Starting phenix.real_space_refine on Wed Sep 17 17:09:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zh8_60096/09_2025/8zh8_60096.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zh8_60096/09_2025/8zh8_60096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zh8_60096/09_2025/8zh8_60096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zh8_60096/09_2025/8zh8_60096.map" model { file = "/net/cci-nas-00/data/ceres_data/8zh8_60096/09_2025/8zh8_60096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zh8_60096/09_2025/8zh8_60096.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6422 2.51 5 N 1720 2.21 5 O 1838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10048 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2635 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2473 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1704 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "S" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.44, per 1000 atoms: 0.24 Number of scatterers: 10048 At special positions: 0 Unit cell: (87.849, 132.795, 148.117, 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 68 16.00 O 1838 8.00 N 1720 7.00 C 6422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 201 " distance=2.03 Simple disulfide: pdb=" SG CYS R 285 " - pdb=" SG CYS R 327 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 413.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 15 sheets defined 37.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'R' and resid 7 through 18 removed outlier: 4.108A pdb=" N ARG R 16 " --> pdb=" O SER R 12 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP R 17 " --> pdb=" O ARG R 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 30 Processing helix chain 'R' and resid 41 through 73 removed outlier: 3.506A pdb=" N THR R 71 " --> pdb=" O PHE R 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 removed outlier: 3.649A pdb=" N ARG R 77 " --> pdb=" O LYS R 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 74 through 77' Processing helix chain 'R' and resid 78 through 98 Processing helix chain 'R' and resid 98 through 107 Processing helix chain 'R' and resid 113 through 149 removed outlier: 4.019A pdb=" N ILE R 117 " --> pdb=" O GLY R 113 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 3.644A pdb=" N THR R 137 " --> pdb=" O ILE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.676A pdb=" N LYS R 154 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 177 removed outlier: 3.599A pdb=" N ALA R 162 " --> pdb=" O THR R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 183 removed outlier: 4.175A pdb=" N HIS R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 195 Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.805A pdb=" N GLN R 211 " --> pdb=" O SER R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 243 Processing helix chain 'R' and resid 264 through 299 removed outlier: 3.814A pdb=" N ALA R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.579A pdb=" N SER R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 306 through 323 Processing helix chain 'R' and resid 323 through 335 Proline residue: R 329 - end of helix Processing helix chain 'R' and resid 336 through 346 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.559A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.987A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.781A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.584A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.649A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.318A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.890A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.643A pdb=" N TYR A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.591A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.082A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 removed outlier: 4.269A pdb=" N GLY Q 14 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 191 Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.926A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.181A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.904A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.085A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.923A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.931A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.036A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.660A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.976A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.724A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.565A pdb=" N THR S 129 " --> pdb=" O ARG S 148 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.837A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1452 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: 1.55 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2254 1.33 - 1.46: 2824 1.46 - 1.58: 5086 1.58 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 10265 Sorted by residual: bond pdb=" CA PRO R 329 " pdb=" CB PRO R 329 " ideal model delta sigma weight residual 1.534 1.477 0.056 1.52e-02 4.33e+03 1.37e+01 bond pdb=" CA ARG Q 25 " pdb=" C ARG Q 25 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.36e+00 bond pdb=" C GLN R 125 " pdb=" O GLN R 125 " ideal model delta sigma weight residual 1.236 1.204 0.033 1.15e-02 7.56e+03 8.21e+00 bond pdb=" C GLN R 125 " pdb=" N SER R 126 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 7.86e+00 bond pdb=" C VAL R 121 " pdb=" N PRO R 122 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.89e+00 ... (remaining 10260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 13498 1.69 - 3.39: 383 3.39 - 5.08: 46 5.08 - 6.77: 12 6.77 - 8.47: 3 Bond angle restraints: 13942 Sorted by residual: angle pdb=" C ASN R 328 " pdb=" N PRO R 329 " pdb=" CA PRO R 329 " ideal model delta sigma weight residual 119.32 114.52 4.80 1.14e+00 7.69e-01 1.77e+01 angle pdb=" C PRO R 329 " pdb=" CA PRO R 329 " pdb=" CB PRO R 329 " ideal model delta sigma weight residual 112.64 106.17 6.47 1.74e+00 3.30e-01 1.38e+01 angle pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta sigma weight residual 120.39 125.45 -5.06 1.39e+00 5.18e-01 1.33e+01 angle pdb=" N SER S 194 " pdb=" CA SER S 194 " pdb=" C SER S 194 " ideal model delta sigma weight residual 108.38 112.67 -4.29 1.35e+00 5.49e-01 1.01e+01 angle pdb=" CA TRP A 96 " pdb=" CB TRP A 96 " pdb=" CG TRP A 96 " ideal model delta sigma weight residual 113.60 119.50 -5.90 1.90e+00 2.77e-01 9.65e+00 ... (remaining 13937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 5496 16.17 - 32.33: 452 32.33 - 48.50: 82 48.50 - 64.66: 13 64.66 - 80.83: 14 Dihedral angle restraints: 6057 sinusoidal: 2247 harmonic: 3810 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -22.52 -63.48 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CA ARG A 94 " pdb=" C ARG A 94 " pdb=" N LYS A 95 " pdb=" CA LYS A 95 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1139 0.041 - 0.082: 345 0.082 - 0.123: 95 0.123 - 0.163: 14 0.163 - 0.204: 3 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ILE R 199 " pdb=" N ILE R 199 " pdb=" C ILE R 199 " pdb=" CB ILE R 199 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN R 328 " pdb=" N ASN R 328 " pdb=" C ASN R 328 " pdb=" CB ASN R 328 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA ILE R 188 " pdb=" N ILE R 188 " pdb=" C ILE R 188 " pdb=" CB ILE R 188 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 1593 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 155 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C ASN B 155 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 155 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN B 156 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 328 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASN R 328 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN R 328 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO R 329 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 225 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO R 226 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " 0.026 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 887 2.75 - 3.28: 9883 3.28 - 3.82: 17145 3.82 - 4.36: 19973 4.36 - 4.90: 34978 Nonbonded interactions: 82866 Sorted by model distance: nonbonded pdb=" OE2 GLU R 142 " pdb=" OH TYR R 157 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR N 117 " pdb=" O CYS B 204 " model vdw 2.218 3.040 nonbonded pdb=" O ASN B 155 " pdb=" ND2 ASN B 155 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.237 3.040 nonbonded pdb=" O SER N 63 " pdb=" NH2 ARG N 67 " model vdw 2.239 3.120 ... (remaining 82861 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 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 0.109 10272 Z= 0.192 Angle : 0.670 8.466 13954 Z= 0.388 Chirality : 0.043 0.204 1596 Planarity : 0.004 0.046 1766 Dihedral : 12.775 80.825 3583 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.24), residues: 1294 helix: 1.54 (0.26), residues: 426 sheet: 0.16 (0.29), residues: 330 loop : -0.33 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.017 0.001 TYR S 60 PHE 0.017 0.002 PHE R 314 TRP 0.022 0.001 TRP N 47 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00290 (10265) covalent geometry : angle 0.66953 (13942) SS BOND : bond 0.00603 ( 6) SS BOND : angle 0.99758 ( 12) hydrogen bonds : bond 0.13456 ( 518) hydrogen bonds : angle 6.00369 ( 1452) Misc. bond : bond 0.10866 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.295 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: N 61 THR cc_start: 0.7475 (t) cc_final: 0.7111 (m) REVERT: A 10 LYS cc_start: 0.7900 (mttp) cc_final: 0.7524 (mttm) REVERT: A 199 ASP cc_start: 0.7787 (p0) cc_final: 0.7093 (p0) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.1156 time to fit residues: 54.8539 Evaluate side-chains 213 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 5 ASN R 63 ASN R 81 ASN B 259 GLN A 123 ASN A 130 ASN A 239 ASN S 82 GLN S 219 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.122313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.099390 restraints weight = 26252.952| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 4.28 r_work: 0.3591 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10272 Z= 0.168 Angle : 0.671 6.526 13954 Z= 0.353 Chirality : 0.044 0.159 1596 Planarity : 0.005 0.051 1766 Dihedral : 4.483 27.285 1417 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.11 % Allowed : 14.45 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.24), residues: 1294 helix: 1.71 (0.26), residues: 420 sheet: 0.08 (0.29), residues: 322 loop : -0.34 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 67 TYR 0.020 0.002 TYR S 95 PHE 0.020 0.002 PHE R 339 TRP 0.018 0.002 TRP R 111 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00384 (10265) covalent geometry : angle 0.66881 (13942) SS BOND : bond 0.00635 ( 6) SS BOND : angle 1.80794 ( 12) hydrogen bonds : bond 0.04305 ( 518) hydrogen bonds : angle 5.22508 ( 1452) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.353 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: R 34 LEU cc_start: 0.8737 (tp) cc_final: 0.8352 (mm) REVERT: R 111 TRP cc_start: 0.7398 (t-100) cc_final: 0.7055 (t60) REVERT: R 312 MET cc_start: 0.8585 (tpp) cc_final: 0.8366 (tpp) REVERT: N 32 TYR cc_start: 0.7953 (m-80) cc_final: 0.7209 (m-80) REVERT: N 53 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6114 (mp10) REVERT: N 61 THR cc_start: 0.8536 (t) cc_final: 0.7855 (m) REVERT: N 73 ASP cc_start: 0.8005 (t0) cc_final: 0.7642 (p0) REVERT: B 82 TRP cc_start: 0.9029 (m100) cc_final: 0.8680 (m-10) REVERT: B 262 MET cc_start: 0.7917 (tpp) cc_final: 0.7505 (tpp) REVERT: B 335 PHE cc_start: 0.8045 (m-10) cc_final: 0.7819 (m-10) REVERT: A 10 LYS cc_start: 0.8250 (mttp) cc_final: 0.7832 (mttp) REVERT: A 14 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7844 (mp0) REVERT: A 21 LYS cc_start: 0.7025 (tttm) cc_final: 0.6711 (ttpp) REVERT: A 25 GLU cc_start: 0.7384 (mp0) cc_final: 0.6958 (mp0) REVERT: A 28 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 131 ASN cc_start: 0.8583 (t0) cc_final: 0.8129 (t0) REVERT: A 199 ASP cc_start: 0.9287 (p0) cc_final: 0.8844 (p0) REVERT: A 230 ASP cc_start: 0.8636 (m-30) cc_final: 0.8286 (m-30) outliers start: 22 outliers final: 10 residues processed: 253 average time/residue: 0.1074 time to fit residues: 37.3710 Evaluate side-chains 223 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain Q residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 342 ASN A 123 ASN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.097143 restraints weight = 26325.489| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 4.29 r_work: 0.3550 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10272 Z= 0.148 Angle : 0.637 6.878 13954 Z= 0.333 Chirality : 0.044 0.179 1596 Planarity : 0.004 0.038 1766 Dihedral : 4.336 26.090 1417 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.78 % Allowed : 16.08 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.24), residues: 1294 helix: 1.78 (0.26), residues: 422 sheet: 0.10 (0.29), residues: 321 loop : -0.41 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 67 TYR 0.018 0.001 TYR S 95 PHE 0.033 0.002 PHE R 11 TRP 0.013 0.001 TRP N 47 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00334 (10265) covalent geometry : angle 0.63369 (13942) SS BOND : bond 0.00996 ( 6) SS BOND : angle 2.36212 ( 12) hydrogen bonds : bond 0.03785 ( 518) hydrogen bonds : angle 5.04015 ( 1452) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.411 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: R 11 PHE cc_start: 0.8977 (m-80) cc_final: 0.8665 (m-80) REVERT: R 15 LEU cc_start: 0.9507 (mm) cc_final: 0.9222 (mm) REVERT: R 228 MET cc_start: 0.7965 (ppp) cc_final: 0.7723 (tmm) REVERT: R 312 MET cc_start: 0.8696 (tpp) cc_final: 0.8484 (tpt) REVERT: N 27 PHE cc_start: 0.6138 (p90) cc_final: 0.5866 (p90) REVERT: N 46 GLU cc_start: 0.5505 (tp30) cc_final: 0.5123 (tp30) REVERT: N 53 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6553 (mp10) REVERT: N 61 THR cc_start: 0.8622 (t) cc_final: 0.7842 (m) REVERT: N 68 PHE cc_start: 0.7604 (m-80) cc_final: 0.7331 (m-10) REVERT: N 73 ASP cc_start: 0.7939 (t0) cc_final: 0.7219 (t0) REVERT: N 76 LYS cc_start: 0.9248 (ttmm) cc_final: 0.8952 (ttpp) REVERT: B 262 MET cc_start: 0.7818 (tpp) cc_final: 0.7350 (tpp) REVERT: A 10 LYS cc_start: 0.8307 (mttp) cc_final: 0.7747 (mttm) REVERT: A 14 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7859 (mp0) REVERT: A 21 LYS cc_start: 0.7187 (tttm) cc_final: 0.6767 (ttpp) REVERT: A 25 GLU cc_start: 0.7519 (mp0) cc_final: 0.7123 (mp0) REVERT: A 120 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 131 ASN cc_start: 0.8559 (t0) cc_final: 0.8040 (t0) REVERT: A 192 PHE cc_start: 0.8439 (t80) cc_final: 0.7920 (t80) REVERT: A 199 ASP cc_start: 0.9324 (p0) cc_final: 0.8827 (p0) REVERT: A 230 ASP cc_start: 0.8681 (m-30) cc_final: 0.8467 (m-30) REVERT: Q 18 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7937 (mmmt) outliers start: 29 outliers final: 10 residues processed: 240 average time/residue: 0.1116 time to fit residues: 36.9053 Evaluate side-chains 216 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 6 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN B 54 HIS S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.120779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.097917 restraints weight = 26363.989| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 4.31 r_work: 0.3561 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10272 Z= 0.127 Angle : 0.604 7.535 13954 Z= 0.317 Chirality : 0.043 0.183 1596 Planarity : 0.004 0.040 1766 Dihedral : 4.177 27.212 1417 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.49 % Allowed : 18.18 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.24), residues: 1294 helix: 1.92 (0.26), residues: 417 sheet: 0.05 (0.28), residues: 332 loop : -0.30 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 67 TYR 0.014 0.001 TYR S 95 PHE 0.026 0.002 PHE R 11 TRP 0.008 0.001 TRP A 96 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00285 (10265) covalent geometry : angle 0.60157 (13942) SS BOND : bond 0.00896 ( 6) SS BOND : angle 1.95244 ( 12) hydrogen bonds : bond 0.03620 ( 518) hydrogen bonds : angle 4.88629 ( 1452) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.269 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: R 11 PHE cc_start: 0.8920 (m-80) cc_final: 0.8617 (m-80) REVERT: R 120 MET cc_start: 0.8530 (tmm) cc_final: 0.8238 (tmm) REVERT: R 228 MET cc_start: 0.7911 (ppp) cc_final: 0.7710 (tmm) REVERT: N 27 PHE cc_start: 0.6451 (p90) cc_final: 0.5958 (p90) REVERT: N 32 TYR cc_start: 0.8053 (m-80) cc_final: 0.6926 (m-80) REVERT: N 53 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6656 (mp10) REVERT: N 61 THR cc_start: 0.8549 (t) cc_final: 0.7765 (m) REVERT: N 68 PHE cc_start: 0.7617 (m-80) cc_final: 0.7320 (m-10) REVERT: N 73 ASP cc_start: 0.8088 (t0) cc_final: 0.7653 (p0) REVERT: N 80 TYR cc_start: 0.7973 (m-10) cc_final: 0.7764 (m-10) REVERT: B 61 MET cc_start: 0.8796 (ppp) cc_final: 0.8543 (ppp) REVERT: B 262 MET cc_start: 0.7585 (tpp) cc_final: 0.7102 (tpp) REVERT: A 10 LYS cc_start: 0.8275 (mttp) cc_final: 0.7671 (mttm) REVERT: A 14 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7815 (mp0) REVERT: A 21 LYS cc_start: 0.7215 (tttm) cc_final: 0.6731 (ttpp) REVERT: A 25 GLU cc_start: 0.7663 (mp0) cc_final: 0.7263 (mp0) REVERT: A 83 MET cc_start: 0.8552 (ttm) cc_final: 0.8183 (ttm) REVERT: A 120 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8219 (mm-30) REVERT: A 131 ASN cc_start: 0.8646 (t0) cc_final: 0.8066 (t0) REVERT: A 195 LYS cc_start: 0.9383 (tptp) cc_final: 0.8981 (tptp) REVERT: A 199 ASP cc_start: 0.9395 (p0) cc_final: 0.8854 (p0) REVERT: A 230 ASP cc_start: 0.8718 (m-30) cc_final: 0.8491 (m-30) REVERT: S 67 ARG cc_start: 0.8322 (ptt-90) cc_final: 0.6462 (ptt-90) REVERT: S 85 SER cc_start: 0.8667 (t) cc_final: 0.8134 (m) REVERT: S 151 LYS cc_start: 0.8319 (pttt) cc_final: 0.8038 (pttm) REVERT: S 174 GLN cc_start: 0.7371 (mm110) cc_final: 0.6976 (mm110) REVERT: Q 13 ASN cc_start: 0.8209 (t0) cc_final: 0.7075 (p0) outliers start: 26 outliers final: 17 residues processed: 229 average time/residue: 0.1088 time to fit residues: 34.1591 Evaluate side-chains 216 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 246 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 293 HIS ** R 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.112767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.090529 restraints weight = 26854.165| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.08 r_work: 0.3430 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 10272 Z= 0.270 Angle : 0.714 8.968 13954 Z= 0.377 Chirality : 0.046 0.204 1596 Planarity : 0.004 0.037 1766 Dihedral : 4.626 28.110 1417 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.73 % Allowed : 17.89 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.24), residues: 1294 helix: 1.62 (0.26), residues: 421 sheet: -0.13 (0.28), residues: 346 loop : -0.48 (0.29), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 251 TYR 0.022 0.002 TYR N 115 PHE 0.031 0.002 PHE A 192 TRP 0.022 0.002 TRP B 169 HIS 0.006 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00621 (10265) covalent geometry : angle 0.71068 (13942) SS BOND : bond 0.01269 ( 6) SS BOND : angle 2.61106 ( 12) hydrogen bonds : bond 0.04423 ( 518) hydrogen bonds : angle 5.19047 ( 1452) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.399 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: R 10 GLN cc_start: 0.7680 (tt0) cc_final: 0.7412 (pt0) REVERT: R 11 PHE cc_start: 0.9049 (m-80) cc_final: 0.8710 (m-80) REVERT: R 15 LEU cc_start: 0.9538 (mm) cc_final: 0.9324 (mp) REVERT: R 291 VAL cc_start: 0.9238 (t) cc_final: 0.9035 (p) REVERT: R 328 ASN cc_start: 0.7681 (m110) cc_final: 0.7443 (m-40) REVERT: N 27 PHE cc_start: 0.6860 (p90) cc_final: 0.6261 (p90) REVERT: N 32 TYR cc_start: 0.8099 (m-80) cc_final: 0.6776 (m-80) REVERT: N 46 GLU cc_start: 0.5902 (tp30) cc_final: 0.5522 (tp30) REVERT: N 53 GLN cc_start: 0.7328 (mp10) cc_final: 0.6965 (mp10) REVERT: N 73 ASP cc_start: 0.8249 (t0) cc_final: 0.8039 (t0) REVERT: B 57 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8011 (ttmt) REVERT: B 61 MET cc_start: 0.9054 (ppp) cc_final: 0.8839 (ppp) REVERT: B 220 GLN cc_start: 0.8635 (mp10) cc_final: 0.8113 (mp10) REVERT: B 234 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.9044 (m-80) REVERT: B 262 MET cc_start: 0.7823 (tpp) cc_final: 0.6954 (tpp) REVERT: A 10 LYS cc_start: 0.8593 (mttp) cc_final: 0.7995 (mttp) REVERT: A 14 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7802 (mp0) REVERT: A 21 LYS cc_start: 0.7550 (tttm) cc_final: 0.6947 (ttpp) REVERT: A 25 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: A 75 GLN cc_start: 0.7523 (pp30) cc_final: 0.7285 (pp30) REVERT: A 83 MET cc_start: 0.8540 (ttm) cc_final: 0.8209 (ttm) REVERT: A 195 LYS cc_start: 0.9438 (tptp) cc_final: 0.9013 (tptp) REVERT: A 199 ASP cc_start: 0.9404 (p0) cc_final: 0.8917 (p0) REVERT: S 88 SER cc_start: 0.9029 (t) cc_final: 0.8782 (p) outliers start: 39 outliers final: 26 residues processed: 236 average time/residue: 0.1113 time to fit residues: 35.5776 Evaluate side-chains 218 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 117 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN S 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.116150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.093435 restraints weight = 27092.538| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.27 r_work: 0.3480 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10272 Z= 0.142 Angle : 0.662 10.306 13954 Z= 0.340 Chirality : 0.043 0.174 1596 Planarity : 0.004 0.069 1766 Dihedral : 4.376 26.064 1417 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.78 % Allowed : 20.67 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.24), residues: 1294 helix: 1.79 (0.26), residues: 423 sheet: 0.09 (0.29), residues: 328 loop : -0.46 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 148 TYR 0.025 0.002 TYR N 115 PHE 0.022 0.001 PHE R 11 TRP 0.011 0.001 TRP R 111 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00324 (10265) covalent geometry : angle 0.65572 (13942) SS BOND : bond 0.01253 ( 6) SS BOND : angle 3.18232 ( 12) hydrogen bonds : bond 0.03781 ( 518) hydrogen bonds : angle 4.89291 ( 1452) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.9086 (m-80) cc_final: 0.8773 (m-80) REVERT: R 120 MET cc_start: 0.8547 (tmm) cc_final: 0.8239 (tmm) REVERT: R 294 MET cc_start: 0.8803 (mmm) cc_final: 0.8601 (mmm) REVERT: N 32 TYR cc_start: 0.8046 (m-80) cc_final: 0.7649 (m-80) REVERT: N 53 GLN cc_start: 0.7331 (mp10) cc_final: 0.7006 (mp10) REVERT: N 61 THR cc_start: 0.8611 (t) cc_final: 0.7854 (m) REVERT: N 73 ASP cc_start: 0.8270 (t0) cc_final: 0.7896 (p0) REVERT: B 57 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8033 (ttmm) REVERT: B 59 TYR cc_start: 0.7630 (m-80) cc_final: 0.7181 (m-80) REVERT: B 220 GLN cc_start: 0.8588 (mp10) cc_final: 0.8242 (mp10) REVERT: B 262 MET cc_start: 0.7700 (tpp) cc_final: 0.6786 (tpp) REVERT: A 10 LYS cc_start: 0.8453 (mttp) cc_final: 0.7821 (mttm) REVERT: A 14 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7790 (mp0) REVERT: A 21 LYS cc_start: 0.7364 (tttm) cc_final: 0.6824 (tttm) REVERT: A 25 GLU cc_start: 0.7766 (mp0) cc_final: 0.7411 (mp0) REVERT: A 83 MET cc_start: 0.8495 (ttm) cc_final: 0.8134 (ttm) REVERT: A 117 ARG cc_start: 0.9200 (mtp180) cc_final: 0.8880 (mmm-85) REVERT: A 131 ASN cc_start: 0.8834 (t0) cc_final: 0.8523 (t0) REVERT: A 195 LYS cc_start: 0.9417 (tptp) cc_final: 0.8900 (tptp) REVERT: A 199 ASP cc_start: 0.9418 (p0) cc_final: 0.8899 (p0) REVERT: S 88 SER cc_start: 0.9009 (t) cc_final: 0.8764 (p) REVERT: S 164 TRP cc_start: 0.6961 (m100) cc_final: 0.6355 (m100) REVERT: Q 13 ASN cc_start: 0.8185 (m-40) cc_final: 0.7747 (m-40) outliers start: 29 outliers final: 17 residues processed: 233 average time/residue: 0.1184 time to fit residues: 37.1930 Evaluate side-chains 210 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 185 GLN ** R 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS A 123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.114016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.091220 restraints weight = 27242.341| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.24 r_work: 0.3447 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10272 Z= 0.189 Angle : 0.683 8.806 13954 Z= 0.352 Chirality : 0.044 0.214 1596 Planarity : 0.004 0.045 1766 Dihedral : 4.438 27.228 1417 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.54 % Allowed : 21.53 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.24), residues: 1294 helix: 1.58 (0.26), residues: 434 sheet: -0.02 (0.28), residues: 351 loop : -0.40 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 67 TYR 0.027 0.002 TYR N 115 PHE 0.039 0.002 PHE R 339 TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00441 (10265) covalent geometry : angle 0.67751 (13942) SS BOND : bond 0.01165 ( 6) SS BOND : angle 3.05329 ( 12) hydrogen bonds : bond 0.03924 ( 518) hydrogen bonds : angle 4.89255 ( 1452) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.417 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: R 11 PHE cc_start: 0.9034 (m-80) cc_final: 0.8748 (m-80) REVERT: R 15 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9234 (tp) REVERT: R 324 ASN cc_start: 0.8975 (t0) cc_final: 0.8771 (t0) REVERT: N 53 GLN cc_start: 0.7522 (mp10) cc_final: 0.7111 (mp10) REVERT: N 73 ASP cc_start: 0.8279 (t0) cc_final: 0.7832 (p0) REVERT: N 76 LYS cc_start: 0.9291 (ttmm) cc_final: 0.8884 (tttp) REVERT: B 57 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8251 (ttmm) REVERT: B 145 TYR cc_start: 0.9096 (p90) cc_final: 0.8594 (p90) REVERT: B 220 GLN cc_start: 0.8556 (mp10) cc_final: 0.8254 (mp10) REVERT: B 262 MET cc_start: 0.7960 (tpp) cc_final: 0.7109 (tpp) REVERT: A 10 LYS cc_start: 0.8559 (mttp) cc_final: 0.7876 (mttm) REVERT: A 14 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7756 (mp0) REVERT: A 21 LYS cc_start: 0.7502 (tttm) cc_final: 0.6956 (tttm) REVERT: A 25 GLU cc_start: 0.7822 (mp0) cc_final: 0.7467 (mp0) REVERT: A 83 MET cc_start: 0.8526 (ttm) cc_final: 0.8172 (ttm) REVERT: A 117 ARG cc_start: 0.9224 (mtp180) cc_final: 0.8986 (mmm-85) REVERT: A 131 ASN cc_start: 0.8816 (t0) cc_final: 0.8472 (t0) REVERT: A 195 LYS cc_start: 0.9434 (tptp) cc_final: 0.8918 (tptp) REVERT: A 199 ASP cc_start: 0.9424 (p0) cc_final: 0.8890 (p0) REVERT: A 231 CYS cc_start: 0.9213 (m) cc_final: 0.8913 (m) REVERT: S 88 SER cc_start: 0.9081 (t) cc_final: 0.8842 (p) REVERT: S 164 TRP cc_start: 0.6925 (m100) cc_final: 0.6320 (m100) outliers start: 37 outliers final: 23 residues processed: 224 average time/residue: 0.1216 time to fit residues: 36.8084 Evaluate side-chains 214 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 15 LEU Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 74 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 210 HIS ** R 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN A 22 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.110661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088623 restraints weight = 27219.663| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.02 r_work: 0.3395 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 10272 Z= 0.267 Angle : 0.766 11.772 13954 Z= 0.394 Chirality : 0.046 0.213 1596 Planarity : 0.005 0.044 1766 Dihedral : 4.839 27.568 1417 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.25 % Allowed : 22.30 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.24), residues: 1294 helix: 1.38 (0.25), residues: 428 sheet: -0.21 (0.28), residues: 355 loop : -0.50 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 67 TYR 0.039 0.002 TYR N 115 PHE 0.031 0.002 PHE R 339 TRP 0.020 0.002 TRP B 169 HIS 0.006 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00618 (10265) covalent geometry : angle 0.75954 (13942) SS BOND : bond 0.01507 ( 6) SS BOND : angle 3.44342 ( 12) hydrogen bonds : bond 0.04432 ( 518) hydrogen bonds : angle 5.17991 ( 1452) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.411 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: R 11 PHE cc_start: 0.9096 (m-80) cc_final: 0.8823 (m-80) REVERT: R 334 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.5036 (t80) REVERT: R 335 MET cc_start: 0.7667 (tpp) cc_final: 0.6910 (tpp) REVERT: N 53 GLN cc_start: 0.7798 (mp10) cc_final: 0.7331 (mp10) REVERT: N 73 ASP cc_start: 0.8393 (t0) cc_final: 0.7773 (p0) REVERT: N 80 TYR cc_start: 0.7992 (m-80) cc_final: 0.7660 (m-10) REVERT: B 220 GLN cc_start: 0.8673 (mp10) cc_final: 0.8348 (mp10) REVERT: B 262 MET cc_start: 0.8102 (tpp) cc_final: 0.7063 (tpp) REVERT: A 21 LYS cc_start: 0.7663 (tttm) cc_final: 0.6980 (ttpp) REVERT: A 25 GLU cc_start: 0.7789 (mp0) cc_final: 0.7265 (mp0) REVERT: A 82 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: A 83 MET cc_start: 0.8517 (ttm) cc_final: 0.8166 (ttm) REVERT: A 117 ARG cc_start: 0.9187 (mtp180) cc_final: 0.8871 (mmm-85) REVERT: A 195 LYS cc_start: 0.9459 (tptp) cc_final: 0.8951 (tptp) REVERT: A 199 ASP cc_start: 0.9413 (p0) cc_final: 0.8925 (p0) REVERT: S 88 SER cc_start: 0.9224 (t) cc_final: 0.9016 (p) REVERT: S 218 MET cc_start: 0.6106 (ttp) cc_final: 0.5320 (tmm) outliers start: 34 outliers final: 25 residues processed: 218 average time/residue: 0.1243 time to fit residues: 36.4973 Evaluate side-chains 209 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.119744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096451 restraints weight = 26449.848| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 4.36 r_work: 0.3461 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10272 Z= 0.145 Angle : 0.713 9.576 13954 Z= 0.359 Chirality : 0.044 0.181 1596 Planarity : 0.004 0.038 1766 Dihedral : 4.525 26.111 1417 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.39 % Allowed : 24.11 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.24), residues: 1294 helix: 1.68 (0.26), residues: 427 sheet: -0.02 (0.29), residues: 338 loop : -0.51 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 179 TYR 0.034 0.002 TYR N 115 PHE 0.025 0.002 PHE N 68 TRP 0.014 0.001 TRP R 111 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00336 (10265) covalent geometry : angle 0.70518 (13942) SS BOND : bond 0.01212 ( 6) SS BOND : angle 3.70662 ( 12) hydrogen bonds : bond 0.03759 ( 518) hydrogen bonds : angle 4.89712 ( 1452) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.394 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: R 11 PHE cc_start: 0.9175 (m-80) cc_final: 0.8874 (m-80) REVERT: R 334 PHE cc_start: 0.5668 (OUTLIER) cc_final: 0.5221 (t80) REVERT: N 32 TYR cc_start: 0.7898 (m-80) cc_final: 0.6713 (m-80) REVERT: N 53 GLN cc_start: 0.7662 (mp10) cc_final: 0.7284 (mp10) REVERT: N 73 ASP cc_start: 0.8275 (t0) cc_final: 0.7984 (t0) REVERT: N 103 PHE cc_start: 0.8611 (m-10) cc_final: 0.8298 (m-80) REVERT: B 145 TYR cc_start: 0.9085 (p90) cc_final: 0.8644 (p90) REVERT: B 220 GLN cc_start: 0.8597 (mp10) cc_final: 0.8264 (mp10) REVERT: B 252 LEU cc_start: 0.9186 (tt) cc_final: 0.8890 (tp) REVERT: B 262 MET cc_start: 0.7947 (tpp) cc_final: 0.6947 (tpp) REVERT: A 14 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7862 (mp0) REVERT: A 21 LYS cc_start: 0.7565 (tttm) cc_final: 0.6916 (ttpp) REVERT: A 25 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7295 (mp0) REVERT: A 75 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 83 MET cc_start: 0.8454 (ttm) cc_final: 0.8132 (ttm) REVERT: A 117 ARG cc_start: 0.9192 (mtp180) cc_final: 0.8953 (mmm-85) REVERT: A 131 ASN cc_start: 0.8873 (t0) cc_final: 0.8505 (t0) REVERT: A 195 LYS cc_start: 0.9418 (tptp) cc_final: 0.8991 (tptp) REVERT: A 199 ASP cc_start: 0.9412 (p0) cc_final: 0.8883 (p0) REVERT: S 164 TRP cc_start: 0.6818 (m100) cc_final: 0.6279 (m100) outliers start: 25 outliers final: 20 residues processed: 218 average time/residue: 0.1238 time to fit residues: 36.3261 Evaluate side-chains 209 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087378 restraints weight = 27467.378| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 4.19 r_work: 0.3379 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 10272 Z= 0.287 Angle : 0.819 10.962 13954 Z= 0.420 Chirality : 0.047 0.250 1596 Planarity : 0.005 0.046 1766 Dihedral : 4.935 29.772 1417 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.11 % Allowed : 24.31 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.24), residues: 1294 helix: 1.43 (0.25), residues: 421 sheet: -0.29 (0.28), residues: 349 loop : -0.59 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 67 TYR 0.038 0.002 TYR N 115 PHE 0.026 0.003 PHE R 339 TRP 0.023 0.002 TRP B 169 HIS 0.006 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00665 (10265) covalent geometry : angle 0.81008 (13942) SS BOND : bond 0.01561 ( 6) SS BOND : angle 4.28978 ( 12) hydrogen bonds : bond 0.04570 ( 518) hydrogen bonds : angle 5.32152 ( 1452) Misc. bond : bond 0.00079 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.9149 (m-80) cc_final: 0.8866 (m-80) REVERT: R 305 TYR cc_start: 0.8975 (m-80) cc_final: 0.8689 (m-80) REVERT: R 334 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5717 (t80) REVERT: N 53 GLN cc_start: 0.7963 (mp10) cc_final: 0.7550 (mp10) REVERT: N 73 ASP cc_start: 0.8328 (t0) cc_final: 0.7807 (p0) REVERT: B 57 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8392 (ttmm) REVERT: B 220 GLN cc_start: 0.8699 (mp10) cc_final: 0.8391 (mp10) REVERT: B 262 MET cc_start: 0.8196 (tpp) cc_final: 0.7041 (tpp) REVERT: A 10 LYS cc_start: 0.8548 (mttp) cc_final: 0.7979 (mmtt) REVERT: A 14 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7730 (mp0) REVERT: A 21 LYS cc_start: 0.7646 (tttm) cc_final: 0.6975 (ttpp) REVERT: A 25 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7284 (mp0) REVERT: A 75 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 83 MET cc_start: 0.8522 (ttm) cc_final: 0.8151 (ttm) REVERT: A 195 LYS cc_start: 0.9470 (tptp) cc_final: 0.8930 (tptp) REVERT: A 199 ASP cc_start: 0.9417 (p0) cc_final: 0.8909 (p0) REVERT: S 211 ASP cc_start: 0.7698 (t0) cc_final: 0.7369 (m-30) REVERT: Q 13 ASN cc_start: 0.8705 (m-40) cc_final: 0.8342 (m-40) outliers start: 22 outliers final: 18 residues processed: 203 average time/residue: 0.1203 time to fit residues: 32.7021 Evaluate side-chains 199 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.115468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093468 restraints weight = 26733.699| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.10 r_work: 0.3481 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10272 Z= 0.146 Angle : 0.746 11.092 13954 Z= 0.377 Chirality : 0.044 0.198 1596 Planarity : 0.004 0.038 1766 Dihedral : 4.602 27.222 1417 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.91 % Allowed : 24.59 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.24), residues: 1294 helix: 1.79 (0.26), residues: 421 sheet: -0.18 (0.28), residues: 350 loop : -0.46 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 117 TYR 0.034 0.002 TYR N 115 PHE 0.025 0.002 PHE N 68 TRP 0.013 0.002 TRP R 286 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00336 (10265) covalent geometry : angle 0.73996 (13942) SS BOND : bond 0.01120 ( 6) SS BOND : angle 3.41910 ( 12) hydrogen bonds : bond 0.03838 ( 518) hydrogen bonds : angle 4.92779 ( 1452) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.94 seconds wall clock time: 55 minutes 33.33 seconds (3333.33 seconds total)