Starting phenix.real_space_refine on Wed Feb 4 05:23:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwg_62610/02_2026/9kwg_62610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwg_62610/02_2026/9kwg_62610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwg_62610/02_2026/9kwg_62610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwg_62610/02_2026/9kwg_62610.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwg_62610/02_2026/9kwg_62610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwg_62610/02_2026/9kwg_62610.cif" } resolution = 3.15 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= 0.015 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 57 5.16 5 C 5606 2.51 5 N 1507 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8774 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2202 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 277} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 3, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1544 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2489 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1656 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 1.55, per 1000 atoms: 0.18 Number of scatterers: 8774 At special positions: 0 Unit cell: (86.698, 120.342, 142.34, 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 57 16.00 O 1604 8.00 N 1507 7.00 C 5606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 54 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 229.3 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 40 through 62 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 70 through 97 removed outlier: 4.239A pdb=" N TRP A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Proline residue: A 90 - end of helix removed outlier: 3.614A pdb=" N LEU A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 140 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 149 through 173 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.574A pdb=" N ALA A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 232 removed outlier: 3.692A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 269 removed outlier: 3.902A pdb=" N LEU A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 275 through 304 removed outlier: 4.023A pdb=" N VAL A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.646A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.521A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 4.041A pdb=" N CYS B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 4 through 26 removed outlier: 3.984A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'F' and resid 1 through 3 No H-bonds generated for 'chain 'F' and resid 1 through 3' Processing helix chain 'F' and resid 4 through 11 Processing helix chain 'F' and resid 15 through 24 Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 45 through 64 removed outlier: 3.720A pdb=" N ARG F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.707A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.791A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.755A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.755A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.532A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.958A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.549A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.637A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 251 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.548A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.701A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.676A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.668A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1275 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: 1.40 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.57: 8886 1.57 - 1.92: 73 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.96: 1 Bond restraints: 8960 Sorted by residual: bond pdb=" C THR F 42 " pdb=" N GLY F 44 " ideal model delta sigma weight residual 1.330 2.965 -1.634 1.49e-02 4.50e+03 1.20e+04 bond pdb=" CB CYS F 47 " pdb=" SG CYS F 47 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" C TYR A 182 " pdb=" N SER A 183 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.73e-02 3.34e+03 2.46e+00 bond pdb=" CB VAL C 71 " pdb=" CG2 VAL C 71 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CB LYS F 20 " pdb=" CG LYS F 20 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 8955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.52: 12221 9.52 - 19.03: 1 19.03 - 28.55: 1 28.55 - 38.07: 0 38.07 - 47.58: 1 Bond angle restraints: 12224 Sorted by residual: angle pdb=" O THR F 42 " pdb=" C THR F 42 " pdb=" N GLY F 44 " ideal model delta sigma weight residual 122.59 75.01 47.58 1.33e+00 5.65e-01 1.28e+03 angle pdb=" C THR F 42 " pdb=" N GLY F 44 " pdb=" CA GLY F 44 " ideal model delta sigma weight residual 121.87 145.06 -23.19 1.57e+00 4.06e-01 2.18e+02 angle pdb=" CA THR F 42 " pdb=" C THR F 42 " pdb=" N GLY F 44 " ideal model delta sigma weight residual 116.84 134.64 -17.80 1.71e+00 3.42e-01 1.08e+02 angle pdb=" CA LYS A 32 " pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 angle pdb=" CB LYS F 20 " pdb=" CG LYS F 20 " pdb=" CD LYS F 20 " ideal model delta sigma weight residual 111.30 118.26 -6.96 2.30e+00 1.89e-01 9.16e+00 ... (remaining 12219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 4953 21.85 - 43.71: 273 43.71 - 65.56: 19 65.56 - 87.41: 3 87.41 - 109.26: 3 Dihedral angle restraints: 5251 sinusoidal: 1793 harmonic: 3458 Sorted by residual: dihedral pdb=" CA THR F 42 " pdb=" C THR F 42 " pdb=" N GLY F 44 " pdb=" CA GLY F 44 " ideal model delta harmonic sigma weight residual -180.00 -70.74 -109.26 0 5.00e+00 4.00e-02 4.78e+02 dihedral pdb=" CA HIS A 185 " pdb=" C HIS A 185 " pdb=" N THR A 186 " pdb=" CA THR A 186 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" N ARG A 33 " pdb=" CA ARG A 33 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 5248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 941 0.036 - 0.072: 359 0.072 - 0.107: 117 0.107 - 0.143: 28 0.143 - 0.179: 3 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CA CYS F 47 " pdb=" N CYS F 47 " pdb=" C CYS F 47 " pdb=" CB CYS F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE H 189 " pdb=" N ILE H 189 " pdb=" C ILE H 189 " pdb=" CB ILE H 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1445 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 42 " 0.171 2.00e-02 2.50e+03 2.11e-01 4.44e+02 pdb=" C THR F 42 " -0.358 2.00e-02 2.50e+03 pdb=" O THR F 42 " 0.131 2.00e-02 2.50e+03 pdb=" N GLY F 44 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 31 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 48 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ILE F 48 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE F 48 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG F 49 " 0.010 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 776 2.74 - 3.28: 8830 3.28 - 3.82: 14481 3.82 - 4.36: 17113 4.36 - 4.90: 30199 Nonbonded interactions: 71399 Sorted by model distance: nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 291 " pdb=" O PRO B 294 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR C 321 " pdb=" OD1 ASP C 323 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN A 71 " pdb=" NH2 ARG A 148 " model vdw 2.246 3.120 ... (remaining 71394 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: 0.950 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.040 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: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.018 1.634 8966 Z= 1.170 Angle : 0.761 47.583 12236 Z= 0.472 Chirality : 0.043 0.179 1448 Planarity : 0.007 0.211 1550 Dihedral : 12.939 109.265 3001 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1176 helix: 1.30 (0.26), residues: 412 sheet: -0.13 (0.33), residues: 261 loop : -0.90 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 40 TYR 0.016 0.002 TYR F 31 PHE 0.020 0.001 PHE A 139 TRP 0.013 0.001 TRP A 102 HIS 0.007 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.01769 ( 8960) covalent geometry : angle 0.75842 (12224) SS BOND : bond 0.00170 ( 6) SS BOND : angle 2.19745 ( 12) hydrogen bonds : bond 0.15364 ( 434) hydrogen bonds : angle 7.16016 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.225 Fit side-chains REVERT: A 100 ASN cc_start: 0.7348 (m-40) cc_final: 0.7069 (m-40) REVERT: A 131 SER cc_start: 0.8014 (t) cc_final: 0.7725 (p) REVERT: A 224 THR cc_start: 0.8666 (m) cc_final: 0.8449 (m) REVERT: B 14 GLU cc_start: 0.7789 (tt0) cc_final: 0.7575 (tt0) REVERT: B 252 ASP cc_start: 0.7492 (t0) cc_final: 0.7176 (t0) REVERT: B 258 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8040 (ptmt) REVERT: C 23 LYS cc_start: 0.8415 (tppt) cc_final: 0.8042 (tppt) REVERT: C 122 SER cc_start: 0.7375 (p) cc_final: 0.7053 (m) REVERT: C 150 ARG cc_start: 0.7803 (mmt-90) cc_final: 0.6874 (mpt180) REVERT: C 155 ASN cc_start: 0.7749 (t0) cc_final: 0.7129 (t0) REVERT: C 251 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7753 (mtt-85) REVERT: C 254 ASP cc_start: 0.8229 (p0) cc_final: 0.7926 (p0) REVERT: C 296 VAL cc_start: 0.8358 (m) cc_final: 0.8092 (t) REVERT: C 317 CYS cc_start: 0.7500 (p) cc_final: 0.7230 (p) REVERT: H 103 TYR cc_start: 0.8188 (t80) cc_final: 0.7727 (t80) REVERT: H 184 SER cc_start: 0.7634 (p) cc_final: 0.7341 (m) REVERT: H 210 THR cc_start: 0.7828 (p) cc_final: 0.7475 (m) REVERT: H 212 PHE cc_start: 0.7503 (m-80) cc_final: 0.7171 (m-10) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1056 time to fit residues: 27.6689 Evaluate side-chains 169 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN B 256 ASN C 175 GLN G 18 GLN H 39 GLN H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117211 restraints weight = 12672.477| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.01 r_work: 0.3368 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8966 Z= 0.267 Angle : 0.675 7.169 12236 Z= 0.356 Chirality : 0.047 0.186 1448 Planarity : 0.005 0.072 1550 Dihedral : 5.694 86.045 1273 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.42 % Allowed : 11.28 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1178 helix: 1.02 (0.26), residues: 410 sheet: -0.33 (0.33), residues: 257 loop : -1.03 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 175 TYR 0.018 0.002 TYR H 190 PHE 0.019 0.002 PHE C 253 TRP 0.024 0.002 TRP C 82 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 8960) covalent geometry : angle 0.67420 (12224) SS BOND : bond 0.00431 ( 6) SS BOND : angle 1.31840 ( 12) hydrogen bonds : bond 0.04602 ( 434) hydrogen bonds : angle 5.48402 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.316 Fit side-chains REVERT: A 100 ASN cc_start: 0.7430 (m-40) cc_final: 0.7214 (m-40) REVERT: A 131 SER cc_start: 0.8212 (t) cc_final: 0.7921 (p) REVERT: A 165 LEU cc_start: 0.7709 (tp) cc_final: 0.7483 (tp) REVERT: B 211 LYS cc_start: 0.8233 (mmmt) cc_final: 0.8000 (mmmt) REVERT: B 258 LYS cc_start: 0.8511 (ptmt) cc_final: 0.8292 (ptmt) REVERT: B 271 LYS cc_start: 0.8255 (ttmt) cc_final: 0.8051 (ttpp) REVERT: C 150 ARG cc_start: 0.8055 (mmt-90) cc_final: 0.7706 (mpt180) REVERT: C 155 ASN cc_start: 0.8036 (t0) cc_final: 0.7623 (t0) REVERT: C 189 SER cc_start: 0.8261 (t) cc_final: 0.8012 (p) REVERT: C 251 ARG cc_start: 0.8448 (mtt90) cc_final: 0.8191 (mtt-85) REVERT: C 314 ARG cc_start: 0.8319 (ttm170) cc_final: 0.7998 (ttm170) REVERT: F 71 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8059 (mm-40) REVERT: H 90 ASP cc_start: 0.8263 (m-30) cc_final: 0.8036 (m-30) REVERT: H 101 TYR cc_start: 0.8625 (m-80) cc_final: 0.8332 (m-80) REVERT: H 166 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7697 (mm) REVERT: H 184 SER cc_start: 0.7790 (p) cc_final: 0.7510 (m) REVERT: H 210 THR cc_start: 0.7943 (p) cc_final: 0.7459 (m) REVERT: H 212 PHE cc_start: 0.7978 (m-80) cc_final: 0.7771 (m-10) REVERT: H 243 THR cc_start: 0.8373 (p) cc_final: 0.8137 (m) outliers start: 21 outliers final: 14 residues processed: 189 average time/residue: 0.1073 time to fit residues: 26.4980 Evaluate side-chains 190 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain F residue 71 GLN Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119036 restraints weight = 12632.428| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.00 r_work: 0.3396 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8966 Z= 0.160 Angle : 0.584 7.773 12236 Z= 0.305 Chirality : 0.043 0.170 1448 Planarity : 0.004 0.053 1550 Dihedral : 5.359 85.132 1273 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.68 % Allowed : 14.50 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1178 helix: 1.30 (0.26), residues: 409 sheet: -0.27 (0.33), residues: 254 loop : -1.04 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 27 TYR 0.017 0.002 TYR H 190 PHE 0.016 0.002 PHE C 253 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8960) covalent geometry : angle 0.58311 (12224) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.96245 ( 12) hydrogen bonds : bond 0.04008 ( 434) hydrogen bonds : angle 5.10599 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.301 Fit side-chains REVERT: A 131 SER cc_start: 0.8214 (t) cc_final: 0.7905 (p) REVERT: B 46 LYS cc_start: 0.6181 (mtmm) cc_final: 0.5894 (mtmm) REVERT: C 150 ARG cc_start: 0.8034 (mmt-90) cc_final: 0.7752 (mpt180) REVERT: C 155 ASN cc_start: 0.8033 (t0) cc_final: 0.7754 (t0) REVERT: C 239 ASN cc_start: 0.7881 (m-40) cc_final: 0.7675 (m-40) REVERT: C 278 PHE cc_start: 0.8367 (m-80) cc_final: 0.7426 (m-80) REVERT: C 314 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7961 (ttm170) REVERT: H 90 ASP cc_start: 0.8197 (m-30) cc_final: 0.7977 (m-30) REVERT: H 101 TYR cc_start: 0.8608 (m-80) cc_final: 0.8305 (m-80) REVERT: H 166 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7804 (mm) REVERT: H 184 SER cc_start: 0.7915 (p) cc_final: 0.7659 (m) REVERT: H 243 THR cc_start: 0.8358 (p) cc_final: 0.8089 (m) outliers start: 32 outliers final: 22 residues processed: 197 average time/residue: 0.1098 time to fit residues: 28.2906 Evaluate side-chains 201 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118231 restraints weight = 12669.143| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.01 r_work: 0.3384 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8966 Z= 0.185 Angle : 0.593 8.275 12236 Z= 0.309 Chirality : 0.044 0.170 1448 Planarity : 0.004 0.058 1550 Dihedral : 5.344 85.254 1273 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Rotamer: Outliers : 4.26 % Allowed : 15.19 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1178 helix: 1.25 (0.26), residues: 407 sheet: -0.35 (0.33), residues: 256 loop : -1.00 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.016 0.002 TYR H 190 PHE 0.016 0.002 PHE C 253 TRP 0.013 0.002 TRP C 339 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8960) covalent geometry : angle 0.59253 (12224) SS BOND : bond 0.00361 ( 6) SS BOND : angle 0.85280 ( 12) hydrogen bonds : bond 0.03969 ( 434) hydrogen bonds : angle 5.03230 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.320 Fit side-chains REVERT: A 131 SER cc_start: 0.8181 (t) cc_final: 0.7894 (p) REVERT: B 46 LYS cc_start: 0.6116 (mtmm) cc_final: 0.5898 (mtmm) REVERT: C 49 ARG cc_start: 0.8250 (mmt90) cc_final: 0.8042 (mmt90) REVERT: C 147 SER cc_start: 0.8122 (m) cc_final: 0.7891 (p) REVERT: C 150 ARG cc_start: 0.8130 (mmt-90) cc_final: 0.7242 (mpt180) REVERT: C 155 ASN cc_start: 0.8011 (t0) cc_final: 0.7732 (t0) REVERT: C 189 SER cc_start: 0.8329 (t) cc_final: 0.8049 (p) REVERT: C 278 PHE cc_start: 0.8346 (m-80) cc_final: 0.7471 (m-80) REVERT: C 314 ARG cc_start: 0.8353 (ttm170) cc_final: 0.7983 (ttm170) REVERT: H 101 TYR cc_start: 0.8643 (m-80) cc_final: 0.8284 (m-80) REVERT: H 184 SER cc_start: 0.7893 (p) cc_final: 0.7645 (m) outliers start: 37 outliers final: 28 residues processed: 197 average time/residue: 0.1137 time to fit residues: 29.2171 Evaluate side-chains 204 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.0670 chunk 24 optimal weight: 0.0270 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119610 restraints weight = 12701.692| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.02 r_work: 0.3399 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8966 Z= 0.144 Angle : 0.569 8.322 12236 Z= 0.295 Chirality : 0.043 0.165 1448 Planarity : 0.004 0.041 1550 Dihedral : 5.212 85.694 1273 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.60 % Allowed : 16.34 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1178 helix: 1.44 (0.26), residues: 407 sheet: -0.37 (0.33), residues: 255 loop : -0.97 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.015 0.001 TYR H 190 PHE 0.014 0.001 PHE C 253 TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8960) covalent geometry : angle 0.56790 (12224) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.04967 ( 12) hydrogen bonds : bond 0.03709 ( 434) hydrogen bonds : angle 4.86314 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.281 Fit side-chains REVERT: A 131 SER cc_start: 0.8162 (t) cc_final: 0.7854 (p) REVERT: A 257 LEU cc_start: 0.7694 (tp) cc_final: 0.7306 (tp) REVERT: B 271 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7774 (ttpp) REVERT: C 49 ARG cc_start: 0.8259 (mmt90) cc_final: 0.8020 (mmt90) REVERT: C 147 SER cc_start: 0.8105 (m) cc_final: 0.7863 (p) REVERT: C 150 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7302 (mpt180) REVERT: C 155 ASN cc_start: 0.7990 (t0) cc_final: 0.7703 (t0) REVERT: C 189 SER cc_start: 0.8352 (t) cc_final: 0.8025 (p) REVERT: C 198 LEU cc_start: 0.7925 (pp) cc_final: 0.7563 (pt) REVERT: C 278 PHE cc_start: 0.8338 (m-80) cc_final: 0.7616 (m-80) REVERT: C 314 ARG cc_start: 0.8341 (ttm170) cc_final: 0.8032 (ttm170) REVERT: F 71 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7910 (mm-40) REVERT: H 101 TYR cc_start: 0.8648 (m-80) cc_final: 0.8276 (m-80) REVERT: H 184 SER cc_start: 0.7870 (p) cc_final: 0.7661 (m) outliers start: 40 outliers final: 30 residues processed: 200 average time/residue: 0.1149 time to fit residues: 30.0282 Evaluate side-chains 206 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain F residue 71 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 61 optimal weight: 0.9980 chunk 114 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119196 restraints weight = 12629.426| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.01 r_work: 0.3394 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8966 Z= 0.166 Angle : 0.581 8.631 12236 Z= 0.300 Chirality : 0.043 0.176 1448 Planarity : 0.004 0.041 1550 Dihedral : 5.214 85.829 1273 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.52 % Allowed : 16.00 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1178 helix: 1.40 (0.26), residues: 408 sheet: -0.56 (0.31), residues: 277 loop : -0.93 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.014 0.001 TYR H 95 PHE 0.016 0.001 PHE C 253 TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8960) covalent geometry : angle 0.58029 (12224) SS BOND : bond 0.00343 ( 6) SS BOND : angle 0.84915 ( 12) hydrogen bonds : bond 0.03752 ( 434) hydrogen bonds : angle 4.86512 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 0.305 Fit side-chains REVERT: A 131 SER cc_start: 0.8172 (t) cc_final: 0.7861 (p) REVERT: A 257 LEU cc_start: 0.7664 (tp) cc_final: 0.7340 (tp) REVERT: B 274 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7607 (pt) REVERT: C 37 ILE cc_start: 0.7621 (mm) cc_final: 0.7335 (tt) REVERT: C 49 ARG cc_start: 0.8278 (mmt90) cc_final: 0.8013 (mmt90) REVERT: C 147 SER cc_start: 0.8099 (m) cc_final: 0.7865 (p) REVERT: C 150 ARG cc_start: 0.8162 (mmt-90) cc_final: 0.7346 (mpt180) REVERT: C 155 ASN cc_start: 0.7981 (t0) cc_final: 0.7692 (t0) REVERT: C 169 TRP cc_start: 0.8418 (m100) cc_final: 0.8214 (m100) REVERT: C 189 SER cc_start: 0.8332 (t) cc_final: 0.8012 (p) REVERT: C 278 PHE cc_start: 0.8330 (m-80) cc_final: 0.7645 (m-80) REVERT: C 314 ARG cc_start: 0.8327 (ttm170) cc_final: 0.7929 (ttm170) REVERT: F 71 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7932 (mm-40) REVERT: H 101 TYR cc_start: 0.8588 (m-80) cc_final: 0.8178 (m-80) REVERT: H 184 SER cc_start: 0.7869 (p) cc_final: 0.7661 (m) outliers start: 48 outliers final: 37 residues processed: 201 average time/residue: 0.1051 time to fit residues: 27.8874 Evaluate side-chains 213 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 71 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 61 optimal weight: 0.1980 chunk 33 optimal weight: 0.0670 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121920 restraints weight = 12661.702| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.03 r_work: 0.3431 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 8966 Z= 0.110 Angle : 0.535 8.446 12236 Z= 0.279 Chirality : 0.041 0.166 1448 Planarity : 0.004 0.041 1550 Dihedral : 4.998 86.423 1273 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.49 % Allowed : 17.03 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1178 helix: 1.62 (0.27), residues: 409 sheet: -0.57 (0.32), residues: 270 loop : -0.90 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.013 0.001 TYR H 190 PHE 0.013 0.001 PHE C 253 TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8960) covalent geometry : angle 0.53393 (12224) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.26367 ( 12) hydrogen bonds : bond 0.03367 ( 434) hydrogen bonds : angle 4.65787 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 100 ASN cc_start: 0.7372 (m-40) cc_final: 0.7166 (m-40) REVERT: A 131 SER cc_start: 0.8211 (t) cc_final: 0.7896 (p) REVERT: A 168 THR cc_start: 0.7326 (p) cc_final: 0.6519 (t) REVERT: B 274 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7523 (pt) REVERT: C 37 ILE cc_start: 0.7573 (mm) cc_final: 0.7176 (tt) REVERT: C 49 ARG cc_start: 0.8220 (mmt90) cc_final: 0.7952 (mmt90) REVERT: C 147 SER cc_start: 0.8100 (m) cc_final: 0.7828 (p) REVERT: C 150 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7361 (mpt180) REVERT: C 155 ASN cc_start: 0.7942 (t0) cc_final: 0.7664 (t0) REVERT: C 169 TRP cc_start: 0.8324 (m100) cc_final: 0.8046 (m100) REVERT: C 189 SER cc_start: 0.8303 (t) cc_final: 0.7960 (p) REVERT: C 314 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7980 (ttm170) REVERT: F 71 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: H 101 TYR cc_start: 0.8577 (m-80) cc_final: 0.8183 (m-80) outliers start: 39 outliers final: 27 residues processed: 200 average time/residue: 0.1062 time to fit residues: 28.1823 Evaluate side-chains 198 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 71 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 33 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118012 restraints weight = 12559.722| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.00 r_work: 0.3378 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8966 Z= 0.240 Angle : 0.622 8.949 12236 Z= 0.324 Chirality : 0.045 0.178 1448 Planarity : 0.004 0.041 1550 Dihedral : 5.297 85.619 1273 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 4.26 % Allowed : 18.30 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1178 helix: 1.24 (0.26), residues: 414 sheet: -0.62 (0.31), residues: 267 loop : -0.97 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 175 TYR 0.013 0.002 TYR H 190 PHE 0.022 0.002 PHE C 253 TRP 0.015 0.002 TRP C 339 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 8960) covalent geometry : angle 0.62046 (12224) SS BOND : bond 0.00393 ( 6) SS BOND : angle 1.60196 ( 12) hydrogen bonds : bond 0.04104 ( 434) hydrogen bonds : angle 4.97286 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.332 Fit side-chains REVERT: A 131 SER cc_start: 0.8134 (t) cc_final: 0.7833 (p) REVERT: B 274 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7637 (pt) REVERT: C 37 ILE cc_start: 0.7699 (mm) cc_final: 0.7399 (tt) REVERT: C 49 ARG cc_start: 0.8296 (mmt90) cc_final: 0.7986 (mmt90) REVERT: C 150 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7296 (mpt180) REVERT: C 155 ASN cc_start: 0.7995 (t0) cc_final: 0.7694 (t0) REVERT: C 314 ARG cc_start: 0.8361 (ttm170) cc_final: 0.8010 (ttm170) REVERT: H 101 TYR cc_start: 0.8567 (m-80) cc_final: 0.8116 (m-80) outliers start: 37 outliers final: 29 residues processed: 189 average time/residue: 0.1103 time to fit residues: 27.2775 Evaluate side-chains 198 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119127 restraints weight = 12547.069| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.98 r_work: 0.3394 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8966 Z= 0.177 Angle : 0.585 8.755 12236 Z= 0.305 Chirality : 0.043 0.173 1448 Planarity : 0.004 0.041 1550 Dihedral : 5.246 86.409 1273 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.57 % Allowed : 19.56 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1178 helix: 1.37 (0.26), residues: 410 sheet: -0.63 (0.31), residues: 266 loop : -1.00 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.013 0.001 TYR H 190 PHE 0.015 0.002 PHE C 253 TRP 0.010 0.001 TRP C 339 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8960) covalent geometry : angle 0.58344 (12224) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.32949 ( 12) hydrogen bonds : bond 0.03823 ( 434) hydrogen bonds : angle 4.89750 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.427 Fit side-chains REVERT: A 131 SER cc_start: 0.8128 (t) cc_final: 0.7814 (p) REVERT: B 274 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7596 (pt) REVERT: C 37 ILE cc_start: 0.7675 (mm) cc_final: 0.7385 (tt) REVERT: C 49 ARG cc_start: 0.8302 (mmt90) cc_final: 0.7996 (mmt90) REVERT: C 150 ARG cc_start: 0.8142 (mmt-90) cc_final: 0.7348 (mpt180) REVERT: C 155 ASN cc_start: 0.7995 (t0) cc_final: 0.7697 (t0) REVERT: C 314 ARG cc_start: 0.8349 (ttm170) cc_final: 0.8075 (ttm170) REVERT: H 101 TYR cc_start: 0.8557 (m-80) cc_final: 0.8130 (m-80) outliers start: 31 outliers final: 30 residues processed: 186 average time/residue: 0.1259 time to fit residues: 30.3170 Evaluate side-chains 196 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 0.0070 chunk 115 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 57 optimal weight: 0.0470 chunk 47 optimal weight: 0.6980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120886 restraints weight = 12522.629| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.01 r_work: 0.3419 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8966 Z= 0.124 Angle : 0.551 8.715 12236 Z= 0.288 Chirality : 0.042 0.171 1448 Planarity : 0.004 0.041 1550 Dihedral : 5.076 87.614 1273 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.68 % Allowed : 20.02 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1178 helix: 1.60 (0.26), residues: 410 sheet: -0.63 (0.31), residues: 266 loop : -0.97 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.012 0.001 TYR H 190 PHE 0.012 0.001 PHE C 253 TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS F 67 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8960) covalent geometry : angle 0.54973 (12224) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.11685 ( 12) hydrogen bonds : bond 0.03476 ( 434) hydrogen bonds : angle 4.70344 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 131 SER cc_start: 0.8148 (t) cc_final: 0.7835 (p) REVERT: A 168 THR cc_start: 0.7320 (p) cc_final: 0.6570 (t) REVERT: B 274 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7556 (pt) REVERT: C 37 ILE cc_start: 0.7643 (mm) cc_final: 0.7365 (tt) REVERT: C 49 ARG cc_start: 0.8281 (mmt90) cc_final: 0.7986 (mmt90) REVERT: C 150 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7366 (mpt180) REVERT: C 155 ASN cc_start: 0.7981 (t0) cc_final: 0.7679 (t0) REVERT: C 219 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7802 (ttm-80) REVERT: C 314 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7927 (ttm170) REVERT: H 101 TYR cc_start: 0.8558 (m-80) cc_final: 0.8107 (m-80) outliers start: 32 outliers final: 28 residues processed: 186 average time/residue: 0.1064 time to fit residues: 25.8183 Evaluate side-chains 198 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119260 restraints weight = 12445.570| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.00 r_work: 0.3389 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8966 Z= 0.184 Angle : 0.584 8.895 12236 Z= 0.304 Chirality : 0.044 0.173 1448 Planarity : 0.004 0.042 1550 Dihedral : 5.199 87.255 1273 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.91 % Allowed : 19.91 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1178 helix: 1.48 (0.26), residues: 410 sheet: -0.67 (0.31), residues: 267 loop : -0.96 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.013 0.001 TYR H 190 PHE 0.016 0.002 PHE C 253 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8960) covalent geometry : angle 0.58324 (12224) SS BOND : bond 0.00355 ( 6) SS BOND : angle 1.24375 ( 12) hydrogen bonds : bond 0.03794 ( 434) hydrogen bonds : angle 4.82457 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.07 seconds wall clock time: 41 minutes 7.83 seconds (2467.83 seconds total)