Starting phenix.real_space_refine on Thu Mar 13 04:11:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbf_24978/03_2025/7sbf_24978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbf_24978/03_2025/7sbf_24978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2025/7sbf_24978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2025/7sbf_24978.map" model { file = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2025/7sbf_24978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2025/7sbf_24978.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 1.000 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 65 5.16 5 C 5452 2.51 5 N 1450 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8525 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1683 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2537 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2157 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'8QY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.23, per 1000 atoms: 0.61 Number of scatterers: 8525 At special positions: 0 Unit cell: (98.58, 116.6, 115.54, 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 65 16.00 O 1558 8.00 N 1450 7.00 C 5452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.932A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.636A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.371A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.714A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.340A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.980A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.066A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.610A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.951A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.976A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.232A pdb=" N THR R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 120 removed outlier: 3.906A pdb=" N THR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 131 removed outlier: 3.548A pdb=" N GLN R 124 " --> pdb=" O THR R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 140 removed outlier: 3.978A pdb=" N LEU R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS R 140 " --> pdb=" O GLY R 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 135 through 140' Processing helix chain 'R' and resid 142 through 171 removed outlier: 3.617A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 179 removed outlier: 3.666A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 206 removed outlier: 3.714A pdb=" N ALA R 197 " --> pdb=" O ILE R 193 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 224 through 241 removed outlier: 4.748A pdb=" N ASN R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 260 removed outlier: 3.870A pdb=" N VAL R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 266 removed outlier: 6.767A pdb=" N MET R 264 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER R 266 " --> pdb=" O ARG R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 306 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 311 through 337 removed outlier: 3.772A pdb=" N THR R 315 " --> pdb=" O THR R 311 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.523A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.572A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.547A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.182A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.836A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.599A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.794A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.801A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.837A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.837A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.456A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 208 through 209 removed outlier: 3.583A pdb=" N ASP R 216 " --> pdb=" O LYS R 209 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2710 1.34 - 1.46: 1866 1.46 - 1.58: 4032 1.58 - 1.69: 3 1.69 - 1.81: 94 Bond restraints: 8705 Sorted by residual: bond pdb=" C02 8QY R 501 " pdb=" N03 8QY R 501 " ideal model delta sigma weight residual 1.365 1.441 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C02 8QY R 501 " pdb=" N12 8QY R 501 " ideal model delta sigma weight residual 1.360 1.423 -0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" N ILE R 142 " pdb=" CA ILE R 142 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" C04 8QY R 501 " pdb=" N03 8QY R 501 " ideal model delta sigma weight residual 1.449 1.500 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C13 8QY R 501 " pdb=" C14 8QY R 501 " ideal model delta sigma weight residual 1.536 1.586 -0.050 2.00e-02 2.50e+03 6.30e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11615 2.02 - 4.04: 171 4.04 - 6.06: 31 6.06 - 8.09: 6 8.09 - 10.11: 3 Bond angle restraints: 11826 Sorted by residual: angle pdb=" N LYS R 141 " pdb=" CA LYS R 141 " pdb=" C LYS R 141 " ideal model delta sigma weight residual 113.17 103.06 10.11 1.26e+00 6.30e-01 6.43e+01 angle pdb=" C ILE B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta sigma weight residual 121.14 114.16 6.98 1.75e+00 3.27e-01 1.59e+01 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.16 108.30 4.86 1.24e+00 6.50e-01 1.54e+01 angle pdb=" C ARG B 19 " pdb=" N ASP B 20 " pdb=" CA ASP B 20 " ideal model delta sigma weight residual 121.58 114.47 7.11 1.95e+00 2.63e-01 1.33e+01 angle pdb=" CA ILE R 142 " pdb=" C ILE R 142 " pdb=" O ILE R 142 " ideal model delta sigma weight residual 120.78 116.33 4.45 1.25e+00 6.40e-01 1.27e+01 ... (remaining 11821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4715 17.74 - 35.48: 366 35.48 - 53.23: 36 53.23 - 70.97: 10 70.97 - 88.71: 7 Dihedral angle restraints: 5134 sinusoidal: 1883 harmonic: 3251 Sorted by residual: dihedral pdb=" CB CYS R 140 " pdb=" SG CYS R 140 " pdb=" SG CYS R 217 " pdb=" CB CYS R 217 " ideal model delta sinusoidal sigma weight residual -86.00 -162.14 76.14 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER R 268 " pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta harmonic sigma weight residual 180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1171 0.065 - 0.131: 192 0.131 - 0.196: 6 0.196 - 0.261: 0 0.261 - 0.327: 3 Chirality restraints: 1372 Sorted by residual: chirality pdb=" C14 8QY R 501 " pdb=" C13 8QY R 501 " pdb=" C15 8QY R 501 " pdb=" N23 8QY R 501 " both_signs ideal model delta sigma weight residual False 2.36 2.69 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASP B 247 " pdb=" N ASP B 247 " pdb=" C ASP B 247 " pdb=" CB ASP B 247 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA LYS R 141 " pdb=" N LYS R 141 " pdb=" C LYS R 141 " pdb=" CB LYS R 141 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1369 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 308 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO R 309 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 309 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 309 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 83 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU R 83 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU R 83 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE R 84 " -0.011 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 724 2.74 - 3.28: 8503 3.28 - 3.82: 14213 3.82 - 4.36: 17111 4.36 - 4.90: 30122 Nonbonded interactions: 70673 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.200 3.040 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.244 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.268 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.299 3.120 ... (remaining 70668 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: 0.850 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.370 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.005 0.082 8705 Z= 0.318 Angle : 0.652 10.106 11826 Z= 0.357 Chirality : 0.047 0.327 1372 Planarity : 0.004 0.058 1485 Dihedral : 12.821 88.712 3027 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 0.23 % Allowed : 0.68 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1103 helix: 0.92 (0.28), residues: 367 sheet: -0.37 (0.28), residues: 289 loop : -0.41 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE A 274 TYR 0.017 0.002 TYR A 296 ARG 0.003 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.895 Fit side-chains REVERT: A 245 GLU cc_start: 0.7139 (mp0) cc_final: 0.6905 (mp0) REVERT: A 247 MET cc_start: 0.8579 (mtp) cc_final: 0.8330 (mtp) REVERT: A 273 LEU cc_start: 0.8744 (tp) cc_final: 0.8522 (tm) REVERT: A 308 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 337 ASP cc_start: 0.7884 (m-30) cc_final: 0.7655 (m-30) REVERT: R 86 ASN cc_start: 0.7868 (m-40) cc_final: 0.7653 (m-40) REVERT: R 87 PHE cc_start: 0.8036 (m-10) cc_final: 0.7423 (m-80) REVERT: R 190 CYS cc_start: 0.8128 (t) cc_final: 0.7834 (t) REVERT: R 342 ASN cc_start: 0.7970 (m-40) cc_final: 0.7714 (m-40) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 1.2377 time to fit residues: 251.7216 Evaluate side-chains 143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 268 ASN C 59 ASN E 167 GLN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104545 restraints weight = 11776.706| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.46 r_work: 0.3148 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8705 Z= 0.200 Angle : 0.560 8.006 11826 Z= 0.295 Chirality : 0.043 0.137 1372 Planarity : 0.003 0.043 1485 Dihedral : 6.327 89.283 1221 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.15 % Allowed : 14.50 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1103 helix: 1.15 (0.28), residues: 364 sheet: -0.29 (0.29), residues: 277 loop : -0.39 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS R 297 PHE 0.013 0.001 PHE R 135 TYR 0.017 0.001 TYR A 296 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: A 245 GLU cc_start: 0.7428 (mp0) cc_final: 0.6869 (mp0) REVERT: A 247 MET cc_start: 0.8836 (mtp) cc_final: 0.8616 (mtp) REVERT: A 273 LEU cc_start: 0.8676 (tp) cc_final: 0.8448 (tm) REVERT: A 337 ASP cc_start: 0.8398 (m-30) cc_final: 0.8109 (m-30) REVERT: B 13 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8207 (pp30) REVERT: B 42 ARG cc_start: 0.7576 (tpt170) cc_final: 0.7275 (tpp-160) REVERT: E 84 THR cc_start: 0.9331 (m) cc_final: 0.9101 (p) REVERT: R 87 PHE cc_start: 0.8282 (m-10) cc_final: 0.7808 (m-80) REVERT: R 130 MET cc_start: 0.8103 (mpp) cc_final: 0.7739 (mpp) REVERT: R 258 ARG cc_start: 0.8011 (tmt170) cc_final: 0.7751 (tmt170) outliers start: 19 outliers final: 10 residues processed: 167 average time/residue: 1.2548 time to fit residues: 222.2964 Evaluate side-chains 159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 ASN ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104678 restraints weight = 11884.363| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.52 r_work: 0.3154 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8705 Z= 0.207 Angle : 0.545 7.928 11826 Z= 0.286 Chirality : 0.042 0.137 1372 Planarity : 0.003 0.045 1485 Dihedral : 6.058 87.285 1221 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.06 % Allowed : 17.21 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1103 helix: 1.35 (0.28), residues: 361 sheet: -0.21 (0.29), residues: 285 loop : -0.50 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR R 149 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: A 20 ASP cc_start: 0.8518 (t0) cc_final: 0.8231 (m-30) REVERT: A 242 ARG cc_start: 0.7302 (mmp-170) cc_final: 0.7020 (mmp-170) REVERT: A 245 GLU cc_start: 0.7500 (mp0) cc_final: 0.6848 (mp0) REVERT: A 337 ASP cc_start: 0.8381 (m-30) cc_final: 0.8075 (m-30) REVERT: B 42 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7392 (tpp-160) REVERT: E 38 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.7842 (ptp90) REVERT: E 43 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8327 (mmmt) REVERT: E 84 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9095 (p) REVERT: R 65 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7187 (tt) REVERT: R 87 PHE cc_start: 0.8297 (m-10) cc_final: 0.7821 (m-80) REVERT: R 258 ARG cc_start: 0.8008 (tmt170) cc_final: 0.7735 (tmt170) outliers start: 27 outliers final: 11 residues processed: 166 average time/residue: 1.1716 time to fit residues: 206.9728 Evaluate side-chains 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 306 GLN B 13 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 HIS ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101869 restraints weight = 11907.397| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.50 r_work: 0.3105 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8705 Z= 0.341 Angle : 0.599 9.405 11826 Z= 0.314 Chirality : 0.044 0.156 1372 Planarity : 0.004 0.048 1485 Dihedral : 6.036 83.792 1221 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.08 % Allowed : 17.33 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1103 helix: 1.33 (0.28), residues: 359 sheet: -0.20 (0.29), residues: 298 loop : -0.47 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS R 297 PHE 0.012 0.001 PHE A 189 TYR 0.020 0.002 TYR A 230 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: A 20 ASP cc_start: 0.8554 (t0) cc_final: 0.8265 (m-30) REVERT: A 33 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: A 188 HIS cc_start: 0.8379 (m90) cc_final: 0.7818 (t70) REVERT: A 245 GLU cc_start: 0.7684 (mp0) cc_final: 0.7118 (mp0) REVERT: A 273 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 337 ASP cc_start: 0.8410 (m-30) cc_final: 0.8103 (m-30) REVERT: E 38 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.7814 (ptp90) REVERT: E 43 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8314 (mmmm) REVERT: E 84 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9066 (p) REVERT: R 65 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7181 (tt) REVERT: R 87 PHE cc_start: 0.8333 (m-10) cc_final: 0.7866 (m-80) REVERT: R 124 GLN cc_start: 0.7605 (mp10) cc_final: 0.6999 (mp10) REVERT: R 258 ARG cc_start: 0.8007 (tmt170) cc_final: 0.7718 (tmt170) outliers start: 36 outliers final: 14 residues processed: 173 average time/residue: 1.1877 time to fit residues: 218.7542 Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 52 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104843 restraints weight = 11867.937| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.48 r_work: 0.3154 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8705 Z= 0.185 Angle : 0.545 8.964 11826 Z= 0.285 Chirality : 0.042 0.148 1372 Planarity : 0.003 0.046 1485 Dihedral : 5.740 79.538 1221 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.72 % Allowed : 20.16 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1103 helix: 1.30 (0.28), residues: 372 sheet: -0.16 (0.30), residues: 280 loop : -0.40 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.026 0.001 TYR A 230 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: A 20 ASP cc_start: 0.8446 (t0) cc_final: 0.8170 (m-30) REVERT: A 33 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: A 242 ARG cc_start: 0.7344 (mmp-170) cc_final: 0.7069 (mmp-170) REVERT: A 245 GLU cc_start: 0.7761 (mp0) cc_final: 0.7087 (mp0) REVERT: A 308 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 337 ASP cc_start: 0.8373 (m-30) cc_final: 0.8073 (m-30) REVERT: B 161 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.8951 (t) REVERT: E 38 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.7784 (ptp90) REVERT: E 83 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8122 (mtp) REVERT: R 65 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7130 (tt) REVERT: R 87 PHE cc_start: 0.8292 (m-10) cc_final: 0.7798 (m-80) REVERT: R 124 GLN cc_start: 0.7608 (mp10) cc_final: 0.7036 (mp10) REVERT: R 258 ARG cc_start: 0.8092 (tmt170) cc_final: 0.7829 (tmt170) outliers start: 24 outliers final: 10 residues processed: 170 average time/residue: 1.2001 time to fit residues: 217.5356 Evaluate side-chains 160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103824 restraints weight = 11804.247| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.46 r_work: 0.3130 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8705 Z= 0.248 Angle : 0.571 10.061 11826 Z= 0.298 Chirality : 0.043 0.156 1372 Planarity : 0.003 0.047 1485 Dihedral : 5.645 75.868 1221 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.74 % Allowed : 20.05 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1103 helix: 1.48 (0.28), residues: 361 sheet: -0.15 (0.30), residues: 287 loop : -0.45 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.027 0.002 TYR A 230 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: A 20 ASP cc_start: 0.8528 (t0) cc_final: 0.8263 (m-30) REVERT: A 33 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: A 188 HIS cc_start: 0.8296 (m90) cc_final: 0.7758 (t70) REVERT: A 245 GLU cc_start: 0.7773 (mp0) cc_final: 0.7082 (mp0) REVERT: A 308 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 337 ASP cc_start: 0.8392 (m-30) cc_final: 0.8080 (m-30) REVERT: B 161 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8974 (t) REVERT: E 38 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.7795 (ptp90) REVERT: R 65 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7118 (tt) REVERT: R 87 PHE cc_start: 0.8259 (m-10) cc_final: 0.7811 (m-80) REVERT: R 124 GLN cc_start: 0.7570 (mp10) cc_final: 0.7028 (mp10) REVERT: R 258 ARG cc_start: 0.8080 (tmt170) cc_final: 0.7776 (tmt170) outliers start: 33 outliers final: 15 residues processed: 173 average time/residue: 1.2355 time to fit residues: 227.4690 Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104324 restraints weight = 11839.319| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.48 r_work: 0.3142 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8705 Z= 0.227 Angle : 0.569 10.583 11826 Z= 0.296 Chirality : 0.043 0.137 1372 Planarity : 0.003 0.047 1485 Dihedral : 5.526 71.737 1221 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.17 % Allowed : 21.86 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1103 helix: 1.51 (0.28), residues: 361 sheet: -0.09 (0.30), residues: 285 loop : -0.45 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE A 189 TYR 0.027 0.001 TYR A 230 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: A 20 ASP cc_start: 0.8443 (t0) cc_final: 0.8169 (m-30) REVERT: A 33 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: A 242 ARG cc_start: 0.7468 (mmp-170) cc_final: 0.7119 (mmp-170) REVERT: A 245 GLU cc_start: 0.7781 (mp0) cc_final: 0.7091 (mp0) REVERT: A 308 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 337 ASP cc_start: 0.8371 (m-30) cc_final: 0.8064 (m-30) REVERT: B 161 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.8963 (t) REVERT: E 38 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.7793 (ptp90) REVERT: R 65 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7120 (tt) REVERT: R 87 PHE cc_start: 0.8235 (m-10) cc_final: 0.7808 (m-80) REVERT: R 124 GLN cc_start: 0.7559 (mp10) cc_final: 0.6985 (mp10) REVERT: R 258 ARG cc_start: 0.8073 (tmt170) cc_final: 0.7778 (tmt170) outliers start: 28 outliers final: 15 residues processed: 167 average time/residue: 1.2147 time to fit residues: 215.6678 Evaluate side-chains 165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 130 MET Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 47 optimal weight: 0.2980 chunk 5 optimal weight: 0.0070 chunk 74 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.145278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109324 restraints weight = 11962.238| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.52 r_work: 0.3225 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8705 Z= 0.140 Angle : 0.542 10.696 11826 Z= 0.281 Chirality : 0.042 0.142 1372 Planarity : 0.003 0.046 1485 Dihedral : 5.073 62.628 1221 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.49 % Allowed : 23.10 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1103 helix: 1.61 (0.28), residues: 364 sheet: -0.03 (0.30), residues: 278 loop : -0.39 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 226 HIS 0.002 0.000 HIS E 35 PHE 0.009 0.001 PHE E 29 TYR 0.022 0.001 TYR A 296 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8428 (t0) cc_final: 0.8147 (m-30) REVERT: A 188 HIS cc_start: 0.8213 (m-70) cc_final: 0.7707 (t70) REVERT: A 242 ARG cc_start: 0.7479 (mmp-170) cc_final: 0.7040 (mmp-170) REVERT: A 245 GLU cc_start: 0.7857 (mp0) cc_final: 0.7211 (mp0) REVERT: A 308 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 337 ASP cc_start: 0.8267 (m-30) cc_final: 0.8008 (m-30) REVERT: B 42 ARG cc_start: 0.7534 (tpt170) cc_final: 0.7244 (tpp-160) REVERT: B 172 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8539 (tp30) REVERT: E 83 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8227 (mtm) REVERT: R 65 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7061 (tt) REVERT: R 87 PHE cc_start: 0.8222 (m-10) cc_final: 0.7743 (m-80) outliers start: 22 outliers final: 11 residues processed: 180 average time/residue: 1.1002 time to fit residues: 212.1134 Evaluate side-chains 159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106508 restraints weight = 11896.061| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.50 r_work: 0.3181 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8705 Z= 0.199 Angle : 0.581 11.437 11826 Z= 0.299 Chirality : 0.042 0.152 1372 Planarity : 0.003 0.047 1485 Dihedral : 5.000 57.016 1221 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.38 % Allowed : 23.56 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1103 helix: 1.62 (0.28), residues: 362 sheet: -0.03 (0.30), residues: 280 loop : -0.36 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE A 189 TYR 0.025 0.001 TYR A 230 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8452 (t0) cc_final: 0.8165 (m-30) REVERT: A 242 ARG cc_start: 0.7405 (mmp-170) cc_final: 0.6889 (mmp-170) REVERT: A 245 GLU cc_start: 0.7850 (mp0) cc_final: 0.7063 (mp0) REVERT: A 306 GLN cc_start: 0.8090 (tt0) cc_final: 0.7855 (mt0) REVERT: A 308 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 337 ASP cc_start: 0.8297 (m-30) cc_final: 0.8019 (m-30) REVERT: B 42 ARG cc_start: 0.7539 (tpt170) cc_final: 0.7264 (tpp-160) REVERT: B 172 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8526 (tp30) REVERT: E 83 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: R 65 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7090 (tt) REVERT: R 87 PHE cc_start: 0.8236 (m-10) cc_final: 0.7772 (m-80) REVERT: R 186 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7238 (mp) REVERT: R 205 MET cc_start: 0.6903 (ttt) cc_final: 0.6702 (ttt) outliers start: 21 outliers final: 12 residues processed: 162 average time/residue: 1.1559 time to fit residues: 199.8343 Evaluate side-chains 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106531 restraints weight = 11842.002| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.49 r_work: 0.3185 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8705 Z= 0.198 Angle : 0.590 11.067 11826 Z= 0.304 Chirality : 0.042 0.174 1372 Planarity : 0.003 0.046 1485 Dihedral : 4.905 52.716 1221 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.15 % Allowed : 24.24 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1103 helix: 1.62 (0.28), residues: 362 sheet: -0.01 (0.30), residues: 278 loop : -0.39 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE A 189 TYR 0.026 0.001 TYR A 230 ARG 0.005 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8453 (t0) cc_final: 0.8163 (m-30) REVERT: A 188 HIS cc_start: 0.8265 (m-70) cc_final: 0.7725 (t70) REVERT: A 242 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.6939 (mmp-170) REVERT: A 245 GLU cc_start: 0.7848 (mp0) cc_final: 0.7128 (mp0) REVERT: A 306 GLN cc_start: 0.8090 (tt0) cc_final: 0.7848 (mt0) REVERT: A 308 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8031 (mt-10) REVERT: A 337 ASP cc_start: 0.8297 (m-30) cc_final: 0.8018 (m-30) REVERT: B 42 ARG cc_start: 0.7505 (tpt170) cc_final: 0.7219 (tpp-160) REVERT: B 172 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8525 (tp30) REVERT: E 83 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: R 65 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7067 (tt) REVERT: R 87 PHE cc_start: 0.8245 (m-10) cc_final: 0.7755 (m-80) REVERT: R 186 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7238 (mp) REVERT: R 205 MET cc_start: 0.6912 (ttt) cc_final: 0.6628 (ttt) outliers start: 19 outliers final: 13 residues processed: 159 average time/residue: 1.2586 time to fit residues: 213.1645 Evaluate side-chains 165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105725 restraints weight = 11979.029| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.50 r_work: 0.3164 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8705 Z= 0.214 Angle : 0.599 11.778 11826 Z= 0.308 Chirality : 0.043 0.142 1372 Planarity : 0.003 0.046 1485 Dihedral : 4.803 45.274 1221 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.72 % Allowed : 23.78 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1103 helix: 1.58 (0.28), residues: 362 sheet: -0.11 (0.29), residues: 294 loop : -0.37 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE A 189 TYR 0.012 0.001 TYR E 178 ARG 0.004 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7216.87 seconds wall clock time: 124 minutes 21.55 seconds (7461.55 seconds total)