Starting phenix.real_space_refine on Fri Sep 27 04:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k99_9947/09_2024/6k99_9947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k99_9947/09_2024/6k99_9947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k99_9947/09_2024/6k99_9947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k99_9947/09_2024/6k99_9947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k99_9947/09_2024/6k99_9947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k99_9947/09_2024/6k99_9947.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8244 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5280 2.51 5 N 1440 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8244 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.36, per 1000 atoms: 0.65 Number of scatterers: 8244 At special positions: 0 Unit cell: (94.6, 93.5, 95.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1500 8.00 N 1440 7.00 C 5280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 0 sheets defined 80.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 123 Processing helix chain 'G' and resid 128 through 137 removed outlier: 4.071A pdb=" N ASP G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 150 removed outlier: 3.653A pdb=" N ARG G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 164 removed outlier: 3.669A pdb=" N LYS G 158 " --> pdb=" O THR G 154 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET G 159 " --> pdb=" O ASN G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 185 Processing helix chain 'G' and resid 187 through 194 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.117A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 removed outlier: 3.562A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.603A pdb=" N ARG A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.721A pdb=" N LYS A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.958A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.165A pdb=" N ASP B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.602A pdb=" N ARG B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.675A pdb=" N LYS B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 185 Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 125 removed outlier: 4.150A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 4.143A pdb=" N ASP C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 150 removed outlier: 3.691A pdb=" N ARG C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.679A pdb=" N LYS C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 126 removed outlier: 4.225A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 137 removed outlier: 4.144A pdb=" N ASP D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.537A pdb=" N ARG D 150 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.615A pdb=" N LYS D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET D 159 " --> pdb=" O ASN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.583A pdb=" N LYS D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP D 175 " --> pdb=" O TRP D 171 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.995A pdb=" N ALA E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 137 removed outlier: 4.133A pdb=" N ASP E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 150 removed outlier: 3.600A pdb=" N ARG E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 164 removed outlier: 3.786A pdb=" N LYS E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 185 removed outlier: 3.804A pdb=" N LYS E 174 " --> pdb=" O ASN E 170 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP E 175 " --> pdb=" O TRP E 171 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 125 removed outlier: 4.049A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 137 removed outlier: 4.085A pdb=" N ASP F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.566A pdb=" N ARG F 150 " --> pdb=" O TYR F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 removed outlier: 3.772A pdb=" N LYS F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 185 removed outlier: 3.772A pdb=" N LYS F 174 " --> pdb=" O ASN F 170 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 175 " --> pdb=" O TRP F 171 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 125 removed outlier: 4.011A pdb=" N ALA H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 137 removed outlier: 3.546A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 150 removed outlier: 3.594A pdb=" N ARG H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 164 removed outlier: 3.649A pdb=" N LYS H 158 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET H 159 " --> pdb=" O ASN H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 169 removed outlier: 3.584A pdb=" N ALA H 168 " --> pdb=" O PHE H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 185 Processing helix chain 'H' and resid 187 through 194 Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 118 through 123 Processing helix chain 'I' and resid 128 through 137 removed outlier: 3.999A pdb=" N ASP I 134 " --> pdb=" O GLU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 150 removed outlier: 3.579A pdb=" N ARG I 150 " --> pdb=" O TYR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 164 removed outlier: 3.659A pdb=" N LYS I 158 " --> pdb=" O THR I 154 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET I 159 " --> pdb=" O ASN I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 185 removed outlier: 3.734A pdb=" N LYS I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP I 175 " --> pdb=" O TRP I 171 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU I 176 " --> pdb=" O THR I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 194 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 118 through 125 removed outlier: 4.173A pdb=" N ALA J 124 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 137 removed outlier: 4.176A pdb=" N ASP J 134 " --> pdb=" O GLU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 150 removed outlier: 3.584A pdb=" N ARG J 150 " --> pdb=" O TYR J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 164 removed outlier: 3.719A pdb=" N LYS J 158 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET J 159 " --> pdb=" O ASN J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 185 Processing helix chain 'J' and resid 187 through 194 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 118 through 126 removed outlier: 4.300A pdb=" N ALA K 124 " --> pdb=" O ALA K 120 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 125 " --> pdb=" O ALA K 121 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 137 removed outlier: 4.076A pdb=" N ASP K 134 " --> pdb=" O GLU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 150 removed outlier: 3.617A pdb=" N ARG K 150 " --> pdb=" O TYR K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 164 removed outlier: 3.730A pdb=" N LYS K 158 " --> pdb=" O THR K 154 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET K 159 " --> pdb=" O ASN K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 removed outlier: 3.606A pdb=" N ALA K 168 " --> pdb=" O PHE K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 185 removed outlier: 3.604A pdb=" N LYS K 174 " --> pdb=" O ASN K 170 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP K 175 " --> pdb=" O TRP K 171 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU K 176 " --> pdb=" O THR K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 194 Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 118 through 125 removed outlier: 3.977A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 removed outlier: 4.055A pdb=" N ASP L 134 " --> pdb=" O GLU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 150 removed outlier: 3.576A pdb=" N ARG L 150 " --> pdb=" O TYR L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 164 removed outlier: 3.704A pdb=" N LYS L 158 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET L 159 " --> pdb=" O ASN L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 185 Processing helix chain 'L' and resid 187 through 194 379 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 2.45 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.730 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- 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= 0.208 Angle : 0.715 8.062 11448 Z= 0.387 Chirality : 0.043 0.169 1260 Planarity : 0.004 0.034 1452 Dihedral : 12.507 74.844 3108 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.46 % Allowed : 10.14 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.24), residues: 972 helix: -1.90 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -1.87 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 169 HIS 0.005 0.001 HIS G 113 PHE 0.014 0.002 PHE D 114 TYR 0.017 0.002 TYR F 187 ARG 0.003 0.001 ARG E 160 *********************** 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 fitting. rotamer outliers: 13 poor density : 533 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 ILE cc_start: 0.9541 (mt) cc_final: 0.9276 (pt) REVERT: G 163 PHE cc_start: 0.8529 (m-80) cc_final: 0.7414 (m-80) REVERT: G 183 GLU cc_start: 0.9838 (mt-10) cc_final: 0.9395 (pt0) REVERT: A 115 ILE cc_start: 0.9636 (mt) cc_final: 0.9186 (pt) REVERT: A 146 TYR cc_start: 0.9201 (t80) cc_final: 0.8579 (t80) REVERT: A 175 ASP cc_start: 0.9381 (m-30) cc_final: 0.9146 (p0) REVERT: A 183 GLU cc_start: 0.9785 (mt-10) cc_final: 0.9528 (mm-30) REVERT: B 174 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8020 (ptpp) REVERT: B 178 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9057 (pp) REVERT: B 183 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9417 (pt0) REVERT: C 119 ARG cc_start: 0.9447 (tmt90) cc_final: 0.8785 (ptt180) REVERT: C 146 TYR cc_start: 0.8751 (t80) cc_final: 0.8497 (t80) REVERT: C 191 ASP cc_start: 0.9826 (t70) cc_final: 0.9514 (m-30) REVERT: D 141 LEU cc_start: 0.7934 (mt) cc_final: 0.7704 (mt) REVERT: D 146 TYR cc_start: 0.9248 (t80) cc_final: 0.8737 (t80) REVERT: D 149 VAL cc_start: 0.9656 (t) cc_final: 0.9194 (m) REVERT: D 161 LYS cc_start: 0.9631 (tppt) cc_final: 0.9317 (tptp) REVERT: D 188 LEU cc_start: 0.9121 (tp) cc_final: 0.8849 (mt) REVERT: E 125 ARG cc_start: 0.9452 (mtt180) cc_final: 0.9173 (tpt170) REVERT: E 154 THR cc_start: 0.8901 (p) cc_final: 0.8654 (t) REVERT: F 141 LEU cc_start: 0.7669 (mt) cc_final: 0.7468 (mt) REVERT: F 146 TYR cc_start: 0.8818 (t80) cc_final: 0.8262 (t80) REVERT: F 155 ASN cc_start: 0.8779 (t0) cc_final: 0.8090 (t0) REVERT: F 163 PHE cc_start: 0.8901 (m-80) cc_final: 0.8372 (m-80) REVERT: F 183 GLU cc_start: 0.9766 (mt-10) cc_final: 0.9519 (pt0) REVERT: H 126 VAL cc_start: 0.8734 (t) cc_final: 0.8496 (p) REVERT: H 137 TYR cc_start: 0.9294 (t80) cc_final: 0.8990 (t80) REVERT: H 157 SER cc_start: 0.9689 (t) cc_final: 0.9481 (p) REVERT: I 114 PHE cc_start: 0.9615 (t80) cc_final: 0.9385 (t80) REVERT: I 119 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8154 (ttp80) REVERT: I 125 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8491 (tpt170) REVERT: I 175 ASP cc_start: 0.9563 (m-30) cc_final: 0.9281 (p0) REVERT: I 192 LEU cc_start: 0.8784 (mp) cc_final: 0.8298 (tp) REVERT: J 146 TYR cc_start: 0.8820 (t80) cc_final: 0.8575 (t80) REVERT: J 149 VAL cc_start: 0.9301 (t) cc_final: 0.8839 (m) REVERT: J 161 LYS cc_start: 0.9638 (tppt) cc_final: 0.9412 (ptmm) REVERT: K 125 ARG cc_start: 0.9126 (mtt180) cc_final: 0.8835 (tpt170) REVERT: L 146 TYR cc_start: 0.9343 (t80) cc_final: 0.9054 (t80) outliers start: 13 outliers final: 0 residues processed: 541 average time/residue: 0.2916 time to fit residues: 193.5579 Evaluate side-chains 299 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 24 optimal weight: 50.0000 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN A 145 GLN D 128 ASN D 145 GLN E 145 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8436 Z= 0.184 Angle : 0.763 8.860 11448 Z= 0.373 Chirality : 0.045 0.143 1260 Planarity : 0.005 0.037 1452 Dihedral : 4.935 15.075 1092 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.24), residues: 972 helix: -1.29 (0.18), residues: 636 sheet: None (None), residues: 0 loop : -1.90 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 169 HIS 0.004 0.001 HIS F 118 PHE 0.023 0.002 PHE J 165 TYR 0.018 0.002 TYR F 146 ARG 0.008 0.001 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 1.054 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 163 PHE cc_start: 0.8588 (m-80) cc_final: 0.7852 (t80) REVERT: A 146 TYR cc_start: 0.9321 (t80) cc_final: 0.8966 (t80) REVERT: A 163 PHE cc_start: 0.8843 (m-80) cc_final: 0.8287 (m-10) REVERT: B 112 LEU cc_start: 0.9510 (tp) cc_final: 0.9198 (pt) REVERT: B 161 LYS cc_start: 0.9465 (tppt) cc_final: 0.9153 (tptm) REVERT: C 141 LEU cc_start: 0.7909 (tp) cc_final: 0.7556 (tp) REVERT: C 143 ASP cc_start: 0.9589 (t0) cc_final: 0.9364 (t0) REVERT: C 146 TYR cc_start: 0.8830 (t80) cc_final: 0.7960 (t80) REVERT: C 177 LEU cc_start: 0.9112 (pp) cc_final: 0.8906 (pp) REVERT: D 185 GLN cc_start: 0.9122 (mm110) cc_final: 0.8843 (mm110) REVERT: E 125 ARG cc_start: 0.9434 (mtt180) cc_final: 0.9185 (tpt170) REVERT: E 163 PHE cc_start: 0.8883 (m-80) cc_final: 0.8658 (m-10) REVERT: F 146 TYR cc_start: 0.8578 (t80) cc_final: 0.8242 (t80) REVERT: F 163 PHE cc_start: 0.9143 (m-80) cc_final: 0.8458 (m-80) REVERT: H 130 GLU cc_start: 0.9591 (pm20) cc_final: 0.9160 (pm20) REVERT: H 137 TYR cc_start: 0.9162 (t80) cc_final: 0.8893 (t80) REVERT: I 125 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8554 (tpt170) REVERT: K 125 ARG cc_start: 0.9095 (mtt180) cc_final: 0.8726 (tpt170) REVERT: K 188 LEU cc_start: 0.8556 (tp) cc_final: 0.8309 (tp) REVERT: L 146 TYR cc_start: 0.9454 (t80) cc_final: 0.9057 (t80) REVERT: L 161 LYS cc_start: 0.9661 (tppt) cc_final: 0.9379 (tptm) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.3018 time to fit residues: 156.6630 Evaluate side-chains 267 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 50.0000 chunk 27 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 50.0000 chunk 87 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 29 optimal weight: 0.0870 chunk 70 optimal weight: 5.9990 overall best weight: 4.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN A 145 GLN D 145 GLN D 147 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN H 147 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8436 Z= 0.186 Angle : 0.745 8.172 11448 Z= 0.370 Chirality : 0.045 0.157 1260 Planarity : 0.005 0.059 1452 Dihedral : 4.930 17.084 1092 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.11 % Allowed : 5.18 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.25), residues: 972 helix: -0.98 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 169 HIS 0.002 0.001 HIS F 118 PHE 0.020 0.002 PHE L 165 TYR 0.009 0.001 TYR L 187 ARG 0.009 0.001 ARG D 182 *********************** 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 390 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 389 time to evaluate : 0.971 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 146 TYR cc_start: 0.9592 (t80) cc_final: 0.9283 (t80) REVERT: A 141 LEU cc_start: 0.8099 (pp) cc_final: 0.7774 (pp) REVERT: A 146 TYR cc_start: 0.9369 (t80) cc_final: 0.8526 (t80) REVERT: B 112 LEU cc_start: 0.9470 (tp) cc_final: 0.9118 (pt) REVERT: B 163 PHE cc_start: 0.8913 (m-80) cc_final: 0.8517 (m-80) REVERT: B 165 PHE cc_start: 0.9371 (m-10) cc_final: 0.9047 (m-10) REVERT: C 119 ARG cc_start: 0.8891 (tpt170) cc_final: 0.7781 (tpt170) REVERT: C 141 LEU cc_start: 0.7942 (tp) cc_final: 0.7639 (tp) REVERT: C 143 ASP cc_start: 0.9633 (t0) cc_final: 0.9411 (p0) REVERT: C 144 GLU cc_start: 0.9463 (pm20) cc_final: 0.9129 (pm20) REVERT: C 146 TYR cc_start: 0.8767 (t80) cc_final: 0.7870 (t80) REVERT: C 158 LYS cc_start: 0.9176 (mttt) cc_final: 0.8960 (mttp) REVERT: C 163 PHE cc_start: 0.8611 (t80) cc_final: 0.8326 (t80) REVERT: D 188 LEU cc_start: 0.8958 (tp) cc_final: 0.8757 (mt) REVERT: E 125 ARG cc_start: 0.9501 (mtt180) cc_final: 0.9253 (tpt170) REVERT: E 163 PHE cc_start: 0.9072 (m-80) cc_final: 0.7470 (m-80) REVERT: F 146 TYR cc_start: 0.8747 (t80) cc_final: 0.8141 (t80) REVERT: H 141 LEU cc_start: 0.8449 (tp) cc_final: 0.8161 (tp) REVERT: H 146 TYR cc_start: 0.9055 (t80) cc_final: 0.8542 (t80) REVERT: I 125 ARG cc_start: 0.9179 (mtt180) cc_final: 0.8586 (tpt170) REVERT: I 161 LYS cc_start: 0.8235 (ptpp) cc_final: 0.7962 (pttm) REVERT: J 137 TYR cc_start: 0.9663 (t80) cc_final: 0.8790 (t80) REVERT: K 125 ARG cc_start: 0.9063 (mtt180) cc_final: 0.8855 (tpt170) REVERT: L 146 TYR cc_start: 0.9440 (t80) cc_final: 0.9000 (t80) REVERT: L 188 LEU cc_start: 0.9623 (tp) cc_final: 0.9324 (tp) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.2917 time to fit residues: 140.1054 Evaluate side-chains 270 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 40.0000 chunk 58 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 25 optimal weight: 50.0000 chunk 77 optimal weight: 6.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN G 179 GLN A 145 GLN B 185 GLN D 145 GLN D 147 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** 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** J 179 GLN K 145 GLN L 147 GLN L 185 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8436 Z= 0.207 Angle : 0.739 8.512 11448 Z= 0.371 Chirality : 0.045 0.143 1260 Planarity : 0.005 0.050 1452 Dihedral : 4.918 22.946 1092 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.26), residues: 972 helix: -0.76 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 169 HIS 0.003 0.001 HIS E 118 PHE 0.032 0.002 PHE G 163 TYR 0.017 0.001 TYR F 146 ARG 0.015 0.001 ARG F 125 *********************** 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 348 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 347 time to evaluate : 0.983 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: G 146 TYR cc_start: 0.9596 (t80) cc_final: 0.9092 (t80) REVERT: A 146 TYR cc_start: 0.9404 (t80) cc_final: 0.9014 (t80) REVERT: B 112 LEU cc_start: 0.9532 (tp) cc_final: 0.9322 (pt) REVERT: B 125 ARG cc_start: 0.9537 (mtp180) cc_final: 0.9254 (mmm-85) REVERT: B 146 TYR cc_start: 0.9138 (t80) cc_final: 0.8919 (t80) REVERT: B 161 LYS cc_start: 0.9554 (tptp) cc_final: 0.9344 (tptp) REVERT: B 188 LEU cc_start: 0.9501 (tp) cc_final: 0.9282 (tp) REVERT: C 119 ARG cc_start: 0.8682 (tpt170) cc_final: 0.8145 (tpt170) REVERT: C 125 ARG cc_start: 0.9177 (mpp-170) cc_final: 0.8498 (ttt90) REVERT: C 143 ASP cc_start: 0.9603 (t0) cc_final: 0.9400 (p0) REVERT: C 144 GLU cc_start: 0.9516 (pm20) cc_final: 0.9280 (pm20) REVERT: C 146 TYR cc_start: 0.8730 (t80) cc_final: 0.8111 (t80) REVERT: C 163 PHE cc_start: 0.8508 (t80) cc_final: 0.8141 (t80) REVERT: D 188 LEU cc_start: 0.9011 (tp) cc_final: 0.8724 (mt) REVERT: D 192 LEU cc_start: 0.9464 (mm) cc_final: 0.8733 (tp) REVERT: E 163 PHE cc_start: 0.8438 (m-80) cc_final: 0.8226 (m-80) REVERT: F 146 TYR cc_start: 0.8841 (t80) cc_final: 0.8259 (t80) REVERT: H 130 GLU cc_start: 0.9594 (pm20) cc_final: 0.9139 (pm20) REVERT: H 133 LEU cc_start: 0.9414 (mt) cc_final: 0.9195 (mt) REVERT: H 146 TYR cc_start: 0.9115 (t80) cc_final: 0.8660 (t80) REVERT: I 125 ARG cc_start: 0.9292 (mtt180) cc_final: 0.8701 (tpt170) REVERT: I 144 GLU cc_start: 0.9650 (pm20) cc_final: 0.9362 (pm20) REVERT: I 179 GLN cc_start: 0.9822 (mt0) cc_final: 0.9604 (tp-100) REVERT: I 183 GLU cc_start: 0.9284 (pm20) cc_final: 0.8968 (pm20) REVERT: J 143 ASP cc_start: 0.9691 (m-30) cc_final: 0.9486 (p0) REVERT: K 125 ARG cc_start: 0.9072 (mtt180) cc_final: 0.8771 (tpt170) REVERT: K 163 PHE cc_start: 0.9305 (m-80) cc_final: 0.9042 (m-80) REVERT: K 177 LEU cc_start: 0.9580 (tt) cc_final: 0.9271 (mt) REVERT: L 134 ASP cc_start: 0.9561 (m-30) cc_final: 0.9276 (m-30) REVERT: L 146 TYR cc_start: 0.9434 (t80) cc_final: 0.8999 (t80) outliers start: 1 outliers final: 0 residues processed: 348 average time/residue: 0.2928 time to fit residues: 125.1602 Evaluate side-chains 231 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 64 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 47 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8436 Z= 0.211 Angle : 0.758 8.455 11448 Z= 0.382 Chirality : 0.045 0.144 1260 Planarity : 0.005 0.069 1452 Dihedral : 4.950 26.902 1092 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.26), residues: 972 helix: -0.79 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.71 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 131 HIS 0.006 0.001 HIS C 118 PHE 0.030 0.002 PHE L 163 TYR 0.017 0.001 TYR C 146 ARG 0.013 0.001 ARG G 150 *********************** 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 316 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 1.070 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: G 146 TYR cc_start: 0.9608 (t80) cc_final: 0.9187 (t80) REVERT: G 163 PHE cc_start: 0.8072 (p90) cc_final: 0.7867 (p90) REVERT: A 123 ILE cc_start: 0.9474 (mm) cc_final: 0.9241 (mm) REVERT: B 146 TYR cc_start: 0.9252 (t80) cc_final: 0.9015 (t80) REVERT: C 144 GLU cc_start: 0.9502 (pm20) cc_final: 0.9157 (pm20) REVERT: C 163 PHE cc_start: 0.8467 (t80) cc_final: 0.8245 (t80) REVERT: D 161 LYS cc_start: 0.9600 (tptp) cc_final: 0.9328 (tptm) REVERT: D 188 LEU cc_start: 0.9133 (tp) cc_final: 0.8816 (mt) REVERT: D 192 LEU cc_start: 0.9437 (mm) cc_final: 0.8761 (tp) REVERT: E 117 GLN cc_start: 0.9657 (tm-30) cc_final: 0.9434 (tm-30) REVERT: E 160 ARG cc_start: 0.9441 (mtt90) cc_final: 0.9183 (ptp-110) REVERT: F 146 TYR cc_start: 0.8907 (t80) cc_final: 0.8347 (t80) REVERT: H 114 PHE cc_start: 0.9371 (t80) cc_final: 0.9153 (t80) REVERT: I 125 ARG cc_start: 0.9301 (mtt180) cc_final: 0.8734 (tpt170) REVERT: I 183 GLU cc_start: 0.9271 (pm20) cc_final: 0.8864 (pm20) REVERT: K 125 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8797 (tpt170) REVERT: K 163 PHE cc_start: 0.9378 (m-80) cc_final: 0.9077 (m-80) REVERT: K 177 LEU cc_start: 0.9561 (tt) cc_final: 0.9262 (mt) REVERT: L 134 ASP cc_start: 0.9561 (m-30) cc_final: 0.9283 (m-30) REVERT: L 146 TYR cc_start: 0.9377 (t80) cc_final: 0.9025 (t80) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.2977 time to fit residues: 116.3380 Evaluate side-chains 227 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 40.0000 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 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 145 GLN A 145 GLN B 179 GLN C 185 GLN D 145 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN F 185 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.8229 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= 0.194 Angle : 0.785 7.895 11448 Z= 0.388 Chirality : 0.046 0.137 1260 Planarity : 0.004 0.058 1452 Dihedral : 4.940 21.356 1092 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 972 helix: -0.63 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.59 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 169 HIS 0.002 0.000 HIS E 118 PHE 0.019 0.002 PHE E 165 TYR 0.012 0.001 TYR C 146 ARG 0.012 0.001 ARG I 182 *********************** 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 318 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9527 (t80) cc_final: 0.8921 (t80) REVERT: A 146 TYR cc_start: 0.9170 (t80) cc_final: 0.8822 (t80) REVERT: B 150 ARG cc_start: 0.9444 (mtm110) cc_final: 0.9175 (mtm180) REVERT: B 165 PHE cc_start: 0.9293 (m-10) cc_final: 0.9090 (m-10) REVERT: C 119 ARG cc_start: 0.8629 (tpt170) cc_final: 0.7407 (tpt170) REVERT: C 137 TYR cc_start: 0.9293 (t80) cc_final: 0.8914 (t80) REVERT: C 158 LYS cc_start: 0.9478 (mttt) cc_final: 0.9246 (mttt) REVERT: C 163 PHE cc_start: 0.8470 (t80) cc_final: 0.8216 (t80) REVERT: D 188 LEU cc_start: 0.9128 (tp) cc_final: 0.8922 (mt) REVERT: E 117 GLN cc_start: 0.9651 (tm-30) cc_final: 0.9417 (tm-30) REVERT: E 149 VAL cc_start: 0.9344 (m) cc_final: 0.9053 (m) REVERT: E 150 ARG cc_start: 0.9428 (mtm180) cc_final: 0.9220 (mtt180) REVERT: E 160 ARG cc_start: 0.9453 (mtt90) cc_final: 0.9107 (ptp-110) REVERT: F 146 TYR cc_start: 0.8754 (t80) cc_final: 0.8486 (t80) REVERT: H 130 GLU cc_start: 0.9604 (pm20) cc_final: 0.9341 (pm20) REVERT: H 137 TYR cc_start: 0.9436 (t80) cc_final: 0.9233 (t80) REVERT: H 146 TYR cc_start: 0.9061 (t80) cc_final: 0.8677 (t80) REVERT: I 125 ARG cc_start: 0.9298 (mtt180) cc_final: 0.8742 (tpt170) REVERT: J 146 TYR cc_start: 0.8693 (t80) cc_final: 0.8205 (t80) REVERT: K 125 ARG cc_start: 0.9105 (mtt180) cc_final: 0.8858 (tpt170) REVERT: K 163 PHE cc_start: 0.9384 (m-80) cc_final: 0.9001 (m-80) REVERT: K 177 LEU cc_start: 0.9558 (tt) cc_final: 0.9267 (mt) REVERT: L 134 ASP cc_start: 0.9589 (m-30) cc_final: 0.9320 (m-30) REVERT: L 146 TYR cc_start: 0.9318 (t80) cc_final: 0.8993 (t80) REVERT: L 160 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8664 (mtt-85) outliers start: 1 outliers final: 1 residues processed: 317 average time/residue: 0.2853 time to fit residues: 111.9800 Evaluate side-chains 220 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 0.0050 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 overall best weight: 4.8002 ------------------------------------------------------------------------------- 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 ** 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** J 185 GLN K 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.8588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8436 Z= 0.190 Angle : 0.816 12.250 11448 Z= 0.403 Chirality : 0.047 0.161 1260 Planarity : 0.004 0.056 1452 Dihedral : 4.992 19.860 1092 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.27), residues: 972 helix: -0.85 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.31 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 169 HIS 0.002 0.000 HIS B 113 PHE 0.016 0.001 PHE G 163 TYR 0.012 0.001 TYR J 146 ARG 0.009 0.001 ARG L 182 *********************** 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 305 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 0.953 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: G 146 TYR cc_start: 0.9560 (t80) cc_final: 0.9289 (t80) REVERT: G 150 ARG cc_start: 0.9164 (mpp80) cc_final: 0.8639 (mpp80) REVERT: A 146 TYR cc_start: 0.9185 (t80) cc_final: 0.8786 (t80) REVERT: A 179 GLN cc_start: 0.9791 (tm-30) cc_final: 0.9520 (tp-100) REVERT: B 150 ARG cc_start: 0.9466 (mtm110) cc_final: 0.9145 (mtm180) REVERT: B 165 PHE cc_start: 0.9259 (m-10) cc_final: 0.9057 (m-10) REVERT: C 119 ARG cc_start: 0.8611 (tpt170) cc_final: 0.7565 (tpt170) REVERT: C 163 PHE cc_start: 0.8474 (t80) cc_final: 0.8211 (t80) REVERT: D 188 LEU cc_start: 0.9134 (tp) cc_final: 0.8842 (mt) REVERT: D 192 LEU cc_start: 0.9429 (mm) cc_final: 0.8666 (tp) REVERT: E 117 GLN cc_start: 0.9649 (tm-30) cc_final: 0.9433 (tm-30) REVERT: E 157 SER cc_start: 0.9629 (t) cc_final: 0.9222 (p) REVERT: E 160 ARG cc_start: 0.9436 (mtt90) cc_final: 0.9171 (ptp-110) REVERT: F 146 TYR cc_start: 0.8950 (t80) cc_final: 0.8474 (t80) REVERT: H 130 GLU cc_start: 0.9564 (pm20) cc_final: 0.9201 (pm20) REVERT: I 125 ARG cc_start: 0.9303 (mtt180) cc_final: 0.8762 (tpt170) REVERT: I 179 GLN cc_start: 0.9740 (tp-100) cc_final: 0.9463 (tp-100) REVERT: I 183 GLU cc_start: 0.9204 (pm20) cc_final: 0.8854 (pm20) REVERT: J 146 TYR cc_start: 0.8381 (t80) cc_final: 0.8016 (t80) REVERT: J 179 GLN cc_start: 0.9665 (mp10) cc_final: 0.9439 (mm-40) REVERT: K 163 PHE cc_start: 0.9401 (m-80) cc_final: 0.9025 (m-80) REVERT: K 177 LEU cc_start: 0.9579 (tt) cc_final: 0.9293 (mt) REVERT: L 146 TYR cc_start: 0.9253 (t80) cc_final: 0.8918 (t80) REVERT: L 160 ARG cc_start: 0.9178 (mtt90) cc_final: 0.8636 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 0.2764 time to fit residues: 104.9051 Evaluate side-chains 202 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 40.0000 chunk 72 optimal weight: 50.0000 chunk 84 optimal weight: 40.0000 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 40.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.9123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8436 Z= 0.277 Angle : 0.833 10.558 11448 Z= 0.421 Chirality : 0.049 0.164 1260 Planarity : 0.005 0.060 1452 Dihedral : 5.293 19.805 1092 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.27), residues: 972 helix: -0.84 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -1.87 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 169 HIS 0.004 0.001 HIS G 113 PHE 0.021 0.002 PHE L 163 TYR 0.012 0.001 TYR F 187 ARG 0.009 0.001 ARG F 125 *********************** 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 273 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 0.973 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: 0.9524 (t80) cc_final: 0.8887 (t80) REVERT: G 150 ARG cc_start: 0.9241 (mpp80) cc_final: 0.8726 (mpp80) REVERT: A 146 TYR cc_start: 0.9164 (t80) cc_final: 0.8709 (t80) REVERT: B 161 LYS cc_start: 0.9596 (tptp) cc_final: 0.9393 (tptp) REVERT: B 165 PHE cc_start: 0.9274 (m-10) cc_final: 0.9073 (m-10) REVERT: C 119 ARG cc_start: 0.8624 (tpt170) cc_final: 0.7487 (tpt170) REVERT: C 163 PHE cc_start: 0.8416 (t80) cc_final: 0.8068 (t80) REVERT: D 161 LYS cc_start: 0.9675 (tptp) cc_final: 0.9398 (tptm) REVERT: D 192 LEU cc_start: 0.9397 (mm) cc_final: 0.8853 (tp) REVERT: F 146 TYR cc_start: 0.9016 (t80) cc_final: 0.8610 (t80) REVERT: H 130 GLU cc_start: 0.9641 (pm20) cc_final: 0.9368 (pm20) REVERT: H 163 PHE cc_start: 0.8517 (m-80) cc_final: 0.8270 (m-80) REVERT: I 125 ARG cc_start: 0.9320 (mtt180) cc_final: 0.8733 (tpt170) REVERT: I 183 GLU cc_start: 0.9260 (pm20) cc_final: 0.9056 (pm20) REVERT: K 163 PHE cc_start: 0.9437 (m-80) cc_final: 0.9095 (m-80) REVERT: L 146 TYR cc_start: 0.9275 (t80) cc_final: 0.8993 (t80) REVERT: L 160 ARG cc_start: 0.9250 (mtt90) cc_final: 0.8723 (mtt-85) REVERT: L 161 LYS cc_start: 0.9475 (pttm) cc_final: 0.9256 (pttm) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2735 time to fit residues: 93.4786 Evaluate side-chains 185 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 26 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN A 145 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 145 GLN D 147 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN H 147 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.9438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8436 Z= 0.225 Angle : 0.854 9.598 11448 Z= 0.424 Chirality : 0.049 0.166 1260 Planarity : 0.004 0.060 1452 Dihedral : 5.213 20.441 1092 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.26), residues: 972 helix: -0.96 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -2.35 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP I 169 HIS 0.004 0.000 HIS I 118 PHE 0.023 0.002 PHE E 165 TYR 0.011 0.001 TYR D 187 ARG 0.010 0.001 ARG F 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 TYR cc_start: 0.9463 (t80) cc_final: 0.8686 (t80) REVERT: G 150 ARG cc_start: 0.9207 (mpp80) cc_final: 0.8922 (mpp80) REVERT: A 146 TYR cc_start: 0.9106 (t80) cc_final: 0.8616 (t80) REVERT: A 163 PHE cc_start: 0.9273 (m-80) cc_final: 0.9063 (m-80) REVERT: B 161 LYS cc_start: 0.9588 (tptp) cc_final: 0.9387 (tptp) REVERT: B 165 PHE cc_start: 0.9252 (m-10) cc_final: 0.9033 (m-10) REVERT: C 119 ARG cc_start: 0.8706 (tpt170) cc_final: 0.7909 (tpt170) REVERT: C 146 TYR cc_start: 0.8013 (t80) cc_final: 0.7517 (t80) REVERT: C 163 PHE cc_start: 0.8425 (t80) cc_final: 0.7992 (t80) REVERT: E 117 GLN cc_start: 0.9691 (tm-30) cc_final: 0.9487 (tm-30) REVERT: F 146 TYR cc_start: 0.9008 (t80) cc_final: 0.8646 (t80) REVERT: H 130 GLU cc_start: 0.9610 (pm20) cc_final: 0.9347 (pm20) REVERT: H 147 GLN cc_start: 0.9377 (pt0) cc_final: 0.9059 (pp30) REVERT: I 125 ARG cc_start: 0.9313 (mtt180) cc_final: 0.8781 (tpt170) REVERT: I 183 GLU cc_start: 0.9230 (pm20) cc_final: 0.8975 (pm20) REVERT: K 163 PHE cc_start: 0.9472 (m-80) cc_final: 0.9197 (m-80) REVERT: L 146 TYR cc_start: 0.9268 (t80) cc_final: 0.8990 (t80) REVERT: L 160 ARG cc_start: 0.9204 (mtt90) cc_final: 0.8715 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2681 time to fit residues: 97.1137 Evaluate side-chains 183 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 0.1980 chunk 60 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 B 185 GLN C 145 GLN D 145 GLN E 145 GLN F 145 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN K 185 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.9692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8436 Z= 0.195 Angle : 0.897 9.872 11448 Z= 0.440 Chirality : 0.050 0.161 1260 Planarity : 0.004 0.053 1452 Dihedral : 5.174 19.557 1092 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.28), residues: 972 helix: -0.77 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.57 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 169 HIS 0.003 0.000 HIS I 118 PHE 0.016 0.002 PHE F 163 TYR 0.013 0.001 TYR D 187 ARG 0.008 0.001 ARG F 125 ********************** 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 302 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.040 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: G 146 TYR cc_start: 0.9394 (t80) cc_final: 0.8638 (t80) REVERT: A 146 TYR cc_start: 0.9016 (t80) cc_final: 0.8407 (t80) REVERT: B 150 ARG cc_start: 0.9455 (mtm110) cc_final: 0.9132 (mtm180) REVERT: C 119 ARG cc_start: 0.8717 (tpt170) cc_final: 0.6946 (tpt170) REVERT: C 179 GLN cc_start: 0.9614 (mp10) cc_final: 0.9338 (mm-40) REVERT: E 150 ARG cc_start: 0.9454 (mtm180) cc_final: 0.9113 (mtt180) REVERT: E 152 GLU cc_start: 0.9544 (pm20) cc_final: 0.8568 (pm20) REVERT: E 159 MET cc_start: 0.9442 (ptp) cc_final: 0.9240 (ptp) REVERT: E 183 GLU cc_start: 0.9411 (pm20) cc_final: 0.9206 (pm20) REVERT: F 146 TYR cc_start: 0.8994 (t80) cc_final: 0.8665 (t80) REVERT: H 130 GLU cc_start: 0.9561 (pm20) cc_final: 0.9277 (pm20) REVERT: I 125 ARG cc_start: 0.9313 (mtt180) cc_final: 0.8813 (tpt170) REVERT: I 165 PHE cc_start: 0.8880 (m-10) cc_final: 0.8665 (m-10) REVERT: I 179 GLN cc_start: 0.9725 (tp-100) cc_final: 0.9488 (tp-100) REVERT: K 163 PHE cc_start: 0.9479 (m-80) cc_final: 0.9184 (m-80) REVERT: L 146 TYR cc_start: 0.9250 (t80) cc_final: 0.9030 (t80) REVERT: L 160 ARG cc_start: 0.9161 (mtt90) cc_final: 0.8678 (mtt-85) REVERT: L 169 TRP cc_start: 0.8775 (m-10) cc_final: 0.8561 (m-10) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2652 time to fit residues: 100.5158 Evaluate side-chains 195 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 0.0030 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 GLN A 145 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN E 145 GLN F 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.025586 restraints weight = 70578.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.026659 restraints weight = 48594.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.027456 restraints weight = 37578.419| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 1.0008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8436 Z= 0.208 Angle : 0.909 9.943 11448 Z= 0.452 Chirality : 0.051 0.188 1260 Planarity : 0.004 0.054 1452 Dihedral : 5.237 20.046 1092 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.28), residues: 972 helix: -0.84 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 169 HIS 0.005 0.001 HIS E 118 PHE 0.017 0.002 PHE C 165 TYR 0.016 0.001 TYR J 146 ARG 0.014 0.001 ARG A 160 =============================================================================== Job complete usr+sys time: 2414.34 seconds wall clock time: 43 minutes 30.84 seconds (2610.84 seconds total)