Starting phenix.real_space_refine on Thu Sep 18 07:27:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k99_9947/09_2025/6k99_9947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k99_9947/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6k99_9947/09_2025/6k99_9947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k99_9947/09_2025/6k99_9947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k99_9947/09_2025/6k99_9947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k99_9947/09_2025/6k99_9947.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.82, per 1000 atoms: 0.22 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: 0.73 Conformation dependent library (CDL) restraints added in 316.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.21 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: 0.92 Time building geometry restraints manager: 0.90 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: 0.00 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.990 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.700 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG E 160 TYR 0.017 0.002 TYR F 187 PHE 0.014 0.002 PHE D 114 TRP 0.012 0.002 TRP J 169 HIS 0.005 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8436) covalent geometry : angle 0.71531 (11448) hydrogen bonds : bond 0.16704 ( 379) hydrogen bonds : angle 6.95098 ( 1131) *********************** 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 : 0.350 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ILE cc_start: 0.9541 (mt) cc_final: 0.9275 (pt) REVERT: G 163 PHE cc_start: 0.8529 (m-80) cc_final: 0.7415 (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: 0.9191 (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: 0.9012 (p0) REVERT: B 174 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8019 (ptpp) REVERT: B 178 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9058 (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: 0.8787 (ptt180) REVERT: C 146 TYR cc_start: 0.8751 (t80) cc_final: 0.8467 (t80) REVERT: C 191 ASP cc_start: 0.9826 (t70) cc_final: 0.9518 (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: 0.8740 (t80) REVERT: D 149 VAL cc_start: 0.9656 (t) cc_final: 0.9193 (m) REVERT: D 161 LYS cc_start: 0.9631 (tppt) cc_final: 0.9318 (tptp) REVERT: D 188 LEU cc_start: 0.9121 (tp) cc_final: 0.8728 (mt) REVERT: D 191 ASP cc_start: 0.9687 (t70) cc_final: 0.9480 (m-30) REVERT: D 192 LEU cc_start: 0.9333 (mp) cc_final: 0.8825 (tp) REVERT: E 125 ARG cc_start: 0.9452 (mtt180) cc_final: 0.9172 (tpt170) REVERT: E 154 THR cc_start: 0.8901 (p) cc_final: 0.8650 (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: 0.8264 (t80) REVERT: F 155 ASN cc_start: 0.8779 (t0) cc_final: 0.8089 (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: 0.8489 (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: 0.9480 (p) REVERT: I 114 PHE cc_start: 0.9615 (t80) cc_final: 0.9333 (t80) REVERT: I 119 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8151 (ttp80) REVERT: I 125 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8490 (tpt170) REVERT: I 175 ASP cc_start: 0.9563 (m-30) cc_final: 0.9299 (p0) REVERT: I 192 LEU cc_start: 0.8784 (mp) cc_final: 0.8267 (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: 0.8837 (m) REVERT: J 161 LYS cc_start: 0.9638 (tppt) cc_final: 0.9409 (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: 0.1322 time to fit residues: 88.3966 Evaluate side-chains 295 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.6942 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 145 GLN E 145 GLN F 118 HIS I 145 GLN ** J 145 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 = 0.2804 r_free = 0.2804 target = 0.038245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.027311 restraints weight = 62303.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028337 restraints weight = 44331.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.029098 restraints weight = 35074.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.029651 restraints weight = 29499.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.030049 restraints weight = 25890.463| |-----------------------------------------------------------------------------| r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4893 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= 0.135 Angle : 0.773 8.823 11448 Z= 0.375 Chirality : 0.044 0.132 1260 Planarity : 0.005 0.036 1452 Dihedral : 4.927 15.042 1092 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.24), residues: 972 helix: -1.32 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -1.90 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 150 TYR 0.013 0.002 TYR F 146 PHE 0.023 0.002 PHE J 165 TRP 0.031 0.001 TRP E 169 HIS 0.003 0.001 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8436) covalent geometry : angle 0.77332 (11448) hydrogen bonds : bond 0.03125 ( 379) hydrogen bonds : angle 4.89640 ( 1131) *********************** 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 432 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 0.333 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: G 115 ILE cc_start: 0.9668 (mt) cc_final: 0.9437 (mp) REVERT: G 146 TYR cc_start: 0.9690 (t80) cc_final: 0.8865 (t80) REVERT: G 163 PHE cc_start: 0.9816 (m-80) cc_final: 0.9198 (t80) REVERT: A 141 LEU cc_start: 0.8947 (pp) cc_final: 0.8581 (pp) REVERT: A 146 TYR cc_start: 0.9539 (t80) cc_final: 0.9051 (t80) REVERT: A 152 GLU cc_start: 0.8857 (mp0) cc_final: 0.8635 (mp0) REVERT: A 161 LYS cc_start: 0.9743 (mmtt) cc_final: 0.9493 (mtmm) REVERT: A 163 PHE cc_start: 0.9692 (m-80) cc_final: 0.8873 (m-10) REVERT: A 178 LEU cc_start: 0.9609 (pp) cc_final: 0.9095 (pp) REVERT: A 182 ARG cc_start: 0.9537 (ptp-110) cc_final: 0.9213 (ptp-110) REVERT: B 112 LEU cc_start: 0.9561 (tp) cc_final: 0.9102 (pt) REVERT: B 146 TYR cc_start: 0.9584 (t80) cc_final: 0.9370 (t80) REVERT: B 161 LYS cc_start: 0.9817 (tppt) cc_final: 0.9314 (tptm) REVERT: B 165 PHE cc_start: 0.9718 (m-10) cc_final: 0.9269 (m-80) REVERT: C 137 TYR cc_start: 0.9729 (t80) cc_final: 0.9424 (t80) REVERT: C 141 LEU cc_start: 0.8600 (tp) cc_final: 0.7588 (tp) REVERT: C 146 TYR cc_start: 0.9670 (t80) cc_final: 0.8617 (t80) REVERT: C 161 LYS cc_start: 0.9049 (ptmt) cc_final: 0.8830 (pttt) REVERT: C 191 ASP cc_start: 0.9697 (t70) cc_final: 0.9439 (m-30) REVERT: D 141 LEU cc_start: 0.9339 (mt) cc_final: 0.9070 (mt) REVERT: D 146 TYR cc_start: 0.9621 (t80) cc_final: 0.9281 (t80) REVERT: D 161 LYS cc_start: 0.9780 (tppt) cc_final: 0.9520 (tppt) REVERT: D 185 GLN cc_start: 0.9370 (mm110) cc_final: 0.9019 (mm110) REVERT: D 188 LEU cc_start: 0.9400 (tp) cc_final: 0.9089 (tp) REVERT: E 139 LYS cc_start: 0.9421 (mppt) cc_final: 0.9183 (mptt) REVERT: E 175 ASP cc_start: 0.9724 (p0) cc_final: 0.9496 (p0) REVERT: F 112 LEU cc_start: 0.9492 (tp) cc_final: 0.9248 (pt) REVERT: F 145 GLN cc_start: 0.9186 (mt0) cc_final: 0.8965 (pt0) REVERT: F 146 TYR cc_start: 0.8881 (t80) cc_final: 0.8161 (t80) REVERT: F 163 PHE cc_start: 0.9752 (m-80) cc_final: 0.9067 (m-80) REVERT: H 130 GLU cc_start: 0.9555 (pm20) cc_final: 0.9118 (pm20) REVERT: H 137 TYR cc_start: 0.9496 (t80) cc_final: 0.9029 (t80) REVERT: H 141 LEU cc_start: 0.9706 (mm) cc_final: 0.9227 (tp) REVERT: H 143 ASP cc_start: 0.9762 (m-30) cc_final: 0.9519 (p0) REVERT: H 144 GLU cc_start: 0.9387 (pm20) cc_final: 0.9184 (pm20) REVERT: I 125 ARG cc_start: 0.9135 (mtt180) cc_final: 0.8755 (tpt170) REVERT: I 182 ARG cc_start: 0.9596 (ptp-110) cc_final: 0.9212 (ptp-110) REVERT: J 137 TYR cc_start: 0.9755 (t80) cc_final: 0.9502 (t80) REVERT: J 161 LYS cc_start: 0.9854 (tppt) cc_final: 0.9343 (ptmm) REVERT: J 163 PHE cc_start: 0.9397 (m-80) cc_final: 0.8900 (m-80) REVERT: J 165 PHE cc_start: 0.9818 (m-10) cc_final: 0.9608 (m-80) REVERT: K 122 LEU cc_start: 0.9829 (mt) cc_final: 0.9518 (pp) REVERT: K 125 ARG cc_start: 0.9253 (mtt180) cc_final: 0.8986 (tpt170) REVERT: K 165 PHE cc_start: 0.9734 (m-10) cc_final: 0.9468 (m-80) REVERT: K 192 LEU cc_start: 0.9347 (mm) cc_final: 0.9017 (tp) REVERT: L 141 LEU cc_start: 0.8672 (pp) cc_final: 0.8394 (pp) REVERT: L 144 GLU cc_start: 0.9710 (pm20) cc_final: 0.9394 (pm20) REVERT: L 146 TYR cc_start: 0.9717 (t80) cc_final: 0.9047 (t80) REVERT: L 161 LYS cc_start: 0.9873 (tppt) cc_final: 0.9305 (tptm) REVERT: L 165 PHE cc_start: 0.9660 (m-10) cc_final: 0.9392 (m-80) outliers start: 1 outliers final: 1 residues processed: 432 average time/residue: 0.1377 time to fit residues: 73.3135 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 40.0000 chunk 57 optimal weight: 50.0000 chunk 52 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 32 optimal weight: 40.0000 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.036190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.026400 restraints weight = 67487.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027390 restraints weight = 46486.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028158 restraints weight = 35977.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.028743 restraints weight = 29593.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029187 restraints weight = 25514.327| |-----------------------------------------------------------------------------| r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8436 Z= 0.166 Angle : 0.751 8.145 11448 Z= 0.379 Chirality : 0.044 0.132 1260 Planarity : 0.004 0.032 1452 Dihedral : 4.931 16.963 1092 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.25), residues: 972 helix: -0.95 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 119 TYR 0.015 0.001 TYR C 146 PHE 0.016 0.002 PHE L 165 TRP 0.025 0.001 TRP E 169 HIS 0.002 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8436) covalent geometry : angle 0.75093 (11448) hydrogen bonds : bond 0.02761 ( 379) hydrogen bonds : angle 5.10660 ( 1131) *********************** 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 369 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.385 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: G 150 ARG cc_start: 0.9076 (ptp90) cc_final: 0.8867 (mtm-85) REVERT: G 154 THR cc_start: 0.9688 (p) cc_final: 0.9427 (p) REVERT: A 159 MET cc_start: 0.9663 (ptp) cc_final: 0.9325 (ptp) REVERT: A 163 PHE cc_start: 0.9484 (m-80) cc_final: 0.9076 (m-80) REVERT: A 169 TRP cc_start: 0.9226 (m-10) cc_final: 0.8835 (m-10) REVERT: B 112 LEU cc_start: 0.9708 (tp) cc_final: 0.9336 (pt) REVERT: B 141 LEU cc_start: 0.8061 (pp) cc_final: 0.7838 (pp) REVERT: B 146 TYR cc_start: 0.9661 (t80) cc_final: 0.9229 (t80) REVERT: B 161 LYS cc_start: 0.9843 (tppt) cc_final: 0.9381 (tptm) REVERT: B 165 PHE cc_start: 0.9729 (m-10) cc_final: 0.9320 (m-80) REVERT: C 137 TYR cc_start: 0.9616 (t80) cc_final: 0.9315 (t80) REVERT: C 144 GLU cc_start: 0.9565 (pm20) cc_final: 0.9163 (pm20) REVERT: C 191 ASP cc_start: 0.9720 (t70) cc_final: 0.9426 (m-30) REVERT: D 141 LEU cc_start: 0.9333 (mt) cc_final: 0.9076 (mt) REVERT: D 146 TYR cc_start: 0.9700 (t80) cc_final: 0.9286 (t80) REVERT: D 161 LYS cc_start: 0.9847 (tppt) cc_final: 0.9541 (tppt) REVERT: E 130 GLU cc_start: 0.9602 (pm20) cc_final: 0.9272 (pm20) REVERT: E 150 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8682 (mtt180) REVERT: E 160 ARG cc_start: 0.9614 (ptp90) cc_final: 0.9093 (ptp-170) REVERT: F 141 LEU cc_start: 0.9208 (mt) cc_final: 0.8962 (tp) REVERT: F 145 GLN cc_start: 0.9444 (mt0) cc_final: 0.9237 (mt0) REVERT: F 146 TYR cc_start: 0.9376 (t80) cc_final: 0.8115 (t80) REVERT: F 161 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8260 (ptpp) REVERT: H 137 TYR cc_start: 0.9572 (t80) cc_final: 0.9148 (t80) REVERT: H 141 LEU cc_start: 0.9700 (mm) cc_final: 0.9192 (pp) REVERT: H 144 GLU cc_start: 0.9475 (pm20) cc_final: 0.9099 (pm20) REVERT: H 146 TYR cc_start: 0.9546 (t80) cc_final: 0.9007 (t80) REVERT: H 163 PHE cc_start: 0.9546 (m-80) cc_final: 0.9074 (m-80) REVERT: I 125 ARG cc_start: 0.9231 (mtt180) cc_final: 0.8860 (tpt170) REVERT: I 161 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7592 (pttm) REVERT: J 137 TYR cc_start: 0.9832 (t80) cc_final: 0.8970 (t80) REVERT: J 141 LEU cc_start: 0.8709 (pp) cc_final: 0.8380 (pp) REVERT: J 163 PHE cc_start: 0.9551 (m-80) cc_final: 0.8950 (m-80) REVERT: J 165 PHE cc_start: 0.9835 (m-10) cc_final: 0.9580 (m-80) REVERT: K 122 LEU cc_start: 0.9849 (mt) cc_final: 0.9580 (pp) REVERT: K 137 TYR cc_start: 0.9797 (t80) cc_final: 0.9511 (t80) REVERT: K 165 PHE cc_start: 0.9792 (m-10) cc_final: 0.9543 (m-80) REVERT: K 192 LEU cc_start: 0.9428 (mm) cc_final: 0.9226 (tp) REVERT: L 112 LEU cc_start: 0.9667 (tp) cc_final: 0.9435 (pt) REVERT: L 141 LEU cc_start: 0.8848 (pp) cc_final: 0.8400 (pp) REVERT: L 146 TYR cc_start: 0.9704 (t80) cc_final: 0.9093 (t80) REVERT: L 161 LYS cc_start: 0.9855 (tppt) cc_final: 0.9133 (tptm) REVERT: L 165 PHE cc_start: 0.9671 (m-10) cc_final: 0.9150 (m-80) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1310 time to fit residues: 59.9771 Evaluate side-chains 254 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 179 GLN A 117 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN L 147 GLN L 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.026749 restraints weight = 68484.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.027784 restraints weight = 47289.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.028567 restraints weight = 36217.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.029013 restraints weight = 30019.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.029511 restraints weight = 26382.486| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.7173 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= 0.137 Angle : 0.735 8.849 11448 Z= 0.367 Chirality : 0.044 0.156 1260 Planarity : 0.004 0.056 1452 Dihedral : 4.840 19.319 1092 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.26), residues: 972 helix: -0.91 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.62 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 160 TYR 0.022 0.001 TYR F 146 PHE 0.013 0.001 PHE G 163 TRP 0.014 0.001 TRP G 131 HIS 0.005 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8436) covalent geometry : angle 0.73456 (11448) hydrogen bonds : bond 0.02690 ( 379) hydrogen bonds : angle 5.02022 ( 1131) *********************** 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 355 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.359 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: G 146 TYR cc_start: 0.9609 (t80) cc_final: 0.9287 (t80) REVERT: G 160 ARG cc_start: 0.9774 (ptp-110) cc_final: 0.9156 (ptp90) REVERT: A 139 LYS cc_start: 0.9449 (mtmm) cc_final: 0.9109 (ptpp) REVERT: A 159 MET cc_start: 0.9652 (ptp) cc_final: 0.9376 (ptp) REVERT: A 163 PHE cc_start: 0.9579 (m-80) cc_final: 0.9065 (m-80) REVERT: B 125 ARG cc_start: 0.9148 (mtp180) cc_final: 0.8568 (mmm-85) REVERT: B 141 LEU cc_start: 0.8164 (pp) cc_final: 0.7873 (pp) REVERT: B 146 TYR cc_start: 0.9728 (t80) cc_final: 0.9331 (t80) REVERT: B 160 ARG cc_start: 0.9518 (ptp-110) cc_final: 0.9181 (ptp-110) REVERT: B 161 LYS cc_start: 0.9858 (tppt) cc_final: 0.9382 (tptm) REVERT: B 165 PHE cc_start: 0.9728 (m-10) cc_final: 0.9285 (m-80) REVERT: C 137 TYR cc_start: 0.9635 (t80) cc_final: 0.9325 (t80) REVERT: C 163 PHE cc_start: 0.9555 (t80) cc_final: 0.9268 (t80) REVERT: C 191 ASP cc_start: 0.9719 (t70) cc_final: 0.9373 (m-30) REVERT: D 141 LEU cc_start: 0.9247 (mt) cc_final: 0.8953 (mt) REVERT: D 146 TYR cc_start: 0.9697 (t80) cc_final: 0.9290 (t80) REVERT: D 192 LEU cc_start: 0.9655 (mm) cc_final: 0.9120 (tp) REVERT: E 150 ARG cc_start: 0.8982 (mtm-85) cc_final: 0.8649 (mtt180) REVERT: E 160 ARG cc_start: 0.9638 (ptp90) cc_final: 0.9090 (ptp-170) REVERT: F 146 TYR cc_start: 0.9343 (t80) cc_final: 0.8835 (t80) REVERT: F 161 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8245 (mttt) REVERT: H 137 TYR cc_start: 0.9661 (t80) cc_final: 0.9102 (t80) REVERT: H 141 LEU cc_start: 0.9638 (mm) cc_final: 0.9130 (tp) REVERT: H 163 PHE cc_start: 0.9599 (m-80) cc_final: 0.9098 (m-80) REVERT: I 122 LEU cc_start: 0.9807 (pp) cc_final: 0.9576 (pp) REVERT: I 125 ARG cc_start: 0.9284 (mtt180) cc_final: 0.8907 (tpt170) REVERT: I 163 PHE cc_start: 0.9182 (m-80) cc_final: 0.8546 (m-10) REVERT: J 141 LEU cc_start: 0.8632 (pp) cc_final: 0.7642 (pp) REVERT: J 146 TYR cc_start: 0.9591 (t80) cc_final: 0.8995 (t80) REVERT: J 163 PHE cc_start: 0.9629 (m-80) cc_final: 0.8987 (m-80) REVERT: J 165 PHE cc_start: 0.9833 (m-10) cc_final: 0.9599 (m-80) REVERT: K 122 LEU cc_start: 0.9826 (mt) cc_final: 0.9582 (pp) REVERT: K 137 TYR cc_start: 0.9759 (t80) cc_final: 0.9426 (t80) REVERT: K 152 GLU cc_start: 0.9591 (mp0) cc_final: 0.9314 (mp0) REVERT: K 161 LYS cc_start: 0.9762 (tppt) cc_final: 0.9378 (mtmm) REVERT: K 165 PHE cc_start: 0.9810 (m-10) cc_final: 0.9575 (m-80) REVERT: L 141 LEU cc_start: 0.8830 (pp) cc_final: 0.8525 (pp) REVERT: L 146 TYR cc_start: 0.9714 (t80) cc_final: 0.9009 (t80) REVERT: L 152 GLU cc_start: 0.9634 (mp0) cc_final: 0.9337 (mp0) REVERT: L 161 LYS cc_start: 0.9881 (tppt) cc_final: 0.9601 (ptpp) REVERT: L 163 PHE cc_start: 0.9457 (m-80) cc_final: 0.9070 (m-80) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.1314 time to fit residues: 58.2793 Evaluate side-chains 251 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 50.0000 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 40.0000 chunk 55 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 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 G 147 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN H 185 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN K 179 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 = 0.036077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.026403 restraints weight = 70549.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.027387 restraints weight = 48560.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.028136 restraints weight = 37715.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.028699 restraints weight = 31203.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.029123 restraints weight = 26950.359| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.7736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8436 Z= 0.153 Angle : 0.769 8.661 11448 Z= 0.385 Chirality : 0.046 0.144 1260 Planarity : 0.004 0.044 1452 Dihedral : 4.984 17.389 1092 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.26), residues: 972 helix: -0.88 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.39 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 160 TYR 0.027 0.001 TYR J 146 PHE 0.031 0.002 PHE G 163 TRP 0.016 0.001 TRP A 169 HIS 0.003 0.000 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8436) covalent geometry : angle 0.76897 (11448) hydrogen bonds : bond 0.02664 ( 379) hydrogen bonds : angle 5.31421 ( 1131) *********************** 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 328 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.361 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 146 TYR cc_start: 0.9480 (t80) cc_final: 0.9145 (t80) REVERT: G 163 PHE cc_start: 0.9303 (p90) cc_final: 0.9014 (p90) REVERT: A 125 ARG cc_start: 0.9222 (mmp80) cc_final: 0.8968 (mmp80) REVERT: A 139 LYS cc_start: 0.9441 (mtmm) cc_final: 0.9142 (ptpp) REVERT: A 149 VAL cc_start: 0.9727 (m) cc_final: 0.9511 (m) REVERT: A 152 GLU cc_start: 0.9187 (mp0) cc_final: 0.8929 (mp0) REVERT: A 161 LYS cc_start: 0.9793 (mmtt) cc_final: 0.9512 (mtmm) REVERT: A 163 PHE cc_start: 0.9656 (m-80) cc_final: 0.9174 (m-80) REVERT: B 141 LEU cc_start: 0.8513 (pp) cc_final: 0.8266 (pp) REVERT: B 146 TYR cc_start: 0.9762 (t80) cc_final: 0.9373 (t80) REVERT: B 161 LYS cc_start: 0.9879 (tppt) cc_final: 0.9430 (tptm) REVERT: B 165 PHE cc_start: 0.9714 (m-10) cc_final: 0.9272 (m-80) REVERT: C 146 TYR cc_start: 0.9345 (t80) cc_final: 0.8832 (t80) REVERT: C 158 LYS cc_start: 0.9701 (mttt) cc_final: 0.9492 (mttt) REVERT: C 163 PHE cc_start: 0.9600 (t80) cc_final: 0.9381 (t80) REVERT: C 179 GLN cc_start: 0.9716 (mm110) cc_final: 0.9499 (mm-40) REVERT: C 191 ASP cc_start: 0.9732 (t70) cc_final: 0.9380 (m-30) REVERT: D 141 LEU cc_start: 0.9243 (mt) cc_final: 0.8960 (mt) REVERT: D 146 TYR cc_start: 0.9719 (t80) cc_final: 0.9336 (t80) REVERT: D 161 LYS cc_start: 0.9886 (tppt) cc_final: 0.9608 (tppt) REVERT: D 192 LEU cc_start: 0.9654 (mm) cc_final: 0.9140 (tp) REVERT: E 150 ARG cc_start: 0.9042 (mtm-85) cc_final: 0.8730 (mtt180) REVERT: F 146 TYR cc_start: 0.9432 (t80) cc_final: 0.8794 (t80) REVERT: F 158 LYS cc_start: 0.9849 (mttt) cc_final: 0.9595 (mttt) REVERT: H 141 LEU cc_start: 0.9623 (mm) cc_final: 0.9177 (tp) REVERT: H 163 PHE cc_start: 0.9664 (m-80) cc_final: 0.9181 (m-80) REVERT: I 125 ARG cc_start: 0.9332 (mtt180) cc_final: 0.8940 (tpt170) REVERT: J 163 PHE cc_start: 0.9676 (m-80) cc_final: 0.9079 (m-80) REVERT: J 165 PHE cc_start: 0.9809 (m-10) cc_final: 0.9607 (m-80) REVERT: K 122 LEU cc_start: 0.9825 (mt) cc_final: 0.9441 (pp) REVERT: K 137 TYR cc_start: 0.9774 (t80) cc_final: 0.9364 (t80) REVERT: K 165 PHE cc_start: 0.9828 (m-10) cc_final: 0.9580 (m-80) REVERT: K 188 LEU cc_start: 0.9403 (tp) cc_final: 0.9195 (mt) REVERT: L 134 ASP cc_start: 0.9182 (m-30) cc_final: 0.8979 (m-30) REVERT: L 146 TYR cc_start: 0.9691 (t80) cc_final: 0.9155 (t80) REVERT: L 161 LYS cc_start: 0.9920 (tppt) cc_final: 0.9483 (tttm) REVERT: L 163 PHE cc_start: 0.9477 (m-80) cc_final: 0.9091 (m-80) REVERT: L 182 ARG cc_start: 0.9470 (ptp-110) cc_final: 0.9236 (ptp-110) outliers start: 1 outliers final: 1 residues processed: 327 average time/residue: 0.1338 time to fit residues: 54.5870 Evaluate side-chains 230 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.027326 restraints weight = 69688.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.028353 restraints weight = 47670.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.029142 restraints weight = 36841.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.029739 restraints weight = 30240.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.030167 restraints weight = 26030.202| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.8084 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= 0.126 Angle : 0.776 8.174 11448 Z= 0.383 Chirality : 0.046 0.148 1260 Planarity : 0.004 0.025 1452 Dihedral : 4.882 17.975 1092 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.34 % Allowed : 2.70 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.26), residues: 972 helix: -0.74 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 182 TYR 0.012 0.001 TYR J 146 PHE 0.039 0.002 PHE G 163 TRP 0.009 0.001 TRP G 131 HIS 0.003 0.000 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8436) covalent geometry : angle 0.77554 (11448) hydrogen bonds : bond 0.02579 ( 379) hydrogen bonds : angle 5.13400 ( 1131) *********************** 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 341 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 338 time to evaluate : 0.349 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: G 169 TRP cc_start: 0.9502 (m-10) cc_final: 0.8627 (m-10) REVERT: A 125 ARG cc_start: 0.9161 (mmp80) cc_final: 0.8870 (mmm-85) REVERT: A 146 TYR cc_start: 0.9628 (t80) cc_final: 0.9316 (t80) REVERT: A 163 PHE cc_start: 0.9675 (m-80) cc_final: 0.9197 (m-80) REVERT: B 141 LEU cc_start: 0.8439 (pp) cc_final: 0.8104 (pp) REVERT: B 146 TYR cc_start: 0.9790 (t80) cc_final: 0.9446 (t80) REVERT: B 161 LYS cc_start: 0.9884 (tppt) cc_final: 0.9549 (tptm) REVERT: B 165 PHE cc_start: 0.9699 (m-10) cc_final: 0.9372 (m-80) REVERT: C 146 TYR cc_start: 0.9348 (t80) cc_final: 0.8804 (t80) REVERT: C 163 PHE cc_start: 0.9628 (t80) cc_final: 0.9387 (t80) REVERT: C 179 GLN cc_start: 0.9719 (mm110) cc_final: 0.9474 (mm-40) REVERT: C 191 ASP cc_start: 0.9723 (t70) cc_final: 0.9357 (m-30) REVERT: D 141 LEU cc_start: 0.9180 (mt) cc_final: 0.8878 (mt) REVERT: D 146 TYR cc_start: 0.9722 (t80) cc_final: 0.9295 (t80) REVERT: D 161 LYS cc_start: 0.9870 (tppt) cc_final: 0.9626 (tppt) REVERT: D 192 LEU cc_start: 0.9602 (mm) cc_final: 0.9075 (tp) REVERT: F 141 LEU cc_start: 0.9205 (mt) cc_final: 0.8984 (mt) REVERT: F 146 TYR cc_start: 0.9459 (t80) cc_final: 0.8801 (t80) REVERT: F 161 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8174 (mttt) REVERT: H 141 LEU cc_start: 0.9571 (mm) cc_final: 0.9130 (tp) REVERT: H 161 LYS cc_start: 0.9023 (ptpt) cc_final: 0.8792 (pttt) REVERT: H 163 PHE cc_start: 0.9654 (m-80) cc_final: 0.9188 (m-80) REVERT: I 125 ARG cc_start: 0.9345 (mtt180) cc_final: 0.8906 (tpt170) REVERT: I 159 MET cc_start: 0.9710 (ptm) cc_final: 0.9430 (ppp) REVERT: J 163 PHE cc_start: 0.9728 (m-80) cc_final: 0.9140 (m-80) REVERT: J 165 PHE cc_start: 0.9837 (m-10) cc_final: 0.9601 (m-80) REVERT: K 122 LEU cc_start: 0.9802 (mt) cc_final: 0.9570 (pp) REVERT: K 137 TYR cc_start: 0.9653 (t80) cc_final: 0.9317 (t80) REVERT: K 161 LYS cc_start: 0.9806 (tppt) cc_final: 0.9463 (mtmm) REVERT: K 188 LEU cc_start: 0.9423 (tp) cc_final: 0.9196 (mt) REVERT: L 145 GLN cc_start: 0.9816 (mt0) cc_final: 0.9603 (mt0) REVERT: L 146 TYR cc_start: 0.9708 (t80) cc_final: 0.9174 (t80) REVERT: L 152 GLU cc_start: 0.9646 (mp0) cc_final: 0.9388 (mp0) REVERT: L 161 LYS cc_start: 0.9922 (tppt) cc_final: 0.9641 (ptpp) REVERT: L 163 PHE cc_start: 0.9560 (m-80) cc_final: 0.9138 (m-80) REVERT: L 182 ARG cc_start: 0.9479 (ptp-110) cc_final: 0.9220 (ptp-110) outliers start: 3 outliers final: 0 residues processed: 338 average time/residue: 0.1331 time to fit residues: 55.8485 Evaluate side-chains 239 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 16 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 50.0000 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 GLN K 145 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.036585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.026714 restraints weight = 69799.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.027759 restraints weight = 47497.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.028552 restraints weight = 36557.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.029128 restraints weight = 29972.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.029567 restraints weight = 25830.969| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.8358 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= 0.130 Angle : 0.815 10.106 11448 Z= 0.401 Chirality : 0.047 0.189 1260 Planarity : 0.004 0.070 1452 Dihedral : 4.991 22.099 1092 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.26), residues: 972 helix: -0.71 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -1.48 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 160 TYR 0.010 0.001 TYR F 146 PHE 0.015 0.001 PHE G 163 TRP 0.010 0.001 TRP G 131 HIS 0.002 0.000 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8436) covalent geometry : angle 0.81502 (11448) hydrogen bonds : bond 0.02603 ( 379) hydrogen bonds : angle 5.23284 ( 1131) *********************** 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 315 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.340 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: G 146 TYR cc_start: 0.9660 (t80) cc_final: 0.9299 (t80) REVERT: G 159 MET cc_start: 0.9528 (ttt) cc_final: 0.8987 (ttm) REVERT: G 169 TRP cc_start: 0.9435 (m-10) cc_final: 0.8626 (m-10) REVERT: A 134 ASP cc_start: 0.9525 (t70) cc_final: 0.9010 (p0) REVERT: A 146 TYR cc_start: 0.9646 (t80) cc_final: 0.9156 (t80) REVERT: A 159 MET cc_start: 0.9555 (ptt) cc_final: 0.9089 (ptt) REVERT: A 163 PHE cc_start: 0.9677 (m-80) cc_final: 0.9055 (m-80) REVERT: A 183 GLU cc_start: 0.9132 (pm20) cc_final: 0.8714 (pm20) REVERT: B 141 LEU cc_start: 0.8531 (pp) cc_final: 0.8181 (pp) REVERT: B 146 TYR cc_start: 0.9783 (t80) cc_final: 0.9428 (t80) REVERT: B 161 LYS cc_start: 0.9906 (tppt) cc_final: 0.9584 (tptm) REVERT: B 165 PHE cc_start: 0.9711 (m-10) cc_final: 0.9343 (m-80) REVERT: C 125 ARG cc_start: 0.9279 (mtm-85) cc_final: 0.8596 (mtp85) REVERT: C 146 TYR cc_start: 0.9305 (t80) cc_final: 0.8828 (t80) REVERT: C 163 PHE cc_start: 0.9607 (t80) cc_final: 0.9386 (t80) REVERT: C 182 ARG cc_start: 0.9776 (mtm110) cc_final: 0.9419 (mtm-85) REVERT: C 191 ASP cc_start: 0.9735 (t70) cc_final: 0.9376 (m-30) REVERT: D 141 LEU cc_start: 0.9108 (mt) cc_final: 0.8838 (mt) REVERT: D 146 TYR cc_start: 0.9742 (t80) cc_final: 0.9319 (t80) REVERT: D 161 LYS cc_start: 0.9882 (tppt) cc_final: 0.9621 (tppt) REVERT: D 192 LEU cc_start: 0.9590 (mm) cc_final: 0.9063 (tp) REVERT: F 141 LEU cc_start: 0.9222 (mt) cc_final: 0.8989 (mt) REVERT: F 146 TYR cc_start: 0.9474 (t80) cc_final: 0.8819 (t80) REVERT: F 161 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8148 (mttt) REVERT: F 163 PHE cc_start: 0.9486 (m-80) cc_final: 0.8977 (m-80) REVERT: H 146 TYR cc_start: 0.9568 (t80) cc_final: 0.9226 (t80) REVERT: H 161 LYS cc_start: 0.8969 (ptpt) cc_final: 0.8697 (pttt) REVERT: H 163 PHE cc_start: 0.9650 (m-80) cc_final: 0.9160 (m-80) REVERT: I 125 ARG cc_start: 0.9363 (mtt180) cc_final: 0.8965 (tpt170) REVERT: I 159 MET cc_start: 0.9688 (ptm) cc_final: 0.9373 (ppp) REVERT: I 163 PHE cc_start: 0.9395 (m-80) cc_final: 0.9183 (m-10) REVERT: J 143 ASP cc_start: 0.9789 (m-30) cc_final: 0.9566 (p0) REVERT: J 144 GLU cc_start: 0.9544 (pm20) cc_final: 0.9310 (pm20) REVERT: J 163 PHE cc_start: 0.9741 (m-80) cc_final: 0.9132 (m-80) REVERT: J 165 PHE cc_start: 0.9816 (m-10) cc_final: 0.9594 (m-80) REVERT: K 122 LEU cc_start: 0.9841 (mt) cc_final: 0.9593 (mt) REVERT: K 133 LEU cc_start: 0.9838 (mp) cc_final: 0.9596 (mp) REVERT: K 158 LYS cc_start: 0.9576 (mttt) cc_final: 0.9371 (mttp) REVERT: K 163 PHE cc_start: 0.9827 (m-80) cc_final: 0.9285 (m-80) REVERT: K 165 PHE cc_start: 0.9835 (m-80) cc_final: 0.9623 (m-80) REVERT: K 188 LEU cc_start: 0.9415 (tp) cc_final: 0.9195 (mt) REVERT: K 192 LEU cc_start: 0.9167 (tp) cc_final: 0.8958 (tp) REVERT: L 141 LEU cc_start: 0.9082 (pp) cc_final: 0.8654 (pp) REVERT: L 146 TYR cc_start: 0.9714 (t80) cc_final: 0.9078 (t80) REVERT: L 152 GLU cc_start: 0.9654 (mp0) cc_final: 0.9449 (mp0) REVERT: L 161 LYS cc_start: 0.9928 (tppt) cc_final: 0.9637 (ptpp) REVERT: L 163 PHE cc_start: 0.9606 (m-80) cc_final: 0.9146 (m-80) REVERT: L 182 ARG cc_start: 0.9486 (ptp-110) cc_final: 0.9282 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.1377 time to fit residues: 53.9088 Evaluate side-chains 232 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 A 179 GLN B 179 GLN B 185 GLN C 145 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.034297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.024974 restraints weight = 72907.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.026012 restraints weight = 48671.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.026775 restraints weight = 36961.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.027323 restraints weight = 30191.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.027731 restraints weight = 25943.846| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.8836 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= 0.162 Angle : 0.835 9.395 11448 Z= 0.421 Chirality : 0.048 0.181 1260 Planarity : 0.005 0.070 1452 Dihedral : 5.144 22.692 1092 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.23 % Allowed : 2.48 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.26), residues: 972 helix: -0.92 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 160 TYR 0.014 0.001 TYR F 146 PHE 0.017 0.002 PHE D 163 TRP 0.009 0.001 TRP A 169 HIS 0.003 0.001 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8436) covalent geometry : angle 0.83493 (11448) hydrogen bonds : bond 0.02899 ( 379) hydrogen bonds : angle 5.60239 ( 1131) *********************** 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 291 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 0.360 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: G 146 TYR cc_start: 0.9482 (t80) cc_final: 0.9275 (t80) REVERT: G 159 MET cc_start: 0.9618 (ttt) cc_final: 0.9321 (ttm) REVERT: G 163 PHE cc_start: 0.9403 (p90) cc_final: 0.9158 (p90) REVERT: A 125 ARG cc_start: 0.9226 (mmp80) cc_final: 0.8957 (mmp80) REVERT: A 134 ASP cc_start: 0.9571 (t70) cc_final: 0.9137 (p0) REVERT: A 146 TYR cc_start: 0.9379 (t80) cc_final: 0.8984 (t80) REVERT: A 159 MET cc_start: 0.9656 (ptt) cc_final: 0.9229 (ptt) REVERT: A 163 PHE cc_start: 0.9700 (m-80) cc_final: 0.9047 (m-80) REVERT: A 179 GLN cc_start: 0.9773 (tp40) cc_final: 0.9505 (tp-100) REVERT: A 183 GLU cc_start: 0.8968 (pm20) cc_final: 0.8679 (pm20) REVERT: B 112 LEU cc_start: 0.9704 (tp) cc_final: 0.9353 (pt) REVERT: B 141 LEU cc_start: 0.8079 (pp) cc_final: 0.7656 (pp) REVERT: B 146 TYR cc_start: 0.9751 (t80) cc_final: 0.9272 (t80) REVERT: B 165 PHE cc_start: 0.9643 (m-10) cc_final: 0.9333 (m-80) REVERT: C 146 TYR cc_start: 0.9210 (t80) cc_final: 0.9000 (t80) REVERT: C 191 ASP cc_start: 0.9745 (t70) cc_final: 0.9381 (m-30) REVERT: D 141 LEU cc_start: 0.8947 (mt) cc_final: 0.8580 (mt) REVERT: D 146 TYR cc_start: 0.9702 (t80) cc_final: 0.9388 (t80) REVERT: D 161 LYS cc_start: 0.9848 (tppt) cc_final: 0.9540 (tptm) REVERT: D 182 ARG cc_start: 0.9748 (mtm110) cc_final: 0.9394 (ptp-110) REVERT: D 192 LEU cc_start: 0.9567 (mm) cc_final: 0.9074 (tp) REVERT: E 160 ARG cc_start: 0.9679 (ptp-170) cc_final: 0.9162 (ptp-170) REVERT: E 163 PHE cc_start: 0.9677 (m-10) cc_final: 0.9249 (m-80) REVERT: E 179 GLN cc_start: 0.9671 (mm-40) cc_final: 0.9445 (mm-40) REVERT: F 141 LEU cc_start: 0.9176 (mt) cc_final: 0.8972 (mt) REVERT: F 146 TYR cc_start: 0.9356 (t80) cc_final: 0.8653 (t80) REVERT: F 161 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8165 (mttt) REVERT: H 133 LEU cc_start: 0.9844 (mp) cc_final: 0.9635 (mp) REVERT: H 134 ASP cc_start: 0.9276 (m-30) cc_final: 0.9012 (m-30) REVERT: H 146 TYR cc_start: 0.9615 (t80) cc_final: 0.9318 (t80) REVERT: H 161 LYS cc_start: 0.8689 (ptpt) cc_final: 0.8216 (pttt) REVERT: I 125 ARG cc_start: 0.9411 (mtt180) cc_final: 0.9021 (tpt170) REVERT: I 159 MET cc_start: 0.9807 (ptm) cc_final: 0.9289 (ppp) REVERT: I 163 PHE cc_start: 0.9566 (m-80) cc_final: 0.9340 (m-80) REVERT: J 163 PHE cc_start: 0.9767 (m-80) cc_final: 0.9149 (m-80) REVERT: K 163 PHE cc_start: 0.9854 (m-80) cc_final: 0.9539 (m-80) REVERT: K 165 PHE cc_start: 0.9876 (m-80) cc_final: 0.9631 (m-80) REVERT: K 188 LEU cc_start: 0.9428 (tp) cc_final: 0.9193 (mt) REVERT: L 134 ASP cc_start: 0.9307 (m-30) cc_final: 0.9097 (m-30) REVERT: L 146 TYR cc_start: 0.9760 (t80) cc_final: 0.9222 (t80) REVERT: L 152 GLU cc_start: 0.9519 (mp0) cc_final: 0.9300 (mp0) REVERT: L 163 PHE cc_start: 0.9649 (m-80) cc_final: 0.9202 (m-80) outliers start: 2 outliers final: 0 residues processed: 291 average time/residue: 0.1367 time to fit residues: 49.3066 Evaluate side-chains 198 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 60 optimal weight: 0.0170 chunk 63 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.027113 restraints weight = 80511.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.028249 restraints weight = 54185.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029066 restraints weight = 41262.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029654 restraints weight = 33654.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.030099 restraints weight = 28811.365| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.9127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8436 Z= 0.143 Angle : 0.843 10.208 11448 Z= 0.418 Chirality : 0.048 0.160 1260 Planarity : 0.005 0.079 1452 Dihedral : 5.177 21.844 1092 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.27), residues: 972 helix: -0.81 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 160 TYR 0.051 0.001 TYR B 146 PHE 0.019 0.002 PHE D 163 TRP 0.008 0.001 TRP G 131 HIS 0.004 0.000 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8436) covalent geometry : angle 0.84293 (11448) hydrogen bonds : bond 0.02905 ( 379) hydrogen bonds : angle 5.43686 ( 1131) *********************** 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 283 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.334 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: G 146 TYR cc_start: 0.9458 (t80) cc_final: 0.9226 (t80) REVERT: G 159 MET cc_start: 0.9439 (ttt) cc_final: 0.9211 (ttm) REVERT: G 163 PHE cc_start: 0.9324 (p90) cc_final: 0.9086 (p90) REVERT: A 134 ASP cc_start: 0.9346 (t70) cc_final: 0.9026 (p0) REVERT: A 150 ARG cc_start: 0.9092 (ttp-110) cc_final: 0.8532 (mtp85) REVERT: A 159 MET cc_start: 0.9530 (ptt) cc_final: 0.9043 (ptt) REVERT: A 163 PHE cc_start: 0.9675 (m-80) cc_final: 0.9041 (m-80) REVERT: B 112 LEU cc_start: 0.9719 (tp) cc_final: 0.9419 (pt) REVERT: B 161 LYS cc_start: 0.9931 (tppt) cc_final: 0.9730 (tttp) REVERT: C 146 TYR cc_start: 0.9325 (t80) cc_final: 0.8895 (t80) REVERT: C 191 ASP cc_start: 0.9763 (t70) cc_final: 0.9413 (m-30) REVERT: D 141 LEU cc_start: 0.9184 (mt) cc_final: 0.8902 (mt) REVERT: D 146 TYR cc_start: 0.9735 (t80) cc_final: 0.9401 (t80) REVERT: D 161 LYS cc_start: 0.9870 (tppt) cc_final: 0.9654 (tptp) REVERT: D 163 PHE cc_start: 0.9739 (m-80) cc_final: 0.9133 (m-80) REVERT: E 163 PHE cc_start: 0.9607 (m-10) cc_final: 0.9203 (m-80) REVERT: F 141 LEU cc_start: 0.9340 (mt) cc_final: 0.9112 (mt) REVERT: F 146 TYR cc_start: 0.9450 (t80) cc_final: 0.8890 (t80) REVERT: F 161 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8170 (mttt) REVERT: H 146 TYR cc_start: 0.9511 (t80) cc_final: 0.9182 (t80) REVERT: H 161 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8555 (pttt) REVERT: I 125 ARG cc_start: 0.9285 (mtt180) cc_final: 0.8991 (tpt170) REVERT: I 159 MET cc_start: 0.9646 (ptm) cc_final: 0.9239 (ppp) REVERT: J 163 PHE cc_start: 0.9716 (m-80) cc_final: 0.9087 (m-80) REVERT: K 158 LYS cc_start: 0.9684 (mttt) cc_final: 0.9375 (mtmm) REVERT: K 163 PHE cc_start: 0.9829 (m-80) cc_final: 0.9416 (m-80) REVERT: K 165 PHE cc_start: 0.9824 (m-80) cc_final: 0.9574 (m-80) REVERT: L 146 TYR cc_start: 0.9593 (t80) cc_final: 0.9048 (t80) REVERT: L 163 PHE cc_start: 0.9600 (m-80) cc_final: 0.9169 (m-80) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.1257 time to fit residues: 44.4270 Evaluate side-chains 207 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 50.0000 chunk 75 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN D 145 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN H 179 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.2797 r_free = 0.2797 target = 0.034713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.025468 restraints weight = 72208.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.026520 restraints weight = 48336.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.027263 restraints weight = 36710.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.027813 restraints weight = 30080.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.028246 restraints weight = 25899.667| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.9397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8436 Z= 0.149 Angle : 0.869 10.066 11448 Z= 0.433 Chirality : 0.049 0.175 1260 Planarity : 0.005 0.083 1452 Dihedral : 5.207 23.379 1092 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.23 % Allowed : 1.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.26), residues: 972 helix: -0.94 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.37 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 160 TYR 0.027 0.001 TYR B 146 PHE 0.019 0.002 PHE D 163 TRP 0.010 0.001 TRP J 131 HIS 0.003 0.000 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8436) covalent geometry : angle 0.86858 (11448) hydrogen bonds : bond 0.02845 ( 379) hydrogen bonds : angle 5.53456 ( 1131) ********************** 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 271 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.346 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: G 146 TYR cc_start: 0.9508 (t80) cc_final: 0.9276 (t80) REVERT: A 125 ARG cc_start: 0.9194 (mmp80) cc_final: 0.8976 (mmp80) REVERT: A 134 ASP cc_start: 0.9580 (t70) cc_final: 0.9243 (p0) REVERT: A 150 ARG cc_start: 0.8971 (ttp-110) cc_final: 0.8401 (mtp85) REVERT: A 159 MET cc_start: 0.9655 (ptt) cc_final: 0.9275 (ptt) REVERT: A 163 PHE cc_start: 0.9724 (m-80) cc_final: 0.9068 (m-80) REVERT: B 112 LEU cc_start: 0.9726 (tp) cc_final: 0.9414 (pt) REVERT: C 146 TYR cc_start: 0.9405 (t80) cc_final: 0.8830 (t80) REVERT: C 163 PHE cc_start: 0.9680 (t80) cc_final: 0.9449 (t80) REVERT: C 191 ASP cc_start: 0.9764 (t70) cc_final: 0.9406 (m-30) REVERT: D 141 LEU cc_start: 0.9012 (mt) cc_final: 0.8687 (mt) REVERT: D 146 TYR cc_start: 0.9720 (t80) cc_final: 0.9370 (t80) REVERT: D 161 LYS cc_start: 0.9849 (tppt) cc_final: 0.9618 (tptp) REVERT: E 160 ARG cc_start: 0.9673 (ptp-170) cc_final: 0.9176 (ptp-170) REVERT: E 163 PHE cc_start: 0.9676 (m-10) cc_final: 0.9236 (m-80) REVERT: F 146 TYR cc_start: 0.9425 (t80) cc_final: 0.8959 (t80) REVERT: F 161 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8055 (mttt) REVERT: H 134 ASP cc_start: 0.9264 (m-30) cc_final: 0.9041 (m-30) REVERT: H 146 TYR cc_start: 0.9617 (t80) cc_final: 0.9271 (t80) REVERT: H 161 LYS cc_start: 0.8683 (ptpt) cc_final: 0.8299 (pttt) REVERT: I 125 ARG cc_start: 0.9415 (mtt180) cc_final: 0.9098 (tpt170) REVERT: I 159 MET cc_start: 0.9794 (ptm) cc_final: 0.9469 (ppp) REVERT: J 163 PHE cc_start: 0.9794 (m-80) cc_final: 0.9172 (m-80) REVERT: J 183 GLU cc_start: 0.8835 (pp20) cc_final: 0.8491 (pp20) REVERT: K 163 PHE cc_start: 0.9907 (m-80) cc_final: 0.9560 (m-80) REVERT: K 165 PHE cc_start: 0.9898 (m-80) cc_final: 0.9613 (m-80) REVERT: L 134 ASP cc_start: 0.9188 (m-30) cc_final: 0.8882 (m-30) REVERT: L 146 TYR cc_start: 0.9702 (t80) cc_final: 0.9216 (t80) REVERT: L 163 PHE cc_start: 0.9674 (m-80) cc_final: 0.9204 (m-80) outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.1278 time to fit residues: 43.8055 Evaluate side-chains 194 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 50.0000 chunk 58 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 40.0000 chunk 16 optimal weight: 40.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN D 145 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.2734 r_free = 0.2734 target = 0.034407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.025293 restraints weight = 73157.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.026213 restraints weight = 51943.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.026913 restraints weight = 40962.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.027456 restraints weight = 34210.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.027842 restraints weight = 29679.423| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.9688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8436 Z= 0.174 Angle : 0.874 11.704 11448 Z= 0.440 Chirality : 0.050 0.214 1260 Planarity : 0.005 0.057 1452 Dihedral : 5.282 23.140 1092 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.23 % Allowed : 2.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.28), residues: 972 helix: -0.60 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 160 TYR 0.012 0.001 TYR L 137 PHE 0.016 0.002 PHE L 163 TRP 0.069 0.001 TRP A 169 HIS 0.002 0.000 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8436) covalent geometry : angle 0.87365 (11448) hydrogen bonds : bond 0.03013 ( 379) hydrogen bonds : angle 5.60121 ( 1131) =============================================================================== Job complete usr+sys time: 1584.17 seconds wall clock time: 28 minutes 1.11 seconds (1681.11 seconds total)