Starting phenix.real_space_refine on Fri Jun 13 12:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k99_9947/06_2025/6k99_9947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k99_9947/06_2025/6k99_9947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k99_9947/06_2025/6k99_9947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k99_9947/06_2025/6k99_9947.map" model { file = "/net/cci-nas-00/data/ceres_data/6k99_9947/06_2025/6k99_9947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k99_9947/06_2025/6k99_9947.cif" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8244 atoms to isotropic. 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 24 5.16 5 C 5280 2.51 5 N 1440 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8244 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.59, per 1000 atoms: 0.68 Number of scatterers: 8244 At special positions: 0 Unit cell: (94.6, 93.5, 95.7, 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 24 16.00 O 1500 8.00 N 1440 7.00 C 5280 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: 2.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 0 sheets defined 80.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 123 Processing helix chain 'G' and resid 128 through 137 removed outlier: 4.071A pdb=" N ASP G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 150 removed outlier: 3.653A pdb=" N ARG G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 164 removed outlier: 3.669A pdb=" N LYS G 158 " --> pdb=" O THR G 154 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET G 159 " --> pdb=" O ASN G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 185 Processing helix chain 'G' and resid 187 through 194 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.117A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 removed outlier: 3.562A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.603A pdb=" N ARG A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.721A pdb=" N LYS A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.958A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.165A pdb=" N ASP B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.602A pdb=" N ARG B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.675A pdb=" N LYS B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 185 Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 125 removed outlier: 4.150A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 4.143A pdb=" N ASP C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 150 removed outlier: 3.691A pdb=" N ARG C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.679A pdb=" N LYS C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 126 removed outlier: 4.225A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 137 removed outlier: 4.144A pdb=" N ASP D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.537A pdb=" N ARG D 150 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.615A pdb=" N LYS D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET D 159 " --> pdb=" O ASN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.583A pdb=" N LYS D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP D 175 " --> pdb=" O TRP D 171 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.995A pdb=" N ALA E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 137 removed outlier: 4.133A pdb=" N ASP E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 150 removed outlier: 3.600A pdb=" N ARG E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 164 removed outlier: 3.786A pdb=" N LYS E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 185 removed outlier: 3.804A pdb=" N LYS E 174 " --> pdb=" O ASN E 170 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP E 175 " --> pdb=" O TRP E 171 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 125 removed outlier: 4.049A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 137 removed outlier: 4.085A pdb=" N ASP F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.566A pdb=" N ARG F 150 " --> pdb=" O TYR F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 removed outlier: 3.772A pdb=" N LYS F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 185 removed outlier: 3.772A pdb=" N LYS F 174 " --> pdb=" O ASN F 170 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 175 " --> pdb=" O TRP F 171 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 125 removed outlier: 4.011A pdb=" N ALA H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 137 removed outlier: 3.546A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 150 removed outlier: 3.594A pdb=" N ARG H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 164 removed outlier: 3.649A pdb=" N LYS H 158 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET H 159 " --> pdb=" O ASN H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 169 removed outlier: 3.584A pdb=" N ALA H 168 " --> pdb=" O PHE H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 185 Processing helix chain 'H' and resid 187 through 194 Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 118 through 123 Processing helix chain 'I' and resid 128 through 137 removed outlier: 3.999A pdb=" N ASP I 134 " --> pdb=" O GLU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 150 removed outlier: 3.579A pdb=" N ARG I 150 " --> pdb=" O TYR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 164 removed outlier: 3.659A pdb=" N LYS I 158 " --> pdb=" O THR I 154 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET I 159 " --> pdb=" O ASN I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 185 removed outlier: 3.734A pdb=" N LYS I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP I 175 " --> pdb=" O TRP I 171 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU I 176 " --> pdb=" O THR I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 194 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 118 through 125 removed outlier: 4.173A pdb=" N ALA J 124 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 137 removed outlier: 4.176A pdb=" N ASP J 134 " --> pdb=" O GLU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 150 removed outlier: 3.584A pdb=" N ARG J 150 " --> pdb=" O TYR J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 164 removed outlier: 3.719A pdb=" N LYS J 158 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET J 159 " --> pdb=" O ASN J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 185 Processing helix chain 'J' and resid 187 through 194 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 118 through 126 removed outlier: 4.300A pdb=" N ALA K 124 " --> pdb=" O ALA K 120 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 125 " --> pdb=" O ALA K 121 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 137 removed outlier: 4.076A pdb=" N ASP K 134 " --> pdb=" O GLU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 150 removed outlier: 3.617A pdb=" N ARG K 150 " --> pdb=" O TYR K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 164 removed outlier: 3.730A pdb=" N LYS K 158 " --> pdb=" O THR K 154 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET K 159 " --> pdb=" O ASN K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 removed outlier: 3.606A pdb=" N ALA K 168 " --> pdb=" O PHE K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 185 removed outlier: 3.604A pdb=" N LYS K 174 " --> pdb=" O ASN K 170 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP K 175 " --> pdb=" O TRP K 171 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU K 176 " --> pdb=" O THR K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 194 Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 118 through 125 removed outlier: 3.977A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 removed outlier: 4.055A pdb=" N ASP L 134 " --> pdb=" O GLU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 150 removed outlier: 3.576A pdb=" N ARG L 150 " --> pdb=" O TYR L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 164 removed outlier: 3.704A pdb=" N LYS L 158 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET L 159 " --> pdb=" O ASN L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 185 Processing helix chain 'L' and resid 187 through 194 379 hydrogen bonds defined for protein. 1131 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: 2.19 Time building geometry restraints manager: 2.53 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: 2678 1.34 - 1.46: 1183 1.46 - 1.57: 4539 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 8436 Sorted by residual: bond pdb=" CA LEU A 112 " pdb=" C LEU A 112 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.45e+00 bond pdb=" CA LEU F 112 " pdb=" C LEU F 112 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.44e+00 bond pdb=" CA VAL F 140 " pdb=" C VAL F 140 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.27e-02 6.20e+03 1.43e+00 bond pdb=" CA LEU B 112 " pdb=" C LEU B 112 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.37e+00 bond pdb=" C ALA E 151 " pdb=" O ALA E 151 " ideal model delta sigma weight residual 1.236 1.224 0.011 9.60e-03 1.09e+04 1.36e+00 ... (remaining 8431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 11079 1.61 - 3.22: 293 3.22 - 4.84: 52 4.84 - 6.45: 13 6.45 - 8.06: 11 Bond angle restraints: 11448 Sorted by residual: angle pdb=" N HIS K 113 " pdb=" CA HIS K 113 " pdb=" C HIS K 113 " ideal model delta sigma weight residual 113.28 110.20 3.08 1.22e+00 6.72e-01 6.38e+00 angle pdb=" N HIS D 113 " pdb=" CA HIS D 113 " pdb=" C HIS D 113 " ideal model delta sigma weight residual 113.18 110.22 2.96 1.21e+00 6.83e-01 5.99e+00 angle pdb=" N HIS J 113 " pdb=" CA HIS J 113 " pdb=" C HIS J 113 " ideal model delta sigma weight residual 113.18 110.34 2.84 1.21e+00 6.83e-01 5.51e+00 angle pdb=" CA LEU I 178 " pdb=" CB LEU I 178 " pdb=" CG LEU I 178 " ideal model delta sigma weight residual 116.30 124.36 -8.06 3.50e+00 8.16e-02 5.31e+00 angle pdb=" CA LEU D 176 " pdb=" CB LEU D 176 " pdb=" CG LEU D 176 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.19e+00 ... (remaining 11443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 4666 14.97 - 29.94: 264 29.94 - 44.91: 108 44.91 - 59.88: 26 59.88 - 74.84: 12 Dihedral angle restraints: 5076 sinusoidal: 2088 harmonic: 2988 Sorted by residual: dihedral pdb=" CA LEU J 112 " pdb=" C LEU J 112 " pdb=" N HIS J 113 " pdb=" CA HIS J 113 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU C 112 " pdb=" C LEU C 112 " pdb=" N HIS C 113 " pdb=" CA HIS C 113 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LEU I 112 " pdb=" C LEU I 112 " pdb=" N HIS I 113 " pdb=" CA HIS I 113 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 770 0.034 - 0.068: 343 0.068 - 0.101: 109 0.101 - 0.135: 35 0.135 - 0.169: 3 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CG LEU B 112 " pdb=" CB LEU B 112 " pdb=" CD1 LEU B 112 " pdb=" CD2 LEU B 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CG LEU F 112 " pdb=" CB LEU F 112 " pdb=" CD1 LEU F 112 " pdb=" CD2 LEU F 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CG LEU C 112 " pdb=" CB LEU C 112 " pdb=" CD1 LEU C 112 " pdb=" CD2 LEU C 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 1257 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 112 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C LEU J 112 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU J 112 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS J 113 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 155 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO D 156 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS J 113 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C HIS J 113 " -0.023 2.00e-02 2.50e+03 pdb=" O HIS J 113 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE J 114 " 0.008 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3193 2.91 - 3.41: 7629 3.41 - 3.90: 12691 3.90 - 4.40: 14721 4.40 - 4.90: 22984 Nonbonded interactions: 61218 Sorted by model distance: nonbonded pdb=" O GLN G 185 " pdb=" OG SER G 186 " model vdw 2.410 3.040 nonbonded pdb=" O GLN C 185 " pdb=" OG SER C 186 " model vdw 2.446 3.040 nonbonded pdb=" O GLN F 185 " pdb=" OG SER F 186 " model vdw 2.449 3.040 nonbonded pdb=" O GLN J 185 " pdb=" OG SER J 186 " model vdw 2.451 3.040 nonbonded pdb=" O GLN E 185 " pdb=" OG SER E 186 " model vdw 2.458 3.040 ... (remaining 61213 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.520 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8436 Z= 0.165 Angle : 0.715 8.062 11448 Z= 0.387 Chirality : 0.043 0.169 1260 Planarity : 0.004 0.034 1452 Dihedral : 12.507 74.844 3108 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.46 % Allowed : 10.14 % Favored : 88.40 % 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: -2.97 (0.24), residues: 972 helix: -1.90 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -1.87 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 169 HIS 0.005 0.001 HIS G 113 PHE 0.014 0.002 PHE D 114 TYR 0.017 0.002 TYR F 187 ARG 0.003 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.16704 ( 379) hydrogen bonds : angle 6.95098 ( 1131) covalent geometry : bond 0.00325 ( 8436) covalent geometry : angle 0.71531 (11448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 533 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ILE cc_start: 0.9541 (mt) cc_final: 0.9276 (pt) REVERT: G 163 PHE cc_start: 0.8529 (m-80) cc_final: 0.7414 (m-80) REVERT: G 183 GLU cc_start: 0.9838 (mt-10) cc_final: 0.9395 (pt0) REVERT: A 115 ILE cc_start: 0.9636 (mt) cc_final: 0.9186 (pt) REVERT: A 146 TYR cc_start: 0.9201 (t80) cc_final: 0.8579 (t80) REVERT: A 175 ASP cc_start: 0.9381 (m-30) cc_final: 0.9146 (p0) REVERT: A 183 GLU cc_start: 0.9785 (mt-10) cc_final: 0.9528 (mm-30) REVERT: B 174 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8020 (ptpp) REVERT: B 178 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9057 (pp) REVERT: B 183 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9417 (pt0) REVERT: C 119 ARG cc_start: 0.9447 (tmt90) cc_final: 0.8785 (ptt180) REVERT: C 146 TYR cc_start: 0.8751 (t80) cc_final: 0.8497 (t80) REVERT: C 191 ASP cc_start: 0.9826 (t70) cc_final: 0.9514 (m-30) REVERT: D 141 LEU cc_start: 0.7934 (mt) cc_final: 0.7704 (mt) REVERT: D 146 TYR cc_start: 0.9248 (t80) cc_final: 0.8737 (t80) REVERT: D 149 VAL cc_start: 0.9656 (t) cc_final: 0.9194 (m) REVERT: D 161 LYS cc_start: 0.9631 (tppt) cc_final: 0.9317 (tptp) REVERT: D 188 LEU cc_start: 0.9121 (tp) cc_final: 0.8849 (mt) REVERT: E 125 ARG cc_start: 0.9452 (mtt180) cc_final: 0.9173 (tpt170) REVERT: E 154 THR cc_start: 0.8901 (p) cc_final: 0.8654 (t) REVERT: F 141 LEU cc_start: 0.7669 (mt) cc_final: 0.7468 (mt) REVERT: F 146 TYR cc_start: 0.8818 (t80) cc_final: 0.8262 (t80) REVERT: F 155 ASN cc_start: 0.8779 (t0) cc_final: 0.8090 (t0) REVERT: F 163 PHE cc_start: 0.8901 (m-80) cc_final: 0.8372 (m-80) REVERT: F 183 GLU cc_start: 0.9766 (mt-10) cc_final: 0.9519 (pt0) REVERT: H 126 VAL cc_start: 0.8734 (t) cc_final: 0.8496 (p) REVERT: H 137 TYR cc_start: 0.9294 (t80) cc_final: 0.8990 (t80) REVERT: H 157 SER cc_start: 0.9689 (t) cc_final: 0.9481 (p) REVERT: I 114 PHE cc_start: 0.9615 (t80) cc_final: 0.9385 (t80) REVERT: I 119 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8154 (ttp80) REVERT: I 125 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8491 (tpt170) REVERT: I 175 ASP cc_start: 0.9563 (m-30) cc_final: 0.9281 (p0) REVERT: I 192 LEU cc_start: 0.8784 (mp) cc_final: 0.8298 (tp) REVERT: J 146 TYR cc_start: 0.8820 (t80) cc_final: 0.8575 (t80) REVERT: J 149 VAL cc_start: 0.9301 (t) cc_final: 0.8839 (m) REVERT: J 161 LYS cc_start: 0.9638 (tppt) cc_final: 0.9412 (ptmm) REVERT: K 125 ARG cc_start: 0.9126 (mtt180) cc_final: 0.8835 (tpt170) REVERT: L 146 TYR cc_start: 0.9343 (t80) cc_final: 0.9054 (t80) outliers start: 13 outliers final: 0 residues processed: 541 average time/residue: 0.3407 time to fit residues: 230.1008 Evaluate side-chains 299 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 24 optimal weight: 50.0000 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN A 145 GLN D 128 ASN D 145 GLN E 145 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.038249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.027275 restraints weight = 62213.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028276 restraints weight = 44097.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.029048 restraints weight = 34924.304| |-----------------------------------------------------------------------------| r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8436 Z= 0.136 Angle : 0.763 8.861 11448 Z= 0.373 Chirality : 0.045 0.143 1260 Planarity : 0.005 0.037 1452 Dihedral : 4.935 15.075 1092 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % 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: -2.39 (0.24), residues: 972 helix: -1.29 (0.18), residues: 636 sheet: None (None), residues: 0 loop : -1.90 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 169 HIS 0.004 0.001 HIS F 118 PHE 0.023 0.002 PHE J 165 TYR 0.018 0.002 TYR F 146 ARG 0.008 0.001 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 379) hydrogen bonds : angle 4.98575 ( 1131) covalent geometry : bond 0.00287 ( 8436) covalent geometry : angle 0.76321 (11448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ILE cc_start: 0.9677 (mt) cc_final: 0.9454 (mp) REVERT: G 163 PHE cc_start: 0.9794 (m-80) cc_final: 0.8975 (t80) REVERT: A 141 LEU cc_start: 0.9034 (pp) cc_final: 0.8705 (pp) REVERT: A 146 TYR cc_start: 0.9577 (t80) cc_final: 0.9087 (t80) REVERT: A 152 GLU cc_start: 0.8928 (mp0) cc_final: 0.8647 (mp0) REVERT: A 161 LYS cc_start: 0.9742 (mmtt) cc_final: 0.9529 (mtmm) REVERT: A 163 PHE cc_start: 0.9678 (m-80) cc_final: 0.8886 (m-10) REVERT: B 112 LEU cc_start: 0.9590 (tp) cc_final: 0.9214 (pt) REVERT: B 146 TYR cc_start: 0.9571 (t80) cc_final: 0.9337 (t80) REVERT: B 161 LYS cc_start: 0.9826 (tppt) cc_final: 0.9321 (tptm) REVERT: B 165 PHE cc_start: 0.9724 (m-10) cc_final: 0.9287 (m-80) REVERT: C 137 TYR cc_start: 0.9740 (t80) cc_final: 0.9289 (t80) REVERT: C 141 LEU cc_start: 0.8624 (tp) cc_final: 0.7759 (tp) REVERT: C 146 TYR cc_start: 0.9664 (t80) cc_final: 0.8600 (t80) REVERT: C 161 LYS cc_start: 0.9041 (ptmt) cc_final: 0.8834 (pttt) REVERT: D 141 LEU cc_start: 0.9316 (mt) cc_final: 0.9077 (mt) REVERT: D 146 TYR cc_start: 0.9642 (t80) cc_final: 0.9282 (t80) REVERT: D 161 LYS cc_start: 0.9794 (tppt) cc_final: 0.9489 (tppt) REVERT: D 185 GLN cc_start: 0.9373 (mm110) cc_final: 0.9010 (mm110) REVERT: E 139 LYS cc_start: 0.9432 (mppt) cc_final: 0.9212 (mptt) REVERT: F 112 LEU cc_start: 0.9484 (tp) cc_final: 0.9223 (pt) REVERT: F 145 GLN cc_start: 0.9224 (mt0) cc_final: 0.9007 (pt0) REVERT: F 146 TYR cc_start: 0.8923 (t80) cc_final: 0.8400 (t80) REVERT: F 163 PHE cc_start: 0.9733 (m-80) cc_final: 0.8989 (m-80) REVERT: H 130 GLU cc_start: 0.9551 (pm20) cc_final: 0.9088 (pm20) REVERT: H 137 TYR cc_start: 0.9501 (t80) cc_final: 0.9059 (t80) REVERT: H 141 LEU cc_start: 0.9708 (mm) cc_final: 0.9248 (tp) REVERT: I 125 ARG cc_start: 0.9111 (mtt180) cc_final: 0.8755 (tpt170) REVERT: J 137 TYR cc_start: 0.9731 (t80) cc_final: 0.9487 (t80) REVERT: J 163 PHE cc_start: 0.9387 (m-80) cc_final: 0.8913 (m-80) REVERT: J 165 PHE cc_start: 0.9801 (m-10) cc_final: 0.9561 (m-80) REVERT: K 122 LEU cc_start: 0.9835 (mt) cc_final: 0.9534 (pp) REVERT: K 125 ARG cc_start: 0.9226 (mtt180) cc_final: 0.8972 (tpt170) REVERT: K 165 PHE cc_start: 0.9727 (m-10) cc_final: 0.9466 (m-80) REVERT: K 192 LEU cc_start: 0.9379 (mm) cc_final: 0.9039 (tp) REVERT: L 141 LEU cc_start: 0.8737 (pp) cc_final: 0.8480 (pp) REVERT: L 144 GLU cc_start: 0.9715 (pm20) cc_final: 0.9418 (pm20) REVERT: L 146 TYR cc_start: 0.9703 (t80) cc_final: 0.9043 (t80) REVERT: L 161 LYS cc_start: 0.9887 (tppt) cc_final: 0.9341 (tptm) REVERT: L 165 PHE cc_start: 0.9650 (m-10) cc_final: 0.9408 (m-80) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.4329 time to fit residues: 233.2586 Evaluate side-chains 279 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 7.9990 chunk 45 optimal weight: 0.1980 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 58 optimal weight: 0.8980 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN A 145 GLN D 145 GLN D 147 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS H 147 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.027398 restraints weight = 65913.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.028458 restraints weight = 45759.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.029266 restraints weight = 35499.353| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8436 Z= 0.133 Angle : 0.738 8.020 11448 Z= 0.365 Chirality : 0.044 0.134 1260 Planarity : 0.005 0.069 1452 Dihedral : 4.891 16.452 1092 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % 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: -1.94 (0.25), residues: 972 helix: -0.93 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.74 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 169 HIS 0.002 0.001 HIS F 118 PHE 0.017 0.002 PHE L 165 TYR 0.009 0.001 TYR L 187 ARG 0.008 0.001 ARG E 182 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 379) hydrogen bonds : angle 4.79774 ( 1131) covalent geometry : bond 0.00284 ( 8436) covalent geometry : angle 0.73777 (11448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9633 (t80) cc_final: 0.9336 (t80) REVERT: A 141 LEU cc_start: 0.8803 (pp) cc_final: 0.8195 (pp) REVERT: A 146 TYR cc_start: 0.9518 (t80) cc_final: 0.8767 (t80) REVERT: A 159 MET cc_start: 0.9628 (ptp) cc_final: 0.9182 (ptp) REVERT: A 163 PHE cc_start: 0.9357 (m-80) cc_final: 0.8819 (m-80) REVERT: A 182 ARG cc_start: 0.9611 (ptp-110) cc_final: 0.9343 (mtm110) REVERT: A 183 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9120 (mm-30) REVERT: B 146 TYR cc_start: 0.9610 (t80) cc_final: 0.9403 (t80) REVERT: B 161 LYS cc_start: 0.9844 (tppt) cc_final: 0.9418 (tptm) REVERT: B 163 PHE cc_start: 0.9463 (m-80) cc_final: 0.8796 (m-80) REVERT: B 165 PHE cc_start: 0.9767 (m-10) cc_final: 0.9384 (m-80) REVERT: C 119 ARG cc_start: 0.8491 (tpt170) cc_final: 0.8051 (tpp-160) REVERT: C 137 TYR cc_start: 0.9719 (t80) cc_final: 0.9418 (t80) REVERT: C 141 LEU cc_start: 0.8499 (tp) cc_final: 0.7728 (tp) REVERT: C 144 GLU cc_start: 0.9568 (pm20) cc_final: 0.9141 (pm20) REVERT: C 146 TYR cc_start: 0.9579 (t80) cc_final: 0.8504 (t80) REVERT: C 158 LYS cc_start: 0.9514 (mttt) cc_final: 0.9276 (mtmm) REVERT: C 163 PHE cc_start: 0.9522 (t80) cc_final: 0.9189 (t80) REVERT: D 141 LEU cc_start: 0.9338 (mt) cc_final: 0.9099 (mt) REVERT: D 146 TYR cc_start: 0.9676 (t80) cc_final: 0.9274 (t80) REVERT: D 161 LYS cc_start: 0.9830 (tppt) cc_final: 0.9534 (tppt) REVERT: E 130 GLU cc_start: 0.9662 (pm20) cc_final: 0.9401 (pm20) REVERT: E 163 PHE cc_start: 0.9823 (m-80) cc_final: 0.8677 (m-80) REVERT: F 145 GLN cc_start: 0.9310 (mt0) cc_final: 0.8995 (pt0) REVERT: F 146 TYR cc_start: 0.9201 (t80) cc_final: 0.8580 (t80) REVERT: H 137 TYR cc_start: 0.9583 (t80) cc_final: 0.9337 (t80) REVERT: H 141 LEU cc_start: 0.9662 (mm) cc_final: 0.9195 (tp) REVERT: H 146 TYR cc_start: 0.9515 (t80) cc_final: 0.9293 (t80) REVERT: H 154 THR cc_start: 0.9811 (p) cc_final: 0.9565 (t) REVERT: H 163 PHE cc_start: 0.9501 (m-80) cc_final: 0.9050 (m-80) REVERT: I 125 ARG cc_start: 0.9169 (mtt180) cc_final: 0.8820 (tpt170) REVERT: I 161 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7513 (pttm) REVERT: J 137 TYR cc_start: 0.9827 (t80) cc_final: 0.9297 (t80) REVERT: J 146 TYR cc_start: 0.9652 (t80) cc_final: 0.9161 (t80) REVERT: J 149 VAL cc_start: 0.9878 (p) cc_final: 0.9514 (m) REVERT: J 152 GLU cc_start: 0.9533 (mp0) cc_final: 0.9317 (mp0) REVERT: J 161 LYS cc_start: 0.9814 (tppt) cc_final: 0.9374 (mtmm) REVERT: J 163 PHE cc_start: 0.9560 (m-80) cc_final: 0.8928 (m-80) REVERT: J 165 PHE cc_start: 0.9831 (m-10) cc_final: 0.9569 (m-80) REVERT: K 122 LEU cc_start: 0.9824 (mt) cc_final: 0.9539 (pp) REVERT: K 137 TYR cc_start: 0.9775 (t80) cc_final: 0.9564 (t80) REVERT: K 161 LYS cc_start: 0.9738 (tppt) cc_final: 0.9395 (ptpt) REVERT: K 192 LEU cc_start: 0.9377 (mm) cc_final: 0.9113 (tp) REVERT: L 112 LEU cc_start: 0.9628 (tp) cc_final: 0.9418 (pt) REVERT: L 125 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8124 (ttt-90) REVERT: L 141 LEU cc_start: 0.8729 (pp) cc_final: 0.8350 (pp) REVERT: L 146 TYR cc_start: 0.9700 (t80) cc_final: 0.9002 (t80) REVERT: L 152 GLU cc_start: 0.9689 (mp0) cc_final: 0.9462 (mp0) REVERT: L 161 LYS cc_start: 0.9854 (tppt) cc_final: 0.9520 (mtmm) REVERT: L 188 LEU cc_start: 0.9742 (tp) cc_final: 0.9441 (tp) outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.3184 time to fit residues: 156.4121 Evaluate side-chains 287 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 32 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 40.0000 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN G 179 GLN A 145 GLN B 185 GLN D 145 GLN D 147 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN K 145 GLN L 147 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.037148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.027069 restraints weight = 67710.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.028086 restraints weight = 46890.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.028840 restraints weight = 36552.775| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8436 Z= 0.149 Angle : 0.728 8.514 11448 Z= 0.368 Chirality : 0.044 0.142 1260 Planarity : 0.005 0.060 1452 Dihedral : 4.891 17.719 1092 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -1.92 (0.26), residues: 972 helix: -0.88 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.86 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.003 0.001 HIS F 118 PHE 0.030 0.002 PHE G 163 TYR 0.017 0.001 TYR F 146 ARG 0.017 0.001 ARG E 119 Details of bonding type rmsd hydrogen bonds : bond 0.02732 ( 379) hydrogen bonds : angle 5.09295 ( 1131) covalent geometry : bond 0.00331 ( 8436) covalent geometry : angle 0.72820 (11448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 169 TRP cc_start: 0.9195 (m-10) cc_final: 0.8457 (m-10) REVERT: A 152 GLU cc_start: 0.9039 (mp0) cc_final: 0.8715 (mp0) REVERT: A 159 MET cc_start: 0.9660 (ptp) cc_final: 0.9334 (ptt) REVERT: A 161 LYS cc_start: 0.9768 (mmtt) cc_final: 0.9523 (mtmm) REVERT: A 163 PHE cc_start: 0.9396 (m-80) cc_final: 0.9057 (m-80) REVERT: A 182 ARG cc_start: 0.9630 (ptp-110) cc_final: 0.9390 (mtm110) REVERT: B 112 LEU cc_start: 0.9692 (tp) cc_final: 0.9425 (pt) REVERT: B 125 ARG cc_start: 0.9211 (mtp180) cc_final: 0.8612 (mmm-85) REVERT: B 141 LEU cc_start: 0.8150 (pp) cc_final: 0.7884 (pp) REVERT: B 146 TYR cc_start: 0.9693 (t80) cc_final: 0.9323 (t80) REVERT: B 161 LYS cc_start: 0.9855 (tppt) cc_final: 0.9371 (tptm) REVERT: B 165 PHE cc_start: 0.9731 (m-10) cc_final: 0.9298 (m-80) REVERT: C 125 ARG cc_start: 0.9250 (mpp-170) cc_final: 0.9024 (mtp-110) REVERT: C 137 TYR cc_start: 0.9858 (t80) cc_final: 0.9436 (t80) REVERT: C 146 TYR cc_start: 0.9616 (t80) cc_final: 0.9327 (t80) REVERT: C 161 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8332 (pttm) REVERT: C 163 PHE cc_start: 0.9488 (t80) cc_final: 0.9104 (t80) REVERT: D 141 LEU cc_start: 0.9363 (mt) cc_final: 0.9078 (mt) REVERT: D 146 TYR cc_start: 0.9689 (t80) cc_final: 0.9281 (t80) REVERT: D 192 LEU cc_start: 0.9645 (mm) cc_final: 0.9091 (tp) REVERT: E 130 GLU cc_start: 0.9666 (pm20) cc_final: 0.9465 (pm20) REVERT: E 163 PHE cc_start: 0.9528 (m-80) cc_final: 0.9140 (m-80) REVERT: F 141 LEU cc_start: 0.9258 (mm) cc_final: 0.9057 (mt) REVERT: F 146 TYR cc_start: 0.9287 (t80) cc_final: 0.8448 (t80) REVERT: F 149 VAL cc_start: 0.9786 (t) cc_final: 0.9545 (p) REVERT: H 130 GLU cc_start: 0.9556 (pm20) cc_final: 0.9125 (pm20) REVERT: H 133 LEU cc_start: 0.9793 (mt) cc_final: 0.9592 (mm) REVERT: H 137 TYR cc_start: 0.9711 (t80) cc_final: 0.8993 (t80) REVERT: H 141 LEU cc_start: 0.9648 (mm) cc_final: 0.9035 (tp) REVERT: H 146 TYR cc_start: 0.9589 (t80) cc_final: 0.9091 (t80) REVERT: H 163 PHE cc_start: 0.9567 (m-80) cc_final: 0.9104 (m-80) REVERT: I 125 ARG cc_start: 0.9302 (mtt180) cc_final: 0.8965 (tpt170) REVERT: I 183 GLU cc_start: 0.9074 (pm20) cc_final: 0.8772 (pm20) REVERT: J 146 TYR cc_start: 0.9625 (t80) cc_final: 0.9133 (t80) REVERT: J 163 PHE cc_start: 0.9643 (m-80) cc_final: 0.9001 (m-80) REVERT: J 165 PHE cc_start: 0.9834 (m-10) cc_final: 0.9554 (m-80) REVERT: K 122 LEU cc_start: 0.9832 (mt) cc_final: 0.9609 (pp) REVERT: K 137 TYR cc_start: 0.9764 (t80) cc_final: 0.9449 (t80) REVERT: K 165 PHE cc_start: 0.9789 (m-80) cc_final: 0.9535 (m-80) REVERT: K 192 LEU cc_start: 0.9366 (mm) cc_final: 0.9166 (tp) REVERT: L 134 ASP cc_start: 0.9170 (m-30) cc_final: 0.8814 (m-30) REVERT: L 141 LEU cc_start: 0.8861 (pp) cc_final: 0.8554 (pp) REVERT: L 146 TYR cc_start: 0.9653 (t80) cc_final: 0.9039 (t80) REVERT: L 161 LYS cc_start: 0.9900 (tppt) cc_final: 0.9436 (tttm) REVERT: L 163 PHE cc_start: 0.9442 (m-80) cc_final: 0.9082 (m-80) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.3264 time to fit residues: 142.0930 Evaluate side-chains 253 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 20.0000 chunk 16 optimal weight: 50.0000 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN A 145 GLN C 118 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN F 185 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.026596 restraints weight = 66365.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.027662 restraints weight = 46075.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.028453 restraints weight = 35454.619| |-----------------------------------------------------------------------------| r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.7591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8436 Z= 0.128 Angle : 0.748 8.025 11448 Z= 0.373 Chirality : 0.045 0.145 1260 Planarity : 0.004 0.050 1452 Dihedral : 4.750 17.839 1092 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.23 % Allowed : 3.83 % Favored : 95.95 % 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: -1.82 (0.26), residues: 972 helix: -0.77 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 131 HIS 0.007 0.001 HIS C 118 PHE 0.020 0.001 PHE G 163 TYR 0.008 0.001 TYR D 187 ARG 0.012 0.001 ARG F 182 Details of bonding type rmsd hydrogen bonds : bond 0.02425 ( 379) hydrogen bonds : angle 4.97762 ( 1131) covalent geometry : bond 0.00274 ( 8436) covalent geometry : angle 0.74839 (11448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9663 (t80) cc_final: 0.9260 (t80) REVERT: G 163 PHE cc_start: 0.9231 (p90) cc_final: 0.8973 (p90) REVERT: G 169 TRP cc_start: 0.9382 (m-10) cc_final: 0.8540 (m-10) REVERT: A 159 MET cc_start: 0.9683 (ptp) cc_final: 0.9252 (ptp) REVERT: A 163 PHE cc_start: 0.9443 (m-80) cc_final: 0.9162 (m-80) REVERT: A 179 GLN cc_start: 0.9731 (tm-30) cc_final: 0.9445 (tp-100) REVERT: B 125 ARG cc_start: 0.9093 (mtp180) cc_final: 0.8586 (mmm160) REVERT: B 146 TYR cc_start: 0.9758 (t80) cc_final: 0.9542 (t80) REVERT: B 165 PHE cc_start: 0.9726 (m-10) cc_final: 0.9500 (m-80) REVERT: C 125 ARG cc_start: 0.9252 (mpp-170) cc_final: 0.9016 (mtp-110) REVERT: C 134 ASP cc_start: 0.9464 (t0) cc_final: 0.9060 (p0) REVERT: C 150 ARG cc_start: 0.9168 (ptp-110) cc_final: 0.8835 (mtm110) REVERT: C 161 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8313 (pttm) REVERT: C 163 PHE cc_start: 0.9516 (t80) cc_final: 0.9192 (t80) REVERT: D 146 TYR cc_start: 0.9607 (t80) cc_final: 0.9222 (t80) REVERT: D 161 LYS cc_start: 0.9860 (tppt) cc_final: 0.9588 (tppt) REVERT: E 130 GLU cc_start: 0.9700 (pm20) cc_final: 0.9499 (pm20) REVERT: E 161 LYS cc_start: 0.9814 (tptp) cc_final: 0.9523 (tptp) REVERT: E 163 PHE cc_start: 0.9568 (m-80) cc_final: 0.9161 (m-80) REVERT: E 165 PHE cc_start: 0.9702 (m-80) cc_final: 0.9442 (m-80) REVERT: F 141 LEU cc_start: 0.9248 (mm) cc_final: 0.8891 (tp) REVERT: F 146 TYR cc_start: 0.9402 (t80) cc_final: 0.7922 (t80) REVERT: F 149 VAL cc_start: 0.9746 (t) cc_final: 0.9510 (p) REVERT: H 130 GLU cc_start: 0.9529 (pm20) cc_final: 0.9171 (pm20) REVERT: H 137 TYR cc_start: 0.9567 (t80) cc_final: 0.8831 (t80) REVERT: H 141 LEU cc_start: 0.9597 (mm) cc_final: 0.9096 (tp) REVERT: H 163 PHE cc_start: 0.9633 (m-80) cc_final: 0.9176 (m-80) REVERT: H 192 LEU cc_start: 0.9475 (mm) cc_final: 0.9261 (tp) REVERT: I 125 ARG cc_start: 0.9351 (mtt180) cc_final: 0.9013 (tpt170) REVERT: I 169 TRP cc_start: 0.9152 (m-10) cc_final: 0.8689 (m-10) REVERT: J 146 TYR cc_start: 0.9656 (t80) cc_final: 0.9237 (t80) REVERT: J 152 GLU cc_start: 0.9491 (mp0) cc_final: 0.9269 (mp0) REVERT: J 161 LYS cc_start: 0.9821 (tppt) cc_final: 0.9562 (mtmm) REVERT: J 163 PHE cc_start: 0.9719 (m-80) cc_final: 0.9055 (m-80) REVERT: J 165 PHE cc_start: 0.9803 (m-10) cc_final: 0.9542 (m-80) REVERT: K 122 LEU cc_start: 0.9816 (mt) cc_final: 0.9572 (pp) REVERT: K 137 TYR cc_start: 0.9749 (t80) cc_final: 0.9411 (t80) REVERT: K 161 LYS cc_start: 0.9822 (tppt) cc_final: 0.9553 (mtmt) REVERT: K 188 LEU cc_start: 0.9438 (tp) cc_final: 0.9174 (mt) REVERT: K 192 LEU cc_start: 0.9285 (mm) cc_final: 0.8982 (tp) REVERT: L 134 ASP cc_start: 0.9173 (m-30) cc_final: 0.8800 (m-30) REVERT: L 141 LEU cc_start: 0.8850 (pp) cc_final: 0.8476 (pp) REVERT: L 146 TYR cc_start: 0.9680 (t80) cc_final: 0.9170 (t80) REVERT: L 161 LYS cc_start: 0.9872 (tppt) cc_final: 0.9447 (tttm) REVERT: L 163 PHE cc_start: 0.9511 (m-80) cc_final: 0.9298 (m-80) REVERT: L 182 ARG cc_start: 0.9437 (ptp-110) cc_final: 0.9232 (ptp-110) outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.2800 time to fit residues: 119.0911 Evaluate side-chains 237 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 80 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 91 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN B 179 GLN C 185 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN F 185 GLN H 185 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN J 145 GLN J 185 GLN K 145 GLN L 185 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.036493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.026846 restraints weight = 69186.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.027875 restraints weight = 47128.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.028621 restraints weight = 36357.204| |-----------------------------------------------------------------------------| r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8436 Z= 0.142 Angle : 0.769 9.671 11448 Z= 0.387 Chirality : 0.046 0.146 1260 Planarity : 0.004 0.049 1452 Dihedral : 4.878 20.241 1092 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % 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: -1.59 (0.27), residues: 972 helix: -0.60 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.09 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 169 HIS 0.007 0.001 HIS C 118 PHE 0.019 0.002 PHE G 163 TYR 0.009 0.001 TYR L 137 ARG 0.009 0.001 ARG F 182 Details of bonding type rmsd hydrogen bonds : bond 0.02645 ( 379) hydrogen bonds : angle 5.10444 ( 1131) covalent geometry : bond 0.00306 ( 8436) covalent geometry : angle 0.76889 (11448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9706 (t80) cc_final: 0.9274 (t80) REVERT: G 163 PHE cc_start: 0.9214 (p90) cc_final: 0.8694 (p90) REVERT: A 150 ARG cc_start: 0.9051 (ttp-110) cc_final: 0.8547 (mtm110) REVERT: A 152 GLU cc_start: 0.9154 (mp0) cc_final: 0.8924 (mp0) REVERT: A 158 LYS cc_start: 0.9711 (mttt) cc_final: 0.9410 (mttm) REVERT: A 159 MET cc_start: 0.9650 (ptp) cc_final: 0.9353 (ptp) REVERT: A 161 LYS cc_start: 0.9810 (mmtt) cc_final: 0.9557 (mtmm) REVERT: A 163 PHE cc_start: 0.9527 (m-80) cc_final: 0.9146 (m-80) REVERT: A 179 GLN cc_start: 0.9560 (tm-30) cc_final: 0.9209 (tp-100) REVERT: B 141 LEU cc_start: 0.8534 (pp) cc_final: 0.8268 (pp) REVERT: B 146 TYR cc_start: 0.9761 (t80) cc_final: 0.9361 (t80) REVERT: B 160 ARG cc_start: 0.9500 (ptp-110) cc_final: 0.9128 (ptp-170) REVERT: B 161 LYS cc_start: 0.9886 (tppt) cc_final: 0.9520 (tptm) REVERT: B 165 PHE cc_start: 0.9705 (m-10) cc_final: 0.9260 (m-10) REVERT: C 134 ASP cc_start: 0.9382 (t0) cc_final: 0.9035 (p0) REVERT: C 137 TYR cc_start: 0.9708 (t80) cc_final: 0.9393 (t80) REVERT: C 163 PHE cc_start: 0.9500 (t80) cc_final: 0.9191 (t80) REVERT: D 141 LEU cc_start: 0.9123 (mt) cc_final: 0.8850 (mt) REVERT: D 146 TYR cc_start: 0.9706 (t80) cc_final: 0.9340 (t80) REVERT: D 161 LYS cc_start: 0.9898 (tppt) cc_final: 0.9622 (tppt) REVERT: D 192 LEU cc_start: 0.9604 (mm) cc_final: 0.9065 (tp) REVERT: E 161 LYS cc_start: 0.9860 (tptp) cc_final: 0.9606 (tptp) REVERT: E 163 PHE cc_start: 0.9574 (m-80) cc_final: 0.9134 (m-80) REVERT: F 141 LEU cc_start: 0.9345 (mm) cc_final: 0.9051 (tp) REVERT: F 146 TYR cc_start: 0.9534 (t80) cc_final: 0.8114 (t80) REVERT: H 130 GLU cc_start: 0.9554 (pm20) cc_final: 0.9235 (pm20) REVERT: H 141 LEU cc_start: 0.9615 (mm) cc_final: 0.9182 (tp) REVERT: H 163 PHE cc_start: 0.9634 (m-80) cc_final: 0.9136 (m-80) REVERT: I 125 ARG cc_start: 0.9334 (mtt180) cc_final: 0.8961 (tpt170) REVERT: I 163 PHE cc_start: 0.9621 (m-80) cc_final: 0.9371 (m-80) REVERT: J 161 LYS cc_start: 0.9845 (tppt) cc_final: 0.9502 (mtmm) REVERT: J 163 PHE cc_start: 0.9731 (m-80) cc_final: 0.9102 (m-80) REVERT: J 165 PHE cc_start: 0.9777 (m-10) cc_final: 0.9511 (m-80) REVERT: K 112 LEU cc_start: 0.9524 (tp) cc_final: 0.9249 (pt) REVERT: K 115 ILE cc_start: 0.9651 (pt) cc_final: 0.9325 (pt) REVERT: K 137 TYR cc_start: 0.9659 (t80) cc_final: 0.9346 (t80) REVERT: K 141 LEU cc_start: 0.9535 (mm) cc_final: 0.9211 (mt) REVERT: K 163 PHE cc_start: 0.9842 (m-80) cc_final: 0.8439 (m-80) REVERT: L 134 ASP cc_start: 0.9136 (m-30) cc_final: 0.8811 (m-30) REVERT: L 146 TYR cc_start: 0.9710 (t80) cc_final: 0.9155 (t80) REVERT: L 160 ARG cc_start: 0.9540 (mtt-85) cc_final: 0.9260 (mtt-85) REVERT: L 163 PHE cc_start: 0.9541 (m-80) cc_final: 0.9241 (m-80) outliers start: 1 outliers final: 1 residues processed: 312 average time/residue: 0.2736 time to fit residues: 106.8333 Evaluate side-chains 222 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 16 optimal weight: 50.0000 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN H 147 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN K 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.025808 restraints weight = 68138.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.026824 restraints weight = 47501.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.027597 restraints weight = 36926.254| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.8443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8436 Z= 0.152 Angle : 0.787 8.922 11448 Z= 0.399 Chirality : 0.046 0.141 1260 Planarity : 0.004 0.043 1452 Dihedral : 4.975 20.393 1092 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -1.50 (0.27), residues: 972 helix: -0.57 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -1.89 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP A 169 HIS 0.004 0.001 HIS C 118 PHE 0.020 0.002 PHE E 165 TYR 0.018 0.001 TYR I 146 ARG 0.007 0.001 ARG G 150 Details of bonding type rmsd hydrogen bonds : bond 0.02671 ( 379) hydrogen bonds : angle 5.35841 ( 1131) covalent geometry : bond 0.00326 ( 8436) covalent geometry : angle 0.78679 (11448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9721 (t80) cc_final: 0.9265 (t80) REVERT: G 163 PHE cc_start: 0.9291 (p90) cc_final: 0.8768 (p90) REVERT: A 146 TYR cc_start: 0.9409 (t80) cc_final: 0.9027 (t80) REVERT: A 159 MET cc_start: 0.9685 (ptp) cc_final: 0.9386 (ptp) REVERT: A 163 PHE cc_start: 0.9556 (m-80) cc_final: 0.9122 (m-80) REVERT: B 141 LEU cc_start: 0.8557 (pp) cc_final: 0.8260 (pp) REVERT: B 146 TYR cc_start: 0.9789 (t80) cc_final: 0.9450 (t80) REVERT: B 161 LYS cc_start: 0.9897 (tppt) cc_final: 0.9573 (tptm) REVERT: B 165 PHE cc_start: 0.9689 (m-10) cc_final: 0.9374 (m-80) REVERT: C 134 ASP cc_start: 0.9381 (t0) cc_final: 0.9063 (p0) REVERT: C 137 TYR cc_start: 0.9593 (t80) cc_final: 0.9341 (t80) REVERT: C 163 PHE cc_start: 0.9532 (t80) cc_final: 0.9230 (t80) REVERT: D 141 LEU cc_start: 0.9105 (mt) cc_final: 0.8787 (mt) REVERT: D 146 TYR cc_start: 0.9718 (t80) cc_final: 0.9338 (t80) REVERT: D 161 LYS cc_start: 0.9897 (tppt) cc_final: 0.9612 (tppt) REVERT: D 192 LEU cc_start: 0.9595 (mm) cc_final: 0.9052 (tp) REVERT: E 161 LYS cc_start: 0.9839 (tptp) cc_final: 0.9623 (tptp) REVERT: E 163 PHE cc_start: 0.9611 (m-80) cc_final: 0.9341 (m-80) REVERT: F 141 LEU cc_start: 0.9401 (mm) cc_final: 0.9095 (tp) REVERT: F 146 TYR cc_start: 0.9622 (t80) cc_final: 0.8712 (t80) REVERT: H 130 GLU cc_start: 0.9594 (pm20) cc_final: 0.9165 (pm20) REVERT: H 133 LEU cc_start: 0.9848 (mp) cc_final: 0.9644 (mp) REVERT: H 146 TYR cc_start: 0.9594 (t80) cc_final: 0.9204 (t80) REVERT: H 163 PHE cc_start: 0.9644 (m-80) cc_final: 0.9108 (m-80) REVERT: I 125 ARG cc_start: 0.9332 (mtt180) cc_final: 0.9021 (tpt170) REVERT: I 163 PHE cc_start: 0.9799 (m-80) cc_final: 0.9405 (m-80) REVERT: J 112 LEU cc_start: 0.9625 (tp) cc_final: 0.9373 (pt) REVERT: J 161 LYS cc_start: 0.9857 (tppt) cc_final: 0.9547 (mtmm) REVERT: J 163 PHE cc_start: 0.9780 (m-80) cc_final: 0.9199 (m-80) REVERT: J 165 PHE cc_start: 0.9776 (m-10) cc_final: 0.9499 (m-80) REVERT: K 112 LEU cc_start: 0.9582 (tp) cc_final: 0.9346 (pt) REVERT: K 137 TYR cc_start: 0.9710 (t80) cc_final: 0.9478 (t80) REVERT: K 141 LEU cc_start: 0.9505 (mm) cc_final: 0.9218 (mt) REVERT: K 152 GLU cc_start: 0.9588 (mp0) cc_final: 0.9280 (mp0) REVERT: K 157 SER cc_start: 0.9779 (t) cc_final: 0.9376 (p) REVERT: K 161 LYS cc_start: 0.9828 (tppt) cc_final: 0.9437 (ptpp) REVERT: K 192 LEU cc_start: 0.9385 (mm) cc_final: 0.9084 (tp) REVERT: L 134 ASP cc_start: 0.9185 (m-30) cc_final: 0.8945 (m-30) REVERT: L 146 TYR cc_start: 0.9645 (t80) cc_final: 0.9090 (t80) REVERT: L 163 PHE cc_start: 0.9571 (m-80) cc_final: 0.9286 (m-80) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2676 time to fit residues: 101.2928 Evaluate side-chains 206 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 63 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 179 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN K 145 GLN K 185 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.035737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.026256 restraints weight = 70070.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.027281 restraints weight = 47876.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.028043 restraints weight = 36984.165| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.8796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8436 Z= 0.145 Angle : 0.802 9.508 11448 Z= 0.401 Chirality : 0.047 0.142 1260 Planarity : 0.004 0.055 1452 Dihedral : 5.032 19.369 1092 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: -1.71 (0.26), residues: 972 helix: -0.71 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 169 HIS 0.003 0.001 HIS C 118 PHE 0.020 0.002 PHE G 163 TYR 0.011 0.001 TYR I 146 ARG 0.009 0.001 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.02649 ( 379) hydrogen bonds : angle 5.28764 ( 1131) covalent geometry : bond 0.00315 ( 8436) covalent geometry : angle 0.80247 (11448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9729 (t80) cc_final: 0.9343 (t80) REVERT: G 163 PHE cc_start: 0.9265 (p90) cc_final: 0.8954 (p90) REVERT: A 146 TYR cc_start: 0.9386 (t80) cc_final: 0.8946 (t80) REVERT: A 159 MET cc_start: 0.9643 (ptp) cc_final: 0.9321 (ptp) REVERT: A 163 PHE cc_start: 0.9541 (m-80) cc_final: 0.9157 (m-80) REVERT: B 141 LEU cc_start: 0.8562 (pp) cc_final: 0.8267 (pp) REVERT: B 146 TYR cc_start: 0.9773 (t80) cc_final: 0.9465 (t80) REVERT: B 160 ARG cc_start: 0.9567 (ptp-110) cc_final: 0.9217 (ptp-170) REVERT: B 161 LYS cc_start: 0.9908 (tppt) cc_final: 0.9585 (tptm) REVERT: B 165 PHE cc_start: 0.9688 (m-10) cc_final: 0.9291 (m-80) REVERT: C 133 LEU cc_start: 0.9890 (mt) cc_final: 0.9568 (tp) REVERT: C 134 ASP cc_start: 0.9320 (t0) cc_final: 0.8999 (p0) REVERT: C 137 TYR cc_start: 0.9553 (t80) cc_final: 0.9252 (t80) REVERT: C 141 LEU cc_start: 0.8839 (tp) cc_final: 0.8244 (tt) REVERT: C 163 PHE cc_start: 0.9489 (t80) cc_final: 0.9167 (t80) REVERT: D 141 LEU cc_start: 0.9186 (mt) cc_final: 0.8920 (mt) REVERT: D 146 TYR cc_start: 0.9731 (t80) cc_final: 0.9370 (t80) REVERT: D 161 LYS cc_start: 0.9866 (tppt) cc_final: 0.9630 (tptp) REVERT: D 192 LEU cc_start: 0.9586 (mm) cc_final: 0.9042 (tp) REVERT: E 160 ARG cc_start: 0.9716 (ptp90) cc_final: 0.9284 (ptp90) REVERT: E 163 PHE cc_start: 0.9618 (m-80) cc_final: 0.9333 (m-80) REVERT: F 141 LEU cc_start: 0.9439 (mm) cc_final: 0.9167 (tp) REVERT: F 146 TYR cc_start: 0.9666 (t80) cc_final: 0.8875 (t80) REVERT: H 130 GLU cc_start: 0.9578 (pm20) cc_final: 0.9268 (pm20) REVERT: H 146 TYR cc_start: 0.9565 (t80) cc_final: 0.9201 (t80) REVERT: H 163 PHE cc_start: 0.9642 (m-80) cc_final: 0.9077 (m-80) REVERT: I 125 ARG cc_start: 0.9282 (mtt180) cc_final: 0.9026 (tpt170) REVERT: I 163 PHE cc_start: 0.9796 (m-80) cc_final: 0.9384 (m-80) REVERT: J 163 PHE cc_start: 0.9767 (m-80) cc_final: 0.9155 (m-80) REVERT: J 165 PHE cc_start: 0.9770 (m-10) cc_final: 0.9449 (m-80) REVERT: K 141 LEU cc_start: 0.9477 (mm) cc_final: 0.9226 (mt) REVERT: K 161 LYS cc_start: 0.9870 (tppt) cc_final: 0.9584 (ptpt) REVERT: K 163 PHE cc_start: 0.9528 (m-80) cc_final: 0.9241 (m-80) REVERT: K 192 LEU cc_start: 0.9469 (mm) cc_final: 0.9048 (tp) REVERT: L 146 TYR cc_start: 0.9587 (t80) cc_final: 0.9006 (t80) REVERT: L 161 LYS cc_start: 0.9899 (tppt) cc_final: 0.9556 (tptp) REVERT: L 163 PHE cc_start: 0.9576 (m-80) cc_final: 0.9290 (m-80) REVERT: L 182 ARG cc_start: 0.9554 (ptp-110) cc_final: 0.9200 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2688 time to fit residues: 96.6050 Evaluate side-chains 192 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN B 179 GLN D 145 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN F 185 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN K 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.025835 restraints weight = 72019.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.026985 restraints weight = 46598.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.027824 restraints weight = 34920.176| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.9100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8436 Z= 0.142 Angle : 0.852 9.120 11448 Z= 0.423 Chirality : 0.048 0.155 1260 Planarity : 0.004 0.057 1452 Dihedral : 5.054 24.705 1092 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % 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: -1.60 (0.27), residues: 972 helix: -0.71 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.52 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 169 HIS 0.005 0.001 HIS I 118 PHE 0.019 0.002 PHE G 163 TYR 0.011 0.001 TYR I 146 ARG 0.015 0.001 ARG J 160 Details of bonding type rmsd hydrogen bonds : bond 0.02743 ( 379) hydrogen bonds : angle 5.27531 ( 1131) covalent geometry : bond 0.00296 ( 8436) covalent geometry : angle 0.85175 (11448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9716 (t80) cc_final: 0.9319 (t80) REVERT: G 163 PHE cc_start: 0.9272 (p90) cc_final: 0.8939 (p90) REVERT: A 146 TYR cc_start: 0.9386 (t80) cc_final: 0.8922 (t80) REVERT: A 159 MET cc_start: 0.9654 (ptp) cc_final: 0.9286 (ptp) REVERT: A 163 PHE cc_start: 0.9587 (m-80) cc_final: 0.9218 (m-80) REVERT: C 119 ARG cc_start: 0.8334 (tpt170) cc_final: 0.8131 (tpt170) REVERT: C 133 LEU cc_start: 0.9866 (mt) cc_final: 0.9432 (tp) REVERT: C 134 ASP cc_start: 0.9364 (t0) cc_final: 0.9032 (p0) REVERT: C 150 ARG cc_start: 0.9663 (ttm110) cc_final: 0.8818 (mmm-85) REVERT: C 163 PHE cc_start: 0.9469 (t80) cc_final: 0.9024 (t80) REVERT: D 141 LEU cc_start: 0.9175 (mt) cc_final: 0.8909 (mt) REVERT: D 146 TYR cc_start: 0.9654 (t80) cc_final: 0.9354 (t80) REVERT: D 192 LEU cc_start: 0.9563 (mm) cc_final: 0.9000 (tp) REVERT: E 163 PHE cc_start: 0.9701 (m-80) cc_final: 0.9213 (m-80) REVERT: F 141 LEU cc_start: 0.9420 (mm) cc_final: 0.9174 (tp) REVERT: F 146 TYR cc_start: 0.9683 (t80) cc_final: 0.8873 (t80) REVERT: F 163 PHE cc_start: 0.9605 (m-80) cc_final: 0.8916 (m-80) REVERT: H 130 GLU cc_start: 0.9476 (pm20) cc_final: 0.9244 (pm20) REVERT: H 146 TYR cc_start: 0.9580 (t80) cc_final: 0.9197 (t80) REVERT: H 161 LYS cc_start: 0.8929 (ptpt) cc_final: 0.8536 (pttt) REVERT: H 163 PHE cc_start: 0.9668 (m-80) cc_final: 0.9184 (m-80) REVERT: H 182 ARG cc_start: 0.9456 (ptp-110) cc_final: 0.9166 (ptp-110) REVERT: I 125 ARG cc_start: 0.9283 (mtt180) cc_final: 0.9076 (tpt170) REVERT: I 163 PHE cc_start: 0.9802 (m-80) cc_final: 0.9356 (m-80) REVERT: J 143 ASP cc_start: 0.9853 (p0) cc_final: 0.9607 (t0) REVERT: J 163 PHE cc_start: 0.9778 (m-80) cc_final: 0.9106 (m-80) REVERT: K 141 LEU cc_start: 0.9460 (mm) cc_final: 0.9195 (mt) REVERT: K 152 GLU cc_start: 0.9581 (mp0) cc_final: 0.9361 (mp0) REVERT: K 161 LYS cc_start: 0.9885 (tppt) cc_final: 0.9539 (ptpp) REVERT: K 192 LEU cc_start: 0.9437 (mm) cc_final: 0.8975 (tp) REVERT: L 146 TYR cc_start: 0.9598 (t80) cc_final: 0.9012 (t80) REVERT: L 161 LYS cc_start: 0.9907 (tppt) cc_final: 0.9589 (tptp) REVERT: L 163 PHE cc_start: 0.9623 (m-80) cc_final: 0.9333 (m-80) REVERT: L 182 ARG cc_start: 0.9543 (ptp-110) cc_final: 0.9211 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.2580 time to fit residues: 93.8148 Evaluate side-chains 196 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 64 optimal weight: 50.0000 chunk 5 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 8 optimal weight: 40.0000 chunk 3 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN C 179 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN J 179 GLN K 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.035567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.026046 restraints weight = 70788.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.027028 restraints weight = 50750.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027769 restraints weight = 40048.062| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.9396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8436 Z= 0.161 Angle : 0.879 10.384 11448 Z= 0.446 Chirality : 0.049 0.184 1260 Planarity : 0.005 0.048 1452 Dihedral : 5.283 24.437 1092 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.26), residues: 972 helix: -0.83 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.46 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 169 HIS 0.009 0.001 HIS C 118 PHE 0.018 0.002 PHE G 163 TYR 0.012 0.001 TYR C 146 ARG 0.013 0.001 ARG J 160 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 379) hydrogen bonds : angle 5.59234 ( 1131) covalent geometry : bond 0.00343 ( 8436) covalent geometry : angle 0.87893 (11448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9713 (t80) cc_final: 0.9272 (t80) REVERT: G 163 PHE cc_start: 0.9281 (p90) cc_final: 0.8756 (p90) REVERT: A 146 TYR cc_start: 0.9405 (t80) cc_final: 0.9012 (t80) REVERT: A 159 MET cc_start: 0.9641 (ptp) cc_final: 0.9256 (ptp) REVERT: A 163 PHE cc_start: 0.9580 (m-80) cc_final: 0.9187 (m-80) REVERT: B 161 LYS cc_start: 0.9923 (tppt) cc_final: 0.9612 (tptm) REVERT: B 183 GLU cc_start: 0.9158 (pm20) cc_final: 0.8632 (pm20) REVERT: C 134 ASP cc_start: 0.9340 (t0) cc_final: 0.9064 (p0) REVERT: C 163 PHE cc_start: 0.9456 (t80) cc_final: 0.9122 (t80) REVERT: D 141 LEU cc_start: 0.9284 (mt) cc_final: 0.9019 (mt) REVERT: D 146 TYR cc_start: 0.9693 (t80) cc_final: 0.9417 (t80) REVERT: D 192 LEU cc_start: 0.9556 (mm) cc_final: 0.9019 (tp) REVERT: E 163 PHE cc_start: 0.9677 (m-80) cc_final: 0.9167 (m-80) REVERT: F 141 LEU cc_start: 0.9493 (mm) cc_final: 0.9233 (tp) REVERT: F 146 TYR cc_start: 0.9701 (t80) cc_final: 0.9226 (t80) REVERT: F 150 ARG cc_start: 0.8999 (ptp90) cc_final: 0.8728 (mtt90) REVERT: F 163 PHE cc_start: 0.9604 (m-80) cc_final: 0.9178 (m-80) REVERT: H 130 GLU cc_start: 0.9482 (pm20) cc_final: 0.9127 (pm20) REVERT: H 133 LEU cc_start: 0.9858 (mp) cc_final: 0.9658 (mp) REVERT: H 146 TYR cc_start: 0.9631 (t80) cc_final: 0.9263 (t80) REVERT: H 161 LYS cc_start: 0.8808 (ptpt) cc_final: 0.8533 (pttt) REVERT: I 125 ARG cc_start: 0.9351 (mtt180) cc_final: 0.9109 (tpt170) REVERT: I 163 PHE cc_start: 0.9803 (m-80) cc_final: 0.9499 (m-10) REVERT: J 143 ASP cc_start: 0.9901 (p0) cc_final: 0.9643 (t0) REVERT: J 163 PHE cc_start: 0.9793 (m-80) cc_final: 0.9344 (m-80) REVERT: K 141 LEU cc_start: 0.9433 (mm) cc_final: 0.9187 (mt) REVERT: K 152 GLU cc_start: 0.9588 (mp0) cc_final: 0.9271 (mp0) REVERT: K 161 LYS cc_start: 0.9900 (tppt) cc_final: 0.9573 (ptpp) REVERT: K 163 PHE cc_start: 0.9573 (m-80) cc_final: 0.9238 (m-80) REVERT: K 192 LEU cc_start: 0.9457 (mm) cc_final: 0.9036 (tp) REVERT: L 134 ASP cc_start: 0.9232 (m-30) cc_final: 0.8913 (m-30) REVERT: L 146 TYR cc_start: 0.9614 (t80) cc_final: 0.9087 (t80) REVERT: L 161 LYS cc_start: 0.9917 (tppt) cc_final: 0.9622 (tptp) REVERT: L 163 PHE cc_start: 0.9637 (m-80) cc_final: 0.9344 (m-80) REVERT: L 182 ARG cc_start: 0.9635 (ptp-110) cc_final: 0.9351 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2685 time to fit residues: 91.5928 Evaluate side-chains 185 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 40.0000 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.0470 chunk 47 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 76 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 30.0000 chunk 13 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 0.0060 overall best weight: 0.9974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN J 145 GLN K 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.037587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.027291 restraints weight = 68676.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.028399 restraints weight = 47740.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.029247 restraints weight = 36963.386| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.9555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8436 Z= 0.153 Angle : 0.920 11.066 11448 Z= 0.456 Chirality : 0.049 0.174 1260 Planarity : 0.005 0.074 1452 Dihedral : 5.162 24.682 1092 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: -1.74 (0.26), residues: 972 helix: -0.81 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 169 HIS 0.006 0.001 HIS C 118 PHE 0.024 0.001 PHE G 163 TYR 0.027 0.001 TYR C 146 ARG 0.012 0.001 ARG I 150 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 379) hydrogen bonds : angle 5.35478 ( 1131) covalent geometry : bond 0.00314 ( 8436) covalent geometry : angle 0.92025 (11448) =============================================================================== Job complete usr+sys time: 3541.70 seconds wall clock time: 64 minutes 13.55 seconds (3853.55 seconds total)