cc_start: 0.5626 (mmp) cc_final: 0.5284 (mpp) REVERT: B 257 GLU cc_start: 0.7485 (tp30) cc_final: 0.7278 (tp30) REVERT: B 261 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 383 MET cc_start: 0.4694 (mmp) cc_final: 0.4376 (mtm) REVERT: C 383 MET cc_start: 0.5509 (mmp) cc_final: 0.5237 (tpp) REVERT: C 391 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7165 (tpt170) REVERT: D 108 TYR cc_start: 0.8944 (m-10) cc_final: 0.8712 (m-80) REVERT: D 383 MET cc_start: 0.4886 (mmp) cc_final: 0.4559 (tpp) REVERT: D 391 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7518 (tpt170) REVERT: E 391 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7691 (tpt170) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 1.3802 time to fit residues: 257.1778 Evaluate side-chains 173 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13155 Z= 0.159 Angle : 0.505 11.310 17785 Z= 0.253 Chirality : 0.037 0.200 2060 Planarity : 0.003 0.034 2250 Dihedral : 3.537 13.972 1740 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.13 % Allowed : 12.68 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.28 (0.22), residues: 1595 helix: 3.52 (0.15), residues: 1105 sheet: 2.85 (0.34), residues: 145 loop : 0.29 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.001 0.000 HIS A 371 PHE 0.020 0.001 PHE E 352 TYR 0.026 0.002 TYR C 154 ARG 0.005 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.814 Fit side-chains REVERT: A 139 TYR cc_start: 0.9258 (p90) cc_final: 0.8922 (p90) REVERT: A 257 GLU cc_start: 0.8045 (tt0) cc_final: 0.7781 (tp30) REVERT: A 297 GLU cc_start: 0.7656 (tt0) cc_final: 0.7382 (tt0) REVERT: A 383 MET cc_start: 0.5578 (mmp) cc_final: 0.5242 (mpp) REVERT: B 257 GLU cc_start: 0.7475 (tp30) cc_final: 0.7223 (tp30) REVERT: B 261 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: B 383 MET cc_start: 0.4672 (mmp) cc_final: 0.4360 (mtm) REVERT: C 383 MET cc_start: 0.5481 (mmp) cc_final: 0.5254 (tpp) REVERT: C 391 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7068 (tpt170) REVERT: D 108 TYR cc_start: 0.8931 (m-10) cc_final: 0.8673 (m-80) REVERT: D 383 MET cc_start: 0.4812 (mmp) cc_final: 0.4486 (tpp) REVERT: E 391 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7646 (tpt170) outliers start: 16 outliers final: 6 residues processed: 184 average time/residue: 1.2364 time to fit residues: 247.8745 Evaluate side-chains 172 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8359 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13155 Z= 0.308 Angle : 0.572 11.542 17785 Z= 0.288 Chirality : 0.039 0.217 2060 Planarity : 0.004 0.032 2250 Dihedral : 3.697 14.373 1740 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.92 % Allowed : 13.38 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.05 (0.22), residues: 1595 helix: 3.34 (0.15), residues: 1105 sheet: 2.77 (0.35), residues: 145 loop : 0.27 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.002 0.001 HIS E 122 PHE 0.017 0.002 PHE C 352 TYR 0.028 0.003 TYR B 108 ARG 0.005 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 1.615 Fit side-chains REVERT: A 139 TYR cc_start: 0.9273 (p90) cc_final: 0.9017 (p90) REVERT: A 257 GLU cc_start: 0.7983 (tt0) cc_final: 0.7740 (tp30) REVERT: A 297 GLU cc_start: 0.7757 (tt0) cc_final: 0.7464 (tt0) REVERT: A 361 MET cc_start: 0.8627 (ptp) cc_final: 0.8200 (ppp) REVERT: A 382 PHE cc_start: 0.8679 (m-80) cc_final: 0.8409 (m-80) REVERT: A 383 MET cc_start: 0.5561 (mmp) cc_final: 0.5243 (mpp) REVERT: B 257 GLU cc_start: 0.7509 (tp30) cc_final: 0.7258 (tp30) REVERT: B 261 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: B 383 MET cc_start: 0.4535 (mmp) cc_final: 0.4250 (mtm) REVERT: C 383 MET cc_start: 0.5529 (mmp) cc_final: 0.5291 (tpp) REVERT: C 391 ARG cc_start: 0.7353 (mtt180) cc_final: 0.6966 (tpt170) REVERT: D 108 TYR cc_start: 0.8951 (m-10) cc_final: 0.8696 (m-80) REVERT: D 391 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7505 (tpt170) REVERT: E 391 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7700 (tpt170) outliers start: 13 outliers final: 6 residues processed: 176 average time/residue: 1.3528 time to fit residues: 258.0708 Evaluate side-chains 167 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN D 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 13155 Z= 0.430 Angle : 0.643 12.424 17785 Z= 0.322 Chirality : 0.041 0.194 2060 Planarity : 0.004 0.032 2250 Dihedral : 3.933 15.209 1740 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.13 % Allowed : 13.38 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.86 (0.21), residues: 1595 helix: 3.34 (0.15), residues: 1075 sheet: 2.60 (0.35), residues: 145 loop : 0.02 (0.37), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 375 HIS 0.003 0.001 HIS A 232 PHE 0.017 0.002 PHE E 86 TYR 0.033 0.003 TYR B 108 ARG 0.005 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9279 (p90) cc_final: 0.9032 (p90) REVERT: A 257 GLU cc_start: 0.7986 (tt0) cc_final: 0.7761 (tp30) REVERT: A 297 GLU cc_start: 0.7824 (tt0) cc_final: 0.7500 (tt0) REVERT: A 361 MET cc_start: 0.8601 (ptp) cc_final: 0.8183 (ppp) REVERT: A 383 MET cc_start: 0.5678 (mmp) cc_final: 0.5337 (mpp) REVERT: B 257 GLU cc_start: 0.7497 (tp30) cc_final: 0.7214 (tp30) REVERT: B 261 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: B 383 MET cc_start: 0.4762 (mmp) cc_final: 0.4406 (mtm) REVERT: C 383 MET cc_start: 0.5509 (mmp) cc_final: 0.5246 (tpp) REVERT: C 391 ARG cc_start: 0.7345 (mtt180) cc_final: 0.7091 (tpt170) REVERT: D 108 TYR cc_start: 0.8949 (m-10) cc_final: 0.8732 (m-80) REVERT: D 352 PHE cc_start: 0.8681 (m-80) cc_final: 0.8229 (m-80) REVERT: D 391 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7520 (tpt170) REVERT: E 190 GLU cc_start: 0.8198 (tt0) cc_final: 0.7808 (tt0) REVERT: E 391 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7712 (tpt170) outliers start: 16 outliers final: 10 residues processed: 173 average time/residue: 1.3669 time to fit residues: 256.3218 Evaluate side-chains 169 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 134 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN D 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13155 Z= 0.159 Angle : 0.534 13.048 17785 Z= 0.263 Chirality : 0.037 0.200 2060 Planarity : 0.003 0.034 2250 Dihedral : 3.549 14.258 1740 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.63 % Allowed : 14.08 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.27 (0.22), residues: 1595 helix: 3.52 (0.15), residues: 1105 sheet: 2.80 (0.35), residues: 145 loop : 0.30 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 162 HIS 0.001 0.000 HIS E 122 PHE 0.014 0.001 PHE B 352 TYR 0.026 0.002 TYR B 154 ARG 0.006 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.636 Fit side-chains revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9259 (p90) cc_final: 0.8947 (p90) REVERT: A 257 GLU cc_start: 0.8047 (tt0) cc_final: 0.7793 (tp30) REVERT: A 297 GLU cc_start: 0.7596 (tt0) cc_final: 0.7321 (tt0) REVERT: A 344 MET cc_start: 0.8423 (mtt) cc_final: 0.8214 (mtm) REVERT: A 383 MET cc_start: 0.5593 (mmp) cc_final: 0.5230 (mpp) REVERT: B 257 GLU cc_start: 0.7405 (tp30) cc_final: 0.6258 (tp30) REVERT: B 261 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: B 383 MET cc_start: 0.4732 (mmp) cc_final: 0.4437 (mtm) REVERT: C 109 GLN cc_start: 0.8317 (tp40) cc_final: 0.8086 (tp40) REVERT: C 383 MET cc_start: 0.5502 (mmp) cc_final: 0.5229 (tpp) REVERT: C 391 ARG cc_start: 0.7411 (mtt180) cc_final: 0.7046 (tpt170) REVERT: D 108 TYR cc_start: 0.8928 (m-10) cc_final: 0.8664 (m-80) REVERT: D 391 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7544 (tpt170) REVERT: E 391 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7763 (tpt-90) outliers start: 9 outliers final: 6 residues processed: 185 average time/residue: 1.2993 time to fit residues: 261.3876 Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.2940 ------------------------------------------------------------------------------- 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: 0.8323 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13155 Z= 0.209 Angle : 0.558 13.066 17785 Z= 0.272 Chirality : 0.038 0.183 2060 Planarity : 0.003 0.033 2250 Dihedral : 3.561 14.303 1740 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.63 % Allowed : 14.37 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.21 (0.22), residues: 1595 helix: 3.46 (0.15), residues: 1105 sheet: 2.81 (0.35), residues: 145 loop : 0.33 (0.41), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 162 HIS 0.001 0.000 HIS A 288 PHE 0.017 0.001 PHE A 352 TYR 0.029 0.002 TYR A 108 ARG 0.006 0.000 ARG E 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9275 (p90) cc_final: 0.8975 (p90) REVERT: A 257 GLU cc_start: 0.7983 (tt0) cc_final: 0.7736 (tp30) REVERT: A 297 GLU cc_start: 0.7665 (tt0) cc_final: 0.7383 (tt0) REVERT: A 344 MET cc_start: 0.8428 (mtt) cc_final: 0.8221 (mtm) REVERT: A 383 MET cc_start: 0.5556 (mmp) cc_final: 0.5242 (mpp) REVERT: B 257 GLU cc_start: 0.7404 (tp30) cc_final: 0.6266 (tp30) REVERT: B 261 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: B 355 MET cc_start: 0.8222 (ttm) cc_final: 0.7967 (ttp) REVERT: B 383 MET cc_start: 0.4486 (mmp) cc_final: 0.4164 (mtm) REVERT: C 383 MET cc_start: 0.5441 (mmp) cc_final: 0.5193 (tpp) REVERT: C 391 ARG cc_start: 0.7416 (mtt180) cc_final: 0.7157 (tpt170) REVERT: D 108 TYR cc_start: 0.8944 (m-10) cc_final: 0.8697 (m-80) REVERT: D 391 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7378 (tpt170) REVERT: E 391 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7693 (tpt170) outliers start: 9 outliers final: 8 residues processed: 180 average time/residue: 1.3052 time to fit residues: 255.5887 Evaluate side-chains 179 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 127 optimal weight: 0.0170 chunk 53 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083919 restraints weight = 65078.460| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.38 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13155 Z= 0.155 Angle : 0.533 13.337 17785 Z= 0.262 Chirality : 0.037 0.197 2060 Planarity : 0.003 0.033 2250 Dihedral : 3.469 13.802 1740 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.63 % Allowed : 14.51 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.29 (0.22), residues: 1595 helix: 3.52 (0.15), residues: 1105 sheet: 2.83 (0.35), residues: 145 loop : 0.35 (0.41), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.001 0.000 HIS C 371 PHE 0.016 0.001 PHE C 352 TYR 0.029 0.002 TYR A 108 ARG 0.005 0.000 ARG E 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.79 seconds wall clock time: 80 minutes 35.11 seconds (4835.11 seconds total)