Starting phenix.real_space_refine on Fri Mar 14 00:35:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijd_60628/03_2025/9ijd_60628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijd_60628/03_2025/9ijd_60628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijd_60628/03_2025/9ijd_60628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijd_60628/03_2025/9ijd_60628.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijd_60628/03_2025/9ijd_60628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijd_60628/03_2025/9ijd_60628.cif" } resolution = 2.76 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= -0.001 sd= 0.098 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 60 5.16 5 C 5953 2.51 5 N 1628 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9371 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1893 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1808 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'CAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.76, per 1000 atoms: 0.61 Number of scatterers: 9371 At special positions: 0 Unit cell: (86.6, 122.322, 124.487, 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 60 16.00 O 1730 8.00 N 1628 7.00 C 5953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " distance=2.06 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 35.5% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 removed outlier: 4.082A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.764A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.695A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.845A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.966A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 65 Processing helix chain 'R' and resid 71 through 90 removed outlier: 3.972A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 removed outlier: 3.621A pdb=" N ALA R 94 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 141 removed outlier: 4.088A pdb=" N GLU R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU R 112 " --> pdb=" O THR R 108 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 149 removed outlier: 4.810A pdb=" N ALA R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 171 Processing helix chain 'R' and resid 202 through 213 Processing helix chain 'R' and resid 213 through 243 Processing helix chain 'R' and resid 290 through 319 removed outlier: 3.580A pdb=" N PHE R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) Proline residue: R 307 - end of helix removed outlier: 3.847A pdb=" N VAL R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 347 removed outlier: 3.802A pdb=" N ALA R 337 " --> pdb=" O TRP R 333 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 3.521A pdb=" N CYS R 347 " --> pdb=" O PRO R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 362 removed outlier: 4.007A pdb=" N ARG R 362 " --> pdb=" O ARG R 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.728A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.628A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.787A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 274 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 275 " --> pdb=" O LEU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.315A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.717A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.743A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.827A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.920A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.680A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.405A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.592A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.512A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.943A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.152A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 148 removed outlier: 6.220A pdb=" N VAL D 147 " --> pdb=" O GLU D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 194 through 195 removed outlier: 6.503A pdb=" N TRP D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR D 190 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 174 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.335A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1350 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: 2.88 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1499 1.30 - 1.43: 2631 1.43 - 1.56: 5354 1.56 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9569 Sorted by residual: bond pdb=" C VAL B 187 " pdb=" O VAL B 187 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.17e-02 7.31e+03 2.44e+01 bond pdb=" C GLY R 335 " pdb=" O GLY R 335 " ideal model delta sigma weight residual 1.234 1.190 0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C TYR D 173 " pdb=" O TYR D 173 " ideal model delta sigma weight residual 1.235 1.195 0.041 1.26e-02 6.30e+03 1.05e+01 bond pdb=" N MET D 192 " pdb=" CA MET D 192 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.47e+00 bond pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.22e-02 6.72e+03 8.87e+00 ... (remaining 9564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12491 1.94 - 3.89: 452 3.89 - 5.83: 45 5.83 - 7.77: 9 7.77 - 9.72: 5 Bond angle restraints: 13002 Sorted by residual: angle pdb=" O LEU D 233 " pdb=" C LEU D 233 " pdb=" N GLU D 234 " ideal model delta sigma weight residual 122.03 130.13 -8.10 1.04e+00 9.25e-01 6.07e+01 angle pdb=" N ASN R 332 " pdb=" CA ASN R 332 " pdb=" C ASN R 332 " ideal model delta sigma weight residual 111.82 104.58 7.24 1.16e+00 7.43e-01 3.89e+01 angle pdb=" C PRO A 316 " pdb=" CA PRO A 316 " pdb=" CB PRO A 316 " ideal model delta sigma weight residual 110.95 102.91 8.04 1.31e+00 5.83e-01 3.76e+01 angle pdb=" CA LEU D 233 " pdb=" C LEU D 233 " pdb=" N GLU D 234 " ideal model delta sigma weight residual 116.92 110.53 6.39 1.16e+00 7.43e-01 3.03e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.72 106.81 5.91 1.14e+00 7.69e-01 2.69e+01 ... (remaining 12997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 5300 27.07 - 54.15: 314 54.15 - 81.22: 32 81.22 - 108.29: 7 108.29 - 135.36: 2 Dihedral angle restraints: 5655 sinusoidal: 2115 harmonic: 3540 Sorted by residual: dihedral pdb=" CB CYS D 159 " pdb=" SG CYS D 159 " pdb=" SG CYS D 229 " pdb=" CB CYS D 229 " ideal model delta sinusoidal sigma weight residual 93.00 43.67 49.33 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -128.66 42.66 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" C PRO A 316 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " pdb=" CB PRO A 316 " ideal model delta harmonic sigma weight residual -120.70 -109.41 -11.29 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 5652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1258 0.070 - 0.140: 202 0.140 - 0.210: 23 0.210 - 0.280: 2 0.280 - 0.350: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA ARG D 98 " pdb=" N ARG D 98 " pdb=" C ARG D 98 " pdb=" CB ARG D 98 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA GLU D 234 " pdb=" N GLU D 234 " pdb=" C GLU D 234 " pdb=" CB GLU D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU B 10 " pdb=" N GLU B 10 " pdb=" C GLU B 10 " pdb=" CB GLU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1483 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 245 " -0.021 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C SER B 245 " 0.080 2.00e-02 2.50e+03 pdb=" O SER B 245 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP B 246 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 233 " -0.017 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C LEU D 233 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 233 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU D 234 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 98 " 0.252 9.50e-02 1.11e+02 1.13e-01 7.79e+00 pdb=" NE ARG D 98 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 98 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 98 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 98 " 0.009 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 608 2.72 - 3.27: 9454 3.27 - 3.81: 15993 3.81 - 4.36: 19900 4.36 - 4.90: 34367 Nonbonded interactions: 80322 Sorted by model distance: nonbonded pdb=" OD1 ASP D 109 " pdb=" N PHE D 110 " model vdw 2.181 3.120 nonbonded pdb=" O SER R 115 " pdb=" OG SER R 169 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.214 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.232 3.040 nonbonded pdb=" O TYR D 235 " pdb=" N LEU D 237 " model vdw 2.239 3.120 ... (remaining 80317 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: 0.010 Normalize map: mean=0, sd=1: 1.650 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.006 0.070 9569 Z= 0.403 Angle : 0.778 9.716 13002 Z= 0.508 Chirality : 0.052 0.350 1486 Planarity : 0.008 0.113 1653 Dihedral : 16.984 135.364 3365 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 1.73 % Allowed : 26.27 % Favored : 72.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1207 helix: 1.15 (0.26), residues: 364 sheet: -0.03 (0.29), residues: 312 loop : -0.37 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 333 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE A 212 TYR 0.021 0.002 TYR N 60 ARG 0.005 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 1.021 Fit side-chains REVERT: B 170 ASP cc_start: 0.6678 (t70) cc_final: 0.6469 (t70) REVERT: B 220 GLN cc_start: 0.7958 (mt0) cc_final: 0.7732 (mt0) REVERT: D 18 ARG cc_start: 0.6164 (tpp80) cc_final: 0.5879 (tpp80) outliers start: 17 outliers final: 11 residues processed: 211 average time/residue: 1.1564 time to fit residues: 261.9362 Evaluate side-chains 184 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 352 PHE Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113853 restraints weight = 12396.628| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.42 r_work: 0.3311 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9569 Z= 0.258 Angle : 0.575 7.345 13002 Z= 0.304 Chirality : 0.043 0.250 1486 Planarity : 0.005 0.074 1653 Dihedral : 7.020 113.811 1358 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.99 % Allowed : 25.56 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.24), residues: 1207 helix: 1.68 (0.26), residues: 365 sheet: -0.08 (0.28), residues: 307 loop : -0.30 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS D 167 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.002 TYR D 235 ARG 0.008 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: B 220 GLN cc_start: 0.8041 (mt0) cc_final: 0.7753 (mt0) REVERT: B 228 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: B 266 HIS cc_start: 0.8772 (t-90) cc_final: 0.8538 (t-90) REVERT: N 28 THR cc_start: 0.8085 (p) cc_final: 0.7773 (p) REVERT: N 95 TYR cc_start: 0.8317 (m-80) cc_final: 0.7720 (m-80) REVERT: D 191 ARG cc_start: 0.8037 (tpp80) cc_final: 0.7754 (mpt-90) REVERT: R 71 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7395 (tmm) REVERT: A 222 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7178 (p90) outliers start: 49 outliers final: 26 residues processed: 204 average time/residue: 1.0600 time to fit residues: 232.7982 Evaluate side-chains 190 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 352 PHE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 31 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 0.0770 chunk 102 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114213 restraints weight = 12414.422| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.41 r_work: 0.3317 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9569 Z= 0.236 Angle : 0.547 6.555 13002 Z= 0.289 Chirality : 0.042 0.202 1486 Planarity : 0.005 0.062 1653 Dihedral : 6.444 102.714 1347 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.11 % Allowed : 25.76 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1207 helix: 1.86 (0.26), residues: 365 sheet: -0.12 (0.28), residues: 308 loop : -0.24 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS D 167 PHE 0.015 0.001 PHE A 212 TYR 0.013 0.001 TYR D 235 ARG 0.004 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: B 220 GLN cc_start: 0.8125 (mt0) cc_final: 0.7909 (mt0) REVERT: B 266 HIS cc_start: 0.8760 (t-90) cc_final: 0.8509 (t-90) REVERT: B 280 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7905 (mtpt) REVERT: N 38 ARG cc_start: 0.8368 (ptt180) cc_final: 0.8146 (ptt180) REVERT: N 53 GLN cc_start: 0.8391 (mp10) cc_final: 0.8182 (mp10) REVERT: N 76 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8566 (mttp) REVERT: N 95 TYR cc_start: 0.8292 (m-80) cc_final: 0.7693 (m-80) REVERT: N 108 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7193 (t80) REVERT: D 140 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8140 (mtp) REVERT: R 67 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7120 (ttt180) REVERT: R 155 ARG cc_start: 0.6875 (mtt180) cc_final: 0.5352 (mmt180) REVERT: A 46 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8618 (mt) REVERT: A 222 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7178 (p90) REVERT: A 346 ARG cc_start: 0.7029 (mtm-85) cc_final: 0.6654 (mtm-85) outliers start: 60 outliers final: 30 residues processed: 210 average time/residue: 1.0765 time to fit residues: 243.3907 Evaluate side-chains 196 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 352 PHE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113921 restraints weight = 12370.483| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.41 r_work: 0.3313 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9569 Z= 0.257 Angle : 0.561 8.997 13002 Z= 0.292 Chirality : 0.043 0.193 1486 Planarity : 0.005 0.065 1653 Dihedral : 6.283 96.905 1347 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.50 % Allowed : 26.07 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1207 helix: 1.88 (0.26), residues: 365 sheet: -0.16 (0.28), residues: 308 loop : -0.25 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 41 PHE 0.015 0.001 PHE A 212 TYR 0.016 0.002 TYR N 80 ARG 0.009 0.001 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: B 220 GLN cc_start: 0.8069 (mt0) cc_final: 0.7741 (mt0) REVERT: B 266 HIS cc_start: 0.8731 (t-90) cc_final: 0.8474 (t-90) REVERT: B 280 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7878 (mtpt) REVERT: N 38 ARG cc_start: 0.8347 (ptt180) cc_final: 0.8057 (ptt180) REVERT: N 53 GLN cc_start: 0.8228 (mp10) cc_final: 0.8015 (mp10) REVERT: N 76 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8564 (mttp) REVERT: N 95 TYR cc_start: 0.8245 (m-80) cc_final: 0.7658 (m-80) REVERT: D 140 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8091 (mtp) REVERT: R 155 ARG cc_start: 0.6830 (mtt180) cc_final: 0.5304 (mmt180) REVERT: A 46 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8517 (mt) REVERT: A 222 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7076 (p90) REVERT: A 346 ARG cc_start: 0.6905 (mtm-85) cc_final: 0.6540 (mtm-85) outliers start: 54 outliers final: 32 residues processed: 198 average time/residue: 1.0807 time to fit residues: 230.6888 Evaluate side-chains 193 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 352 PHE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 88 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 237 ASN N 39 GLN D 186 GLN A 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117315 restraints weight = 12364.158| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.41 r_work: 0.3358 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9569 Z= 0.153 Angle : 0.515 7.786 13002 Z= 0.268 Chirality : 0.041 0.166 1486 Planarity : 0.004 0.060 1653 Dihedral : 5.783 80.530 1347 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.40 % Allowed : 26.68 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1207 helix: 2.20 (0.27), residues: 365 sheet: -0.15 (0.28), residues: 310 loop : -0.21 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR D 235 ARG 0.004 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7619 (mtt90) REVERT: B 59 TYR cc_start: 0.8858 (m-80) cc_final: 0.7153 (m-80) REVERT: B 134 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7651 (ptp90) REVERT: B 266 HIS cc_start: 0.8728 (t-90) cc_final: 0.8360 (t-90) REVERT: B 280 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7824 (mtpm) REVERT: B 325 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7783 (tpp) REVERT: B 333 ASP cc_start: 0.7752 (p0) cc_final: 0.7370 (p0) REVERT: N 91 THR cc_start: 0.8629 (p) cc_final: 0.8386 (p) REVERT: N 95 TYR cc_start: 0.8220 (m-80) cc_final: 0.7689 (m-80) REVERT: N 108 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7124 (t80) REVERT: R 155 ARG cc_start: 0.6483 (mtt180) cc_final: 0.5140 (mmt180) REVERT: A 222 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.6939 (p90) REVERT: A 346 ARG cc_start: 0.6979 (mtm-85) cc_final: 0.6713 (mtm-85) outliers start: 53 outliers final: 27 residues processed: 207 average time/residue: 1.6592 time to fit residues: 369.6441 Evaluate side-chains 189 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 39 GLN D 142 GLN D 186 GLN R 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115992 restraints weight = 12314.798| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.41 r_work: 0.3340 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9569 Z= 0.206 Angle : 0.545 9.558 13002 Z= 0.282 Chirality : 0.042 0.168 1486 Planarity : 0.004 0.062 1653 Dihedral : 5.591 78.833 1345 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.79 % Allowed : 27.90 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.24), residues: 1207 helix: 2.14 (0.26), residues: 365 sheet: -0.18 (0.28), residues: 310 loop : -0.21 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR N 80 ARG 0.005 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7735 (mtt90) REVERT: B 59 TYR cc_start: 0.8946 (m-80) cc_final: 0.7275 (m-80) REVERT: B 266 HIS cc_start: 0.8732 (t-90) cc_final: 0.8400 (t-90) REVERT: B 280 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7907 (mtpt) REVERT: B 325 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7829 (tpp) REVERT: N 34 MET cc_start: 0.8590 (mmm) cc_final: 0.8089 (mmm) REVERT: N 95 TYR cc_start: 0.8269 (m-80) cc_final: 0.7783 (m-80) REVERT: R 67 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7291 (ttt180) REVERT: R 155 ARG cc_start: 0.6577 (mtt180) cc_final: 0.5283 (mmt180) REVERT: A 222 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7023 (p90) REVERT: A 346 ARG cc_start: 0.7022 (mtm-85) cc_final: 0.6751 (mtm-85) outliers start: 47 outliers final: 31 residues processed: 195 average time/residue: 1.2433 time to fit residues: 261.0137 Evaluate side-chains 191 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 3 GLN N 39 GLN D 142 GLN D 186 GLN R 141 ASN R 332 ASN A 35 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115262 restraints weight = 12492.755| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.42 r_work: 0.3330 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9569 Z= 0.235 Angle : 0.564 10.201 13002 Z= 0.290 Chirality : 0.043 0.180 1486 Planarity : 0.004 0.061 1653 Dihedral : 5.646 78.921 1345 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.68 % Allowed : 28.51 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1207 helix: 2.06 (0.26), residues: 365 sheet: -0.25 (0.28), residues: 314 loop : -0.23 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR D 235 ARG 0.006 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7743 (mtt90) REVERT: B 59 TYR cc_start: 0.8966 (m-80) cc_final: 0.7579 (m-80) REVERT: B 176 GLN cc_start: 0.8976 (mt0) cc_final: 0.8728 (mt0) REVERT: B 266 HIS cc_start: 0.8727 (t-90) cc_final: 0.8386 (t-90) REVERT: B 280 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7950 (mtpt) REVERT: B 325 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7820 (tpp) REVERT: N 3 GLN cc_start: 0.7391 (tp40) cc_final: 0.7125 (tp40) REVERT: N 76 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8510 (mttp) REVERT: N 95 TYR cc_start: 0.8355 (m-80) cc_final: 0.7793 (m-80) REVERT: R 155 ARG cc_start: 0.6623 (mtt180) cc_final: 0.5319 (mmt180) REVERT: A 222 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7028 (p90) REVERT: A 346 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.6770 (mtm-85) outliers start: 46 outliers final: 33 residues processed: 193 average time/residue: 1.1376 time to fit residues: 235.2831 Evaluate side-chains 194 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN B 237 ASN N 39 GLN D 186 GLN R 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115407 restraints weight = 12566.988| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.43 r_work: 0.3334 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9569 Z= 0.221 Angle : 0.564 10.317 13002 Z= 0.290 Chirality : 0.042 0.172 1486 Planarity : 0.004 0.062 1653 Dihedral : 5.593 76.947 1345 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.99 % Allowed : 29.12 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1207 helix: 2.05 (0.26), residues: 365 sheet: -0.19 (0.28), residues: 318 loop : -0.21 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.001 TYR N 80 ARG 0.008 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7770 (mtt90) REVERT: B 59 TYR cc_start: 0.8906 (m-80) cc_final: 0.7626 (m-80) REVERT: B 266 HIS cc_start: 0.8748 (t-90) cc_final: 0.8402 (t-90) REVERT: B 280 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7880 (mtpt) REVERT: B 325 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7764 (tpp) REVERT: N 76 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8496 (mttp) REVERT: N 95 TYR cc_start: 0.8355 (m-80) cc_final: 0.7782 (m-80) REVERT: D 140 MET cc_start: 0.8311 (mmm) cc_final: 0.8031 (mmm) REVERT: R 155 ARG cc_start: 0.6509 (mtt180) cc_final: 0.5241 (mmt180) REVERT: A 222 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.6985 (p90) REVERT: A 346 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6767 (mtm-85) outliers start: 49 outliers final: 34 residues processed: 196 average time/residue: 1.0718 time to fit residues: 226.6098 Evaluate side-chains 193 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 3 GLN N 39 GLN D 142 GLN R 332 ASN A 35 GLN A 41 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111470 restraints weight = 12393.442| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.40 r_work: 0.3283 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9569 Z= 0.402 Angle : 0.653 11.800 13002 Z= 0.335 Chirality : 0.046 0.215 1486 Planarity : 0.005 0.063 1653 Dihedral : 5.913 93.193 1343 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.58 % Allowed : 29.53 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1207 helix: 1.61 (0.26), residues: 365 sheet: -0.28 (0.28), residues: 319 loop : -0.30 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.008 0.002 HIS B 225 PHE 0.015 0.002 PHE A 212 TYR 0.014 0.002 TYR N 117 ARG 0.010 0.001 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 GLN cc_start: 0.8980 (mt0) cc_final: 0.8751 (mt0) REVERT: B 280 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7933 (mtpp) REVERT: N 38 ARG cc_start: 0.8271 (ptt180) cc_final: 0.7986 (ptt180) REVERT: N 76 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8474 (mttp) REVERT: N 95 TYR cc_start: 0.8362 (m-80) cc_final: 0.7825 (m-80) REVERT: R 155 ARG cc_start: 0.6525 (mtt180) cc_final: 0.5095 (mmt180) REVERT: A 222 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7153 (p90) outliers start: 45 outliers final: 35 residues processed: 187 average time/residue: 1.2735 time to fit residues: 256.1990 Evaluate side-chains 193 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.0030 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 3 GLN N 39 GLN D 142 GLN R 332 ASN A 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117301 restraints weight = 12453.940| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.40 r_work: 0.3353 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9569 Z= 0.170 Angle : 0.562 11.990 13002 Z= 0.288 Chirality : 0.042 0.166 1486 Planarity : 0.004 0.060 1653 Dihedral : 5.315 75.269 1343 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.05 % Allowed : 30.96 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1207 helix: 2.06 (0.27), residues: 365 sheet: -0.36 (0.28), residues: 312 loop : -0.27 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR N 80 ARG 0.005 0.000 ARG R 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8823 (m-80) cc_final: 0.7463 (m-80) REVERT: B 189 SER cc_start: 0.8563 (t) cc_final: 0.8307 (p) REVERT: B 280 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7845 (mtpt) REVERT: N 95 TYR cc_start: 0.8327 (m-80) cc_final: 0.7828 (m-80) REVERT: D 140 MET cc_start: 0.8312 (mmm) cc_final: 0.8059 (mmm) REVERT: R 155 ARG cc_start: 0.6425 (mtt180) cc_final: 0.5172 (mmt180) REVERT: A 222 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.6818 (p90) outliers start: 30 outliers final: 24 residues processed: 181 average time/residue: 1.1509 time to fit residues: 224.8799 Evaluate side-chains 181 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN B 266 HIS N 3 GLN N 39 GLN D 142 GLN R 332 ASN A 35 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117274 restraints weight = 12377.342| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.39 r_work: 0.3358 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9569 Z= 0.178 Angle : 0.555 11.386 13002 Z= 0.284 Chirality : 0.042 0.160 1486 Planarity : 0.004 0.063 1653 Dihedral : 5.182 69.533 1343 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.56 % Allowed : 30.75 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1207 helix: 2.18 (0.26), residues: 365 sheet: -0.33 (0.28), residues: 312 loop : -0.25 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR A 37 ARG 0.005 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9192.83 seconds wall clock time: 160 minutes 20.78 seconds (9620.78 seconds total)