Starting phenix.real_space_refine on Wed Apr 30 21:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soy_40671/04_2025/8soy_40671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soy_40671/04_2025/8soy_40671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8soy_40671/04_2025/8soy_40671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soy_40671/04_2025/8soy_40671.map" model { file = "/net/cci-nas-00/data/ceres_data/8soy_40671/04_2025/8soy_40671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soy_40671/04_2025/8soy_40671.cif" } resolution = 2.85 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= 0.003 sd= 0.159 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 6390 2.51 5 N 1801 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1679 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1663 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1684 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1683 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 56 Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1690 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 6.66, per 1000 atoms: 0.66 Number of scatterers: 10074 At special positions: 0 Unit cell: (86.86, 89.44, 97.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1853 8.00 N 1801 7.00 C 6390 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 - 3.00 Amino acid : True - 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 12 sheets defined 58.3% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.782A pdb=" N ASP A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 229 through 248 removed outlier: 3.713A pdb=" N VAL A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 Proline residue: B 39 - end of helix removed outlier: 3.709A pdb=" N PHE B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.524A pdb=" N ASP B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 164 through 175 Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 195 through 211 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 229 through 248 removed outlier: 3.681A pdb=" N VAL B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.927A pdb=" N ALA B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 Proline residue: C 39 - end of helix removed outlier: 3.530A pdb=" N LEU C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 removed outlier: 3.549A pdb=" N ASP C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.696A pdb=" N ARG C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 195 through 211 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.638A pdb=" N ALA C 219 " --> pdb=" O PRO C 215 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 248 removed outlier: 3.796A pdb=" N VAL C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.940A pdb=" N ALA C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.576A pdb=" N TRP D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 82 through 105 removed outlier: 3.784A pdb=" N ASP D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 229 through 248 removed outlier: 3.714A pdb=" N VAL D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.899A pdb=" N ALA D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 46 removed outlier: 3.796A pdb=" N TRP E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) Proline residue: E 39 - end of helix Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.577A pdb=" N ASP E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 96 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 127 Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 195 through 211 removed outlier: 3.838A pdb=" N SER E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.778A pdb=" N ALA E 219 " --> pdb=" O PRO E 215 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 248 removed outlier: 3.792A pdb=" N VAL E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.896A pdb=" N ALA E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 48 Proline residue: F 39 - end of helix removed outlier: 3.636A pdb=" N PHE F 42 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 105 removed outlier: 3.903A pdb=" N ASP F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 100 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 164 through 175 Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 195 through 212 removed outlier: 3.702A pdb=" N SER F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS F 204 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 227 removed outlier: 3.700A pdb=" N ALA F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 248 removed outlier: 3.761A pdb=" N VAL F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.894A pdb=" N ALA F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 4.557A pdb=" N GLY A 58 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 131 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 191 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 8 through 12 removed outlier: 4.579A pdb=" N GLY B 58 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 131 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 191 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 13 removed outlier: 4.584A pdb=" N GLY C 58 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 131 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 135 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP C 191 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 117 through 119 removed outlier: 6.855A pdb=" N CYS C 118 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 8 through 13 removed outlier: 4.555A pdb=" N GLY D 58 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 131 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP D 191 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AA9, first strand: chain 'E' and resid 8 through 12 removed outlier: 4.569A pdb=" N GLY E 58 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 131 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 135 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP E 191 " --> pdb=" O ARG E 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 117 through 119 removed outlier: 6.801A pdb=" N CYS E 118 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 8 through 12 removed outlier: 4.561A pdb=" N GLY F 58 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 131 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP F 191 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 117 through 119 611 hydrogen bonds defined for protein. 1770 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: 3.45 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3355 1.34 - 1.46: 1298 1.46 - 1.57: 5535 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 10236 Sorted by residual: bond pdb=" C LEU A 159 " pdb=" N PRO A 160 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.19e-02 7.06e+03 4.00e+00 bond pdb=" CG LEU A 21 " pdb=" CD1 LEU A 21 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CG LEU F 21 " pdb=" CD1 LEU F 21 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" CG LEU C 21 " pdb=" CD1 LEU C 21 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CG LEU E 21 " pdb=" CD1 LEU E 21 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 ... (remaining 10231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 13496 1.73 - 3.46: 404 3.46 - 5.19: 49 5.19 - 6.92: 5 6.92 - 8.66: 6 Bond angle restraints: 13960 Sorted by residual: angle pdb=" CB ARG A 92 " pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " ideal model delta sigma weight residual 111.30 117.24 -5.94 2.30e+00 1.89e-01 6.68e+00 angle pdb=" N PRO A 160 " pdb=" CA PRO A 160 " pdb=" C PRO A 160 " ideal model delta sigma weight residual 113.84 117.06 -3.22 1.30e+00 5.92e-01 6.13e+00 angle pdb=" CA LEU E 21 " pdb=" CB LEU E 21 " pdb=" CG LEU E 21 " ideal model delta sigma weight residual 116.30 124.96 -8.66 3.50e+00 8.16e-02 6.12e+00 angle pdb=" CA LEU C 21 " pdb=" CB LEU C 21 " pdb=" CG LEU C 21 " ideal model delta sigma weight residual 116.30 124.92 -8.62 3.50e+00 8.16e-02 6.06e+00 angle pdb=" CA ALA B 211 " pdb=" C ALA B 211 " pdb=" N ALA B 212 " ideal model delta sigma weight residual 118.59 122.25 -3.66 1.63e+00 3.76e-01 5.04e+00 ... (remaining 13955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.47: 5462 14.47 - 28.94: 442 28.94 - 43.41: 133 43.41 - 57.89: 11 57.89 - 72.36: 8 Dihedral angle restraints: 6056 sinusoidal: 1994 harmonic: 4062 Sorted by residual: dihedral pdb=" CA ALA A 246 " pdb=" C ALA A 246 " pdb=" N PHE A 247 " pdb=" CA PHE A 247 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA VAL B 142 " pdb=" C VAL B 142 " pdb=" N ARG B 143 " pdb=" CA ARG B 143 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ALA C 246 " pdb=" C ALA C 246 " pdb=" N PHE C 247 " pdb=" CA PHE C 247 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 960 0.039 - 0.077: 535 0.077 - 0.116: 140 0.116 - 0.154: 73 0.154 - 0.193: 2 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CB VAL C 153 " pdb=" CA VAL C 153 " pdb=" CG1 VAL C 153 " pdb=" CG2 VAL C 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA PRO A 160 " pdb=" N PRO A 160 " pdb=" C PRO A 160 " pdb=" CB PRO A 160 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA VAL E 142 " pdb=" N VAL E 142 " pdb=" C VAL E 142 " pdb=" CB VAL E 142 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1707 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 159 " -0.051 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PRO B 160 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 115 " -0.020 2.00e-02 2.50e+03 2.46e-02 9.10e+00 pdb=" CG HIS E 115 " 0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS E 115 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS E 115 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS E 115 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 115 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 159 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO D 160 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " 0.040 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3504 2.88 - 3.38: 8740 3.38 - 3.89: 15804 3.89 - 4.39: 17515 4.39 - 4.90: 31507 Nonbonded interactions: 77070 Sorted by model distance: nonbonded pdb=" O GLU A 170 " pdb=" OG1 THR A 174 " model vdw 2.374 3.040 nonbonded pdb=" O GLU F 170 " pdb=" OG1 THR F 174 " model vdw 2.382 3.040 nonbonded pdb=" OD2 ASP C 130 " pdb=" NZ LYS C 222 " model vdw 2.406 3.120 nonbonded pdb=" O GLU C 170 " pdb=" OG1 THR C 174 " model vdw 2.436 3.040 nonbonded pdb=" OE1 GLN D 18 " pdb=" NE2 HIS D 204 " model vdw 2.469 3.120 ... (remaining 77065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 83 or (resid 84 throug \ h 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 92 through 129 or (resid 130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 131 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 193 or (resid 194 through 196 and \ (name N or name CA or name C or name O or name CB )) or resid 197 through 231 o \ r (resid 232 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 33 through 256)) selection = (chain 'B' and (resid 5 through 83 or (resid 84 through 85 and (name N or name C \ A or name C or name O or name CB )) or resid 86 through 90 or (resid 91 and (nam \ e N or name CA or name C or name O or name CB )) or resid 92 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 136 or (resid 137 through 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 164 or (resid 165 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 184 or (resid 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 25 \ 6)) selection = (chain 'C' and (resid 5 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 129 or (resid 130 and \ (name N or name CA or name C or name O or name CB )) or resid 131 through 231 or \ (resid 232 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 3 through 256)) selection = (chain 'D' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 83 or (resid 84 throug \ h 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 92 through 94 or (resid 95 and (name N or name CA or name C or name O or nam \ e CB )) or resid 96 through 136 or (resid 137 through 138 and (name N or name CA \ or name C or name O or name CB )) or resid 139 through 164 or (resid 165 and (n \ ame N or name CA or name C or name O or name CB )) or resid 166 through 184 or ( \ resid 185 and (name N or name CA or name C or name O or name CB )) or resid 186 \ through 231 or (resid 232 and (name N or name CA or name C or name O or name CB \ )) or resid 233 through 249 or (resid 250 through 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 through 256)) selection = (chain 'E' and (resid 5 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 67 or (resid 68 through 81 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 82 through 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 86 through 90 or (res \ id 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throu \ gh 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or r \ esid 96 through 129 or (resid 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 through 136 or (resid 137 through 138 and (name N or nam \ e CA or name C or name O or name CB )) or resid 139 through 184 or (resid 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 through 231 \ or (resid 232 and (name N or name CA or name C or name O or name CB )) or resid \ 233 through 249 or (resid 250 through 251 and (name N or name CA or name C or na \ me O or name CB )) or resid 252 through 256)) selection = (chain 'F' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 45 or (resid 46 through 48 and (nam \ e N or name CA or name C or name O or name CB )) or resid 49 through 84 or (resi \ d 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 92 through 94 or (resid 95 and (name N or name CA or name C or name O or nam \ e CB )) or resid 96 through 129 or (resid 130 and (name N or name CA or name C o \ r name O or name CB )) or resid 131 through 136 or (resid 137 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 164 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 184 or (resid 185 and (name N or name CA or name C or name O or name CB \ )) or resid 186 through 231 or (resid 232 and (name N or name CA or name C or na \ me O or name CB )) or resid 233 through 249 or (resid 250 through 251 and (name \ N or name CA or name C or name O or name CB )) or resid 252 through 256)) } 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=1.00 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: 1.650 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 28.530 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:23.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.005 0.052 10236 Z= 0.239 Angle : 0.726 8.656 13960 Z= 0.395 Chirality : 0.052 0.193 1710 Planarity : 0.007 0.077 1786 Dihedral : 12.140 72.357 3428 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.69 (0.21), residues: 1386 helix: 0.20 (0.19), residues: 702 sheet: 1.16 (0.35), residues: 180 loop : -2.00 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 243 HIS 0.030 0.003 HIS E 115 PHE 0.018 0.003 PHE D 42 TYR 0.015 0.001 TYR C 65 ARG 0.007 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.19388 ( 611) hydrogen bonds : angle 5.94847 ( 1770) covalent geometry : bond 0.00538 (10236) covalent geometry : angle 0.72578 (13960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 1.2657 time to fit residues: 196.1358 Evaluate side-chains 128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN C 190 ASN F 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.180322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.169509 restraints weight = 9614.139| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 0.61 r_work: 0.3689 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10236 Z= 0.175 Angle : 0.612 7.520 13960 Z= 0.338 Chirality : 0.047 0.142 1710 Planarity : 0.006 0.073 1786 Dihedral : 4.713 17.862 1500 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.45 % Allowed : 9.28 % Favored : 88.27 % 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: -0.42 (0.22), residues: 1386 helix: 0.42 (0.19), residues: 738 sheet: 1.39 (0.34), residues: 180 loop : -2.08 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 243 HIS 0.009 0.002 HIS E 115 PHE 0.015 0.002 PHE E 42 TYR 0.005 0.001 TYR D 65 ARG 0.003 0.001 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.07397 ( 611) hydrogen bonds : angle 4.74040 ( 1770) covalent geometry : bond 0.00375 (10236) covalent geometry : angle 0.61157 (13960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.031 Fit side-chains REVERT: E 137 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7064 (p0) REVERT: F 88 ASP cc_start: 0.7895 (m-30) cc_final: 0.7630 (m-30) REVERT: F 223 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7879 (t70) outliers start: 23 outliers final: 11 residues processed: 148 average time/residue: 1.1096 time to fit residues: 178.3427 Evaluate side-chains 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN B 90 HIS B 228 GLN C 115 HIS D 228 GLN F 190 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.175618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.164390 restraints weight = 9770.236| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 0.63 r_work: 0.3656 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10236 Z= 0.275 Angle : 0.768 8.954 13960 Z= 0.424 Chirality : 0.053 0.153 1710 Planarity : 0.008 0.076 1786 Dihedral : 5.241 19.038 1500 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.05 % Allowed : 13.97 % Favored : 81.98 % 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: -0.89 (0.21), residues: 1386 helix: -0.05 (0.19), residues: 738 sheet: 1.19 (0.32), residues: 180 loop : -2.13 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 243 HIS 0.006 0.002 HIS D 90 PHE 0.020 0.003 PHE D 42 TYR 0.010 0.001 TYR D 65 ARG 0.005 0.001 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.09631 ( 611) hydrogen bonds : angle 4.84264 ( 1770) covalent geometry : bond 0.00632 (10236) covalent geometry : angle 0.76785 (13960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.039 Fit side-chains REVERT: B 200 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8250 (tp) REVERT: C 232 GLN cc_start: 0.7689 (pt0) cc_final: 0.7388 (pt0) REVERT: D 200 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8268 (tp) REVERT: E 137 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7040 (p0) REVERT: E 232 GLN cc_start: 0.7669 (pt0) cc_final: 0.7382 (pt0) REVERT: F 88 ASP cc_start: 0.8063 (m-30) cc_final: 0.7807 (m-30) outliers start: 38 outliers final: 24 residues processed: 147 average time/residue: 1.1069 time to fit residues: 175.7333 Evaluate side-chains 154 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 129 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS C 115 HIS F 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.186903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.177051 restraints weight = 9682.356| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 0.57 r_work: 0.3742 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10236 Z= 0.128 Angle : 0.524 6.824 13960 Z= 0.289 Chirality : 0.044 0.143 1710 Planarity : 0.005 0.068 1786 Dihedral : 4.413 16.714 1500 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.88 % Allowed : 16.63 % Favored : 80.49 % 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: -0.09 (0.22), residues: 1386 helix: 0.65 (0.19), residues: 738 sheet: 1.70 (0.33), residues: 180 loop : -1.96 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 117 HIS 0.004 0.001 HIS E 90 PHE 0.013 0.002 PHE A 42 TYR 0.004 0.001 TYR D 65 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05513 ( 611) hydrogen bonds : angle 4.48853 ( 1770) covalent geometry : bond 0.00259 (10236) covalent geometry : angle 0.52361 (13960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.925 Fit side-chains REVERT: E 137 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6819 (p0) REVERT: E 200 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8204 (tt) REVERT: F 88 ASP cc_start: 0.7687 (m-30) cc_final: 0.7421 (m-30) REVERT: F 184 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8247 (tp30) REVERT: F 223 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7726 (t70) outliers start: 27 outliers final: 8 residues processed: 154 average time/residue: 1.0202 time to fit residues: 170.7175 Evaluate side-chains 142 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS C 115 HIS D 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.167743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.157975 restraints weight = 9596.857| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 0.56 r_work: 0.3545 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10236 Z= 0.263 Angle : 0.741 8.680 13960 Z= 0.409 Chirality : 0.052 0.156 1710 Planarity : 0.007 0.072 1786 Dihedral : 5.160 18.553 1500 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.26 % Allowed : 17.48 % Favored : 78.25 % 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: -0.67 (0.21), residues: 1386 helix: 0.10 (0.19), residues: 738 sheet: 1.46 (0.32), residues: 180 loop : -2.07 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 117 HIS 0.007 0.002 HIS A 115 PHE 0.020 0.003 PHE D 42 TYR 0.009 0.001 TYR D 65 ARG 0.005 0.001 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.09247 ( 611) hydrogen bonds : angle 4.74686 ( 1770) covalent geometry : bond 0.00604 (10236) covalent geometry : angle 0.74129 (13960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.039 Fit side-chains REVERT: B 200 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8218 (tp) REVERT: C 232 GLN cc_start: 0.7770 (pt0) cc_final: 0.7465 (pt0) REVERT: D 200 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8235 (tp) REVERT: E 137 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7077 (p0) REVERT: E 232 GLN cc_start: 0.7773 (pt0) cc_final: 0.7466 (pt0) outliers start: 40 outliers final: 17 residues processed: 150 average time/residue: 1.0568 time to fit residues: 171.7668 Evaluate side-chains 148 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.180280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.169158 restraints weight = 9763.733| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 0.63 r_work: 0.3714 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10236 Z= 0.169 Angle : 0.596 7.479 13960 Z= 0.330 Chirality : 0.047 0.156 1710 Planarity : 0.006 0.069 1786 Dihedral : 4.734 17.579 1500 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.62 % Allowed : 18.76 % Favored : 77.61 % 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: -0.32 (0.22), residues: 1386 helix: 0.40 (0.19), residues: 738 sheet: 1.72 (0.32), residues: 180 loop : -2.00 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 117 HIS 0.006 0.001 HIS E 90 PHE 0.017 0.002 PHE A 42 TYR 0.007 0.001 TYR B 65 ARG 0.003 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.07036 ( 611) hydrogen bonds : angle 4.56429 ( 1770) covalent geometry : bond 0.00363 (10236) covalent geometry : angle 0.59628 (13960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.051 Fit side-chains REVERT: B 200 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8224 (tp) REVERT: D 200 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8266 (tp) REVERT: E 137 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7004 (p0) REVERT: E 200 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8292 (tt) REVERT: F 223 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7947 (t70) outliers start: 34 outliers final: 17 residues processed: 153 average time/residue: 1.2978 time to fit residues: 216.3335 Evaluate side-chains 148 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 130 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS C 204 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.178600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.167240 restraints weight = 9789.551| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 0.64 r_work: 0.3672 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10236 Z= 0.191 Angle : 0.628 7.668 13960 Z= 0.347 Chirality : 0.048 0.142 1710 Planarity : 0.006 0.069 1786 Dihedral : 4.842 17.589 1500 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.69 % Allowed : 18.66 % Favored : 76.65 % 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: -0.37 (0.22), residues: 1386 helix: 0.35 (0.19), residues: 738 sheet: 1.74 (0.32), residues: 180 loop : -2.03 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 117 HIS 0.005 0.002 HIS A 115 PHE 0.018 0.002 PHE D 42 TYR 0.007 0.001 TYR B 65 ARG 0.003 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.07634 ( 611) hydrogen bonds : angle 4.59579 ( 1770) covalent geometry : bond 0.00418 (10236) covalent geometry : angle 0.62837 (13960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.258 Fit side-chains REVERT: B 200 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8248 (tp) REVERT: D 200 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8247 (tp) REVERT: E 137 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7008 (p0) REVERT: E 200 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8312 (tt) REVERT: F 184 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8313 (tp30) outliers start: 44 outliers final: 26 residues processed: 161 average time/residue: 1.2743 time to fit residues: 223.6868 Evaluate side-chains 157 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.178081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.166602 restraints weight = 9749.178| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 0.65 r_work: 0.3665 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10236 Z= 0.203 Angle : 0.649 7.862 13960 Z= 0.358 Chirality : 0.049 0.149 1710 Planarity : 0.006 0.069 1786 Dihedral : 4.917 17.802 1500 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.22 % Allowed : 18.34 % Favored : 76.44 % 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: -0.44 (0.22), residues: 1386 helix: 0.29 (0.19), residues: 738 sheet: 1.71 (0.32), residues: 180 loop : -2.04 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 117 HIS 0.006 0.002 HIS B 115 PHE 0.018 0.002 PHE D 42 TYR 0.008 0.001 TYR B 65 ARG 0.003 0.001 ARG E 169 Details of bonding type rmsd hydrogen bonds : bond 0.07926 ( 611) hydrogen bonds : angle 4.62546 ( 1770) covalent geometry : bond 0.00449 (10236) covalent geometry : angle 0.64876 (13960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.038 Fit side-chains REVERT: A 12 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8232 (t) REVERT: B 200 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8256 (tp) REVERT: D 200 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8262 (tp) REVERT: E 137 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7029 (p0) REVERT: E 200 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8321 (tt) outliers start: 49 outliers final: 30 residues processed: 164 average time/residue: 0.9694 time to fit residues: 173.7155 Evaluate side-chains 162 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 74 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.178211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.166966 restraints weight = 9683.710| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 0.63 r_work: 0.3696 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10236 Z= 0.205 Angle : 0.654 7.826 13960 Z= 0.361 Chirality : 0.049 0.151 1710 Planarity : 0.006 0.069 1786 Dihedral : 4.937 17.838 1500 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.22 % Allowed : 18.34 % Favored : 76.44 % 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: -0.47 (0.21), residues: 1386 helix: 0.26 (0.19), residues: 738 sheet: 1.70 (0.32), residues: 180 loop : -2.06 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 117 HIS 0.006 0.002 HIS A 115 PHE 0.018 0.002 PHE D 42 TYR 0.009 0.001 TYR D 65 ARG 0.003 0.001 ARG E 169 Details of bonding type rmsd hydrogen bonds : bond 0.07976 ( 611) hydrogen bonds : angle 4.63455 ( 1770) covalent geometry : bond 0.00454 (10236) covalent geometry : angle 0.65428 (13960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.052 Fit side-chains REVERT: B 200 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8262 (tp) REVERT: D 200 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8261 (tp) REVERT: E 137 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7019 (p0) REVERT: E 200 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8329 (tt) REVERT: F 184 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8321 (tp30) outliers start: 49 outliers final: 34 residues processed: 164 average time/residue: 1.0193 time to fit residues: 182.7181 Evaluate side-chains 165 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.180886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.169987 restraints weight = 9708.878| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 0.62 r_work: 0.3705 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10236 Z= 0.153 Angle : 0.569 7.165 13960 Z= 0.313 Chirality : 0.046 0.148 1710 Planarity : 0.006 0.066 1786 Dihedral : 4.625 17.288 1500 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.26 % Allowed : 19.51 % Favored : 76.23 % 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: -0.13 (0.22), residues: 1386 helix: 0.58 (0.19), residues: 738 sheet: 1.88 (0.32), residues: 180 loop : -1.99 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 117 HIS 0.006 0.001 HIS D 115 PHE 0.016 0.002 PHE D 42 TYR 0.006 0.001 TYR D 65 ARG 0.002 0.000 ARG E 158 Details of bonding type rmsd hydrogen bonds : bond 0.06466 ( 611) hydrogen bonds : angle 4.50886 ( 1770) covalent geometry : bond 0.00323 (10236) covalent geometry : angle 0.56886 (13960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.064 Fit side-chains REVERT: B 200 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8235 (tp) REVERT: D 200 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8253 (tp) REVERT: E 137 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6974 (p0) REVERT: F 184 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8300 (tp30) outliers start: 40 outliers final: 23 residues processed: 163 average time/residue: 0.9581 time to fit residues: 170.8017 Evaluate side-chains 158 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 117 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 132 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS D 115 HIS E 204 HIS F 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.174247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.163733 restraints weight = 9589.008| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 0.64 r_work: 0.3641 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10236 Z= 0.132 Angle : 0.530 6.849 13960 Z= 0.290 Chirality : 0.044 0.134 1710 Planarity : 0.005 0.064 1786 Dihedral : 4.398 16.977 1500 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.30 % Allowed : 20.79 % Favored : 75.91 % 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: 0.16 (0.22), residues: 1386 helix: 0.84 (0.19), residues: 738 sheet: 2.02 (0.33), residues: 180 loop : -1.90 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 117 HIS 0.005 0.001 HIS D 115 PHE 0.014 0.002 PHE D 42 TYR 0.005 0.001 TYR B 65 ARG 0.002 0.000 ARG F 169 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 611) hydrogen bonds : angle 4.42658 ( 1770) covalent geometry : bond 0.00272 (10236) covalent geometry : angle 0.52957 (13960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6362.56 seconds wall clock time: 111 minutes 34.77 seconds (6694.77 seconds total)