Starting phenix.real_space_refine on Sat Aug 23 14:34:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bht_44552/08_2025/9bht_44552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bht_44552/08_2025/9bht_44552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bht_44552/08_2025/9bht_44552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bht_44552/08_2025/9bht_44552.map" model { file = "/net/cci-nas-00/data/ceres_data/9bht_44552/08_2025/9bht_44552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bht_44552/08_2025/9bht_44552.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.044 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 74 5.16 5 C 8024 2.51 5 N 2203 2.21 5 O 2410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12725 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1773 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 4 Chain: "B" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2272 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2265 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2166 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2308 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1765 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.64, per 1000 atoms: 0.21 Number of scatterers: 12725 At special positions: 0 Unit cell: (61.202, 74.994, 258.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 14 15.00 O 2410 8.00 N 2203 7.00 C 8024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 568.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2954 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 14 sheets defined 45.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.596A pdb=" N ILE A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 235 through 253 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'B' and resid 34 through 47 removed outlier: 3.839A pdb=" N GLN B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 122 through 141 removed outlier: 3.771A pdb=" N VAL B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 181 Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.877A pdb=" N MET B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 300 through 314 removed outlier: 3.768A pdb=" N LEU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 23 through 36 removed outlier: 4.265A pdb=" N LYS C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 115 through 135 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 188 through 206 Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.721A pdb=" N LEU C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.584A pdb=" N PHE D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 135 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 188 through 206 removed outlier: 3.864A pdb=" N HIS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 283 through 292 Processing helix chain 'D' and resid 294 through 305 Processing helix chain 'E' and resid 34 through 47 Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 122 through 141 Processing helix chain 'E' and resid 170 through 181 Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.693A pdb=" N ILE E 195 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 196 " --> pdb=" O ALA E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 196' Processing helix chain 'E' and resid 197 through 216 Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 277 through 286 Processing helix chain 'E' and resid 289 through 300 Processing helix chain 'E' and resid 301 through 314 Processing helix chain 'F' and resid 96 through 105 removed outlier: 4.011A pdb=" N PHE F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.171A pdb=" N ILE F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR F 168 " --> pdb=" O PRO F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 219 Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 235 through 253 Processing helix chain 'F' and resid 271 through 281 Processing helix chain 'F' and resid 319 through 341 removed outlier: 5.462A pdb=" N GLN F 332 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP F 333 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 133 removed outlier: 6.392A pdb=" N LEU A 87 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER A 195 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 198 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 284 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 97 removed outlier: 6.865A pdb=" N PHE B 48 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR B 105 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE B 50 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL B 107 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 52 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER B 109 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS B 54 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N ALA B 157 " --> pdb=" O CYS B 49 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 51 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU B 159 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 53 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE B 161 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B 55 " --> pdb=" O PHE B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 90 removed outlier: 3.671A pdb=" N CYS C 148 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS C 149 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 180 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR C 151 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AA7, first strand: chain 'C' and resid 252 through 255 Processing sheet with id=AA8, first strand: chain 'D' and resid 82 through 90 removed outlier: 6.691A pdb=" N PHE D 37 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR D 98 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE D 39 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASP D 100 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 41 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N CYS D 148 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR D 40 " --> pdb=" O CYS D 148 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU D 150 " --> pdb=" O THR D 40 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET D 42 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE D 152 " --> pdb=" O MET D 42 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 44 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS D 149 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU D 180 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR D 151 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AB1, first strand: chain 'E' and resid 87 through 97 removed outlier: 7.069A pdb=" N PHE E 48 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR E 105 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE E 50 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL E 107 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE E 52 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N SER E 109 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N CYS E 54 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR E 160 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 250 through 253 Processing sheet with id=AB3, first strand: chain 'F' and resid 131 through 133 removed outlier: 6.488A pdb=" N PHE F 85 " --> pdb=" O THR F 145 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL F 147 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU F 87 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR F 86 " --> pdb=" O SER F 195 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE F 197 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N MET F 88 " --> pdb=" O PHE F 197 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE F 199 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA F 90 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N CYS F 196 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL F 227 " --> pdb=" O CYS F 196 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR F 198 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AB5, first strand: chain 'F' and resid 303 through 305 597 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2130 1.31 - 1.44: 3327 1.44 - 1.56: 7375 1.56 - 1.69: 24 1.69 - 1.82: 117 Bond restraints: 12973 Sorted by residual: bond pdb=" CA SER E 27 " pdb=" CB SER E 27 " ideal model delta sigma weight residual 1.530 1.355 0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" CA LYS D 77 " pdb=" C LYS D 77 " ideal model delta sigma weight residual 1.520 1.556 -0.037 4.80e-03 4.34e+04 5.87e+01 bond pdb=" C GLY C 20 " pdb=" O GLY C 20 " ideal model delta sigma weight residual 1.239 1.195 0.043 7.10e-03 1.98e+04 3.75e+01 bond pdb=" N GLY E 31 " pdb=" CA GLY E 31 " ideal model delta sigma weight residual 1.448 1.493 -0.045 8.80e-03 1.29e+04 2.56e+01 bond pdb=" C ARG C 30 " pdb=" N LYS C 31 " ideal model delta sigma weight residual 1.335 1.271 0.064 1.38e-02 5.25e+03 2.18e+01 ... (remaining 12968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.39: 17507 7.39 - 14.77: 30 14.77 - 22.16: 4 22.16 - 29.54: 5 29.54 - 36.93: 1 Bond angle restraints: 17547 Sorted by residual: angle pdb=" CA PHE D 21 " pdb=" CB PHE D 21 " pdb=" CG PHE D 21 " ideal model delta sigma weight residual 113.80 124.73 -10.93 1.00e+00 1.00e+00 1.20e+02 angle pdb=" O1A GDP D 501 " pdb=" PA GDP D 501 " pdb=" O3A GDP D 501 " ideal model delta sigma weight residual 109.50 80.91 28.59 3.00e+00 1.11e-01 9.08e+01 angle pdb=" O5' GDP D 501 " pdb=" PA GDP D 501 " pdb=" O3A GDP D 501 " ideal model delta sigma weight residual 102.60 74.45 28.15 3.00e+00 1.11e-01 8.81e+01 angle pdb=" N PRO A 306 " pdb=" CA PRO A 306 " pdb=" C PRO A 306 " ideal model delta sigma weight residual 112.47 93.14 19.33 2.06e+00 2.36e-01 8.80e+01 angle pdb=" O1A GDP D 501 " pdb=" PA GDP D 501 " pdb=" O2A GDP D 501 " ideal model delta sigma weight residual 109.50 82.38 27.12 3.00e+00 1.11e-01 8.17e+01 ... (remaining 17542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 7408 33.71 - 67.41: 400 67.41 - 101.12: 20 101.12 - 134.83: 6 134.83 - 168.53: 3 Dihedral angle restraints: 7837 sinusoidal: 3286 harmonic: 4551 Sorted by residual: dihedral pdb=" C TYR D 18 " pdb=" N TYR D 18 " pdb=" CA TYR D 18 " pdb=" CB TYR D 18 " ideal model delta harmonic sigma weight residual -122.60 -104.31 -18.29 0 2.50e+00 1.60e-01 5.35e+01 dihedral pdb=" O3B GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual -68.92 99.61 -168.53 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -92.22 -163.19 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 7834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1665 0.071 - 0.143: 278 0.143 - 0.214: 20 0.214 - 0.285: 5 0.285 - 0.357: 3 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA ARG A 301 " pdb=" N ARG A 301 " pdb=" C ARG A 301 " pdb=" CB ARG A 301 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA TYR A 305 " pdb=" N TYR A 305 " pdb=" C TYR A 305 " pdb=" CB TYR A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CG LEU F 234 " pdb=" CB LEU F 234 " pdb=" CD1 LEU F 234 " pdb=" CD2 LEU F 234 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1968 not shown) Planarity restraints: 2221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 305 " 0.172 5.00e-02 4.00e+02 2.56e-01 1.05e+02 pdb=" N PRO A 306 " -0.440 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " 0.172 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " 0.097 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 304 " 0.030 2.00e-02 2.50e+03 6.14e-02 3.76e+01 pdb=" C LEU A 304 " -0.106 2.00e-02 2.50e+03 pdb=" O LEU A 304 " 0.040 2.00e-02 2.50e+03 pdb=" N TYR A 305 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 29 " 0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C TYR C 29 " -0.091 2.00e-02 2.50e+03 pdb=" O TYR C 29 " 0.034 2.00e-02 2.50e+03 pdb=" N ARG C 30 " 0.031 2.00e-02 2.50e+03 ... (remaining 2218 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 264 2.63 - 3.20: 11693 3.20 - 3.76: 20466 3.76 - 4.33: 27085 4.33 - 4.90: 44404 Nonbonded interactions: 103912 Sorted by model distance: nonbonded pdb=" OG1 THR C 241 " pdb=" O GLY C 252 " model vdw 2.058 3.040 nonbonded pdb=" OE2 GLU C 191 " pdb=" O3' GDP D 501 " model vdw 2.124 3.040 nonbonded pdb=" NE1 TRP D 115 " pdb=" OE2 GLU D 166 " model vdw 2.130 3.120 nonbonded pdb=" O SER E 63 " pdb=" ND2 ASN E 67 " model vdw 2.150 3.120 nonbonded pdb=" O TYR D 18 " pdb=" C VAL D 19 " model vdw 2.158 3.270 ... (remaining 103907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 84 and (name N or name CA or name C or name O or name CB \ )) or resid 85 through 108 or resid 130 through 133 or (resid 142 and (name N or \ name CA or name C or name O or name CB )) or resid 143 through 261 or resid 274 \ through 501)) selection = (chain 'F' and (resid 84 through 261 or resid 274 through 501)) } ncs_group { reference = chain 'B' selection = (chain 'E' and (resid 32 through 254 or (resid 255 through 257 and (name N or na \ me CA or name C or name O or name CB )) or resid 258 through 500)) } ncs_group { reference = (chain 'C' and (resid 18 through 214 or (resid 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 230 through 244 or resid 249 through 501)) selection = (chain 'D' and (resid 18 through 63 or resid 70 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.700 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 0.175 12975 Z= 0.304 Angle : 1.129 36.928 17547 Z= 0.573 Chirality : 0.053 0.357 1971 Planarity : 0.008 0.256 2221 Dihedral : 19.394 168.535 4883 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 1.05 % Allowed : 5.96 % Favored : 93.00 % Rotamer: Outliers : 2.05 % Allowed : 33.00 % Favored : 64.94 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.21), residues: 1528 helix: 0.60 (0.20), residues: 647 sheet: 0.14 (0.34), residues: 212 loop : -1.73 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 244 TYR 0.033 0.002 TYR A 305 PHE 0.032 0.002 PHE C 21 TRP 0.030 0.002 TRP A 307 HIS 0.010 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00552 (12973) covalent geometry : angle 1.12861 (17547) hydrogen bonds : bond 0.16288 ( 597) hydrogen bonds : angle 6.51274 ( 1686) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 232 average time/residue: 0.1141 time to fit residues: 36.6905 Evaluate side-chains 138 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN B 151 HIS ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN F 172 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.053388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.043071 restraints weight = 86095.999| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 5.81 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 12975 Z= 0.156 Angle : 0.910 31.370 17547 Z= 0.415 Chirality : 0.048 0.212 1971 Planarity : 0.006 0.180 2221 Dihedral : 12.441 170.852 1773 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.69 % Favored : 93.78 % Rotamer: Outliers : 5.67 % Allowed : 26.98 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.21), residues: 1528 helix: 0.97 (0.20), residues: 652 sheet: 0.19 (0.36), residues: 205 loop : -1.51 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 194 TYR 0.019 0.002 TYR C 29 PHE 0.026 0.002 PHE B 148 TRP 0.024 0.002 TRP A 307 HIS 0.006 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00359 (12973) covalent geometry : angle 0.91002 (17547) hydrogen bonds : bond 0.04475 ( 597) hydrogen bonds : angle 5.28185 ( 1686) Misc. bond : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 141 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6069 (ptm-80) REVERT: A 218 LEU cc_start: 0.8959 (mm) cc_final: 0.8738 (mm) REVERT: A 292 MET cc_start: 0.8281 (mmt) cc_final: 0.7982 (mmp) REVERT: B 101 ARG cc_start: 0.8686 (mtm180) cc_final: 0.8485 (ptt90) REVERT: B 177 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: B 290 MET cc_start: 0.8962 (mmm) cc_final: 0.8583 (mmm) REVERT: C 28 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9179 (mt) REVERT: C 198 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 200 MET cc_start: 0.8459 (mmm) cc_final: 0.7539 (mmm) REVERT: D 21 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8444 (p90) REVERT: D 200 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8452 (mpp) REVERT: D 282 MET cc_start: 0.8586 (tpp) cc_final: 0.8202 (tpp) REVERT: D 290 ASN cc_start: 0.9405 (OUTLIER) cc_final: 0.9162 (m110) REVERT: E 66 MET cc_start: 0.8633 (mtt) cc_final: 0.8021 (mtt) REVERT: E 83 MET cc_start: 0.8075 (tpp) cc_final: 0.7704 (tpp) REVERT: E 202 HIS cc_start: 0.9227 (t70) cc_final: 0.8986 (t-90) REVERT: E 222 PHE cc_start: 0.6917 (m-80) cc_final: 0.6684 (m-80) REVERT: E 284 MET cc_start: 0.8062 (mmt) cc_final: 0.7416 (mmt) REVERT: E 296 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9211 (mmmm) REVERT: F 215 MET cc_start: 0.9019 (mtm) cc_final: 0.8811 (mtm) outliers start: 80 outliers final: 25 residues processed: 212 average time/residue: 0.0877 time to fit residues: 27.1903 Evaluate side-chains 150 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 296 LYS Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 0.0000 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 116 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.052765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.042738 restraints weight = 86309.456| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 5.61 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12975 Z= 0.138 Angle : 0.846 31.162 17547 Z= 0.377 Chirality : 0.046 0.242 1971 Planarity : 0.005 0.162 2221 Dihedral : 12.061 169.164 1757 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.97 % Favored : 94.50 % Rotamer: Outliers : 3.90 % Allowed : 27.34 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.21), residues: 1528 helix: 1.08 (0.20), residues: 657 sheet: 0.23 (0.36), residues: 206 loop : -1.39 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 145 TYR 0.017 0.001 TYR F 152 PHE 0.018 0.001 PHE D 21 TRP 0.012 0.001 TRP A 307 HIS 0.022 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00310 (12973) covalent geometry : angle 0.84591 (17547) hydrogen bonds : bond 0.03923 ( 597) hydrogen bonds : angle 5.15996 ( 1686) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8361 (mmt) cc_final: 0.8143 (mmp) REVERT: B 101 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8578 (mtm180) REVERT: B 202 HIS cc_start: 0.9025 (m-70) cc_final: 0.8600 (m-70) REVERT: C 135 MET cc_start: 0.8273 (mmm) cc_final: 0.8037 (mmm) REVERT: C 198 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 135 MET cc_start: 0.8547 (tmm) cc_final: 0.8244 (tmm) REVERT: D 200 MET cc_start: 0.8726 (mpp) cc_final: 0.7939 (mpp) REVERT: D 282 MET cc_start: 0.8519 (tpp) cc_final: 0.8055 (tpp) REVERT: E 66 MET cc_start: 0.8606 (mtt) cc_final: 0.8215 (mtt) REVERT: E 145 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8246 (ptm-80) REVERT: E 244 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9278 (m) REVERT: E 296 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9242 (mmmm) REVERT: F 215 MET cc_start: 0.8991 (mtm) cc_final: 0.8780 (mtm) REVERT: F 331 MET cc_start: 0.8460 (tpp) cc_final: 0.8171 (tpt) outliers start: 55 outliers final: 29 residues processed: 172 average time/residue: 0.0938 time to fit residues: 23.9207 Evaluate side-chains 149 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 296 LYS Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.050781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.040763 restraints weight = 90473.998| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 5.59 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12975 Z= 0.231 Angle : 0.858 32.142 17547 Z= 0.388 Chirality : 0.046 0.176 1971 Planarity : 0.005 0.150 2221 Dihedral : 11.919 167.113 1755 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.69 % Favored : 93.78 % Rotamer: Outliers : 4.67 % Allowed : 25.78 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1528 helix: 1.19 (0.20), residues: 658 sheet: 0.14 (0.35), residues: 206 loop : -1.38 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 145 TYR 0.018 0.002 TYR C 29 PHE 0.013 0.002 PHE C 167 TRP 0.010 0.001 TRP B 265 HIS 0.007 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00503 (12973) covalent geometry : angle 0.85818 (17547) hydrogen bonds : bond 0.04065 ( 597) hydrogen bonds : angle 5.16544 ( 1686) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 112 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8509 (mt) REVERT: A 218 LEU cc_start: 0.8886 (mm) cc_final: 0.8471 (mm) REVERT: A 292 MET cc_start: 0.8608 (mmt) cc_final: 0.8344 (mmp) REVERT: B 32 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6338 (m-10) REVERT: B 101 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8475 (ptt90) REVERT: C 135 MET cc_start: 0.8403 (mmm) cc_final: 0.8183 (mmm) REVERT: C 198 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8280 (tm-30) REVERT: C 280 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8715 (p) REVERT: D 82 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: D 276 MET cc_start: 0.6062 (ttm) cc_final: 0.5446 (ttm) REVERT: D 282 MET cc_start: 0.8617 (tpp) cc_final: 0.8170 (tpp) REVERT: E 244 VAL cc_start: 0.9474 (OUTLIER) cc_final: 0.9266 (m) REVERT: E 296 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9273 (mmmm) REVERT: F 178 HIS cc_start: 0.7565 (p90) cc_final: 0.7360 (p90) REVERT: F 197 PHE cc_start: 0.9092 (m-80) cc_final: 0.7895 (m-80) REVERT: F 215 MET cc_start: 0.9044 (mtm) cc_final: 0.8819 (mtm) outliers start: 66 outliers final: 36 residues processed: 171 average time/residue: 0.0903 time to fit residues: 22.9744 Evaluate side-chains 149 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 296 LYS Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.051254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.041356 restraints weight = 89531.326| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 5.47 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12975 Z= 0.158 Angle : 0.831 32.300 17547 Z= 0.372 Chirality : 0.045 0.181 1971 Planarity : 0.004 0.101 2221 Dihedral : 11.738 168.260 1755 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.56 % Favored : 93.98 % Rotamer: Outliers : 4.18 % Allowed : 25.99 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.22), residues: 1528 helix: 1.43 (0.20), residues: 654 sheet: -0.05 (0.33), residues: 218 loop : -1.30 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 248 TYR 0.020 0.002 TYR C 29 PHE 0.016 0.001 PHE E 222 TRP 0.007 0.001 TRP B 265 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00352 (12973) covalent geometry : angle 0.83120 (17547) hydrogen bonds : bond 0.03663 ( 597) hydrogen bonds : angle 5.06980 ( 1686) Misc. bond : bond 0.00046 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 110 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8921 (mm) cc_final: 0.8706 (mm) REVERT: A 292 MET cc_start: 0.8627 (mmt) cc_final: 0.8352 (mmp) REVERT: B 101 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8478 (ptt90) REVERT: B 138 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8446 (mm110) REVERT: C 198 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 19 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8512 (t) REVERT: D 82 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: D 282 MET cc_start: 0.8545 (tpp) cc_final: 0.8177 (tpp) REVERT: E 177 MET cc_start: 0.9204 (mmm) cc_final: 0.8993 (mmm) REVERT: E 244 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9193 (m) REVERT: F 85 PHE cc_start: 0.7984 (t80) cc_final: 0.7705 (t80) REVERT: F 87 LEU cc_start: 0.9467 (tt) cc_final: 0.9252 (mm) REVERT: F 178 HIS cc_start: 0.7631 (p90) cc_final: 0.7376 (p-80) REVERT: F 197 PHE cc_start: 0.9027 (m-80) cc_final: 0.7869 (m-80) REVERT: F 215 MET cc_start: 0.9031 (mtm) cc_final: 0.8801 (mtm) REVERT: F 331 MET cc_start: 0.8210 (tpt) cc_final: 0.7423 (tpt) outliers start: 59 outliers final: 42 residues processed: 162 average time/residue: 0.0893 time to fit residues: 21.4893 Evaluate side-chains 152 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 327 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.051145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.041228 restraints weight = 88363.926| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 5.48 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12975 Z= 0.154 Angle : 0.834 32.937 17547 Z= 0.371 Chirality : 0.045 0.214 1971 Planarity : 0.004 0.051 2221 Dihedral : 11.618 168.269 1755 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.57 % Rotamer: Outliers : 4.60 % Allowed : 26.27 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.22), residues: 1528 helix: 1.52 (0.20), residues: 655 sheet: -0.00 (0.33), residues: 221 loop : -1.21 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 248 TYR 0.013 0.002 TYR C 297 PHE 0.024 0.001 PHE B 148 TRP 0.007 0.001 TRP B 265 HIS 0.007 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00338 (12973) covalent geometry : angle 0.83415 (17547) hydrogen bonds : bond 0.03625 ( 597) hydrogen bonds : angle 5.01077 ( 1686) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 109 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8883 (mm) cc_final: 0.8681 (mm) REVERT: A 236 MET cc_start: 0.8615 (mmm) cc_final: 0.8310 (mmm) REVERT: A 292 MET cc_start: 0.8614 (mmt) cc_final: 0.8317 (mmp) REVERT: B 101 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8437 (ptt90) REVERT: D 82 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: D 168 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8617 (mpp) REVERT: D 282 MET cc_start: 0.8579 (tpp) cc_final: 0.8230 (tpp) REVERT: E 145 ARG cc_start: 0.8520 (ptm-80) cc_final: 0.8097 (ptm-80) REVERT: E 296 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9267 (mmmm) REVERT: F 215 MET cc_start: 0.9009 (mtm) cc_final: 0.8799 (mtm) outliers start: 65 outliers final: 45 residues processed: 167 average time/residue: 0.0952 time to fit residues: 23.6058 Evaluate side-chains 149 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 296 LYS Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.050330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.040510 restraints weight = 88990.815| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 5.42 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12975 Z= 0.184 Angle : 0.834 33.483 17547 Z= 0.375 Chirality : 0.046 0.201 1971 Planarity : 0.004 0.050 2221 Dihedral : 11.572 167.429 1755 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 4.67 % Allowed : 25.92 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.22), residues: 1528 helix: 1.58 (0.20), residues: 654 sheet: 0.17 (0.34), residues: 208 loop : -1.26 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.022 0.002 TYR C 29 PHE 0.025 0.002 PHE B 148 TRP 0.018 0.002 TRP D 115 HIS 0.009 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00405 (12973) covalent geometry : angle 0.83428 (17547) hydrogen bonds : bond 0.03669 ( 597) hydrogen bonds : angle 5.08599 ( 1686) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 105 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8904 (mm) cc_final: 0.8541 (mm) REVERT: A 292 MET cc_start: 0.8526 (mmt) cc_final: 0.8196 (mmp) REVERT: B 101 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8382 (ptt90) REVERT: C 187 MET cc_start: 0.8629 (mpp) cc_final: 0.8089 (mpp) REVERT: D 82 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: D 168 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8585 (mpp) REVERT: D 282 MET cc_start: 0.8563 (tpp) cc_final: 0.8256 (tpp) REVERT: E 145 ARG cc_start: 0.8535 (ptm-80) cc_final: 0.8118 (ptm-80) REVERT: F 197 PHE cc_start: 0.9293 (m-80) cc_final: 0.8083 (m-80) REVERT: F 215 MET cc_start: 0.8991 (mtm) cc_final: 0.8772 (mtm) outliers start: 66 outliers final: 49 residues processed: 158 average time/residue: 0.0962 time to fit residues: 22.4260 Evaluate side-chains 154 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 102 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.0040 chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.051035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.041244 restraints weight = 87805.425| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 5.46 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12975 Z= 0.130 Angle : 0.836 33.930 17547 Z= 0.371 Chirality : 0.045 0.206 1971 Planarity : 0.004 0.049 2221 Dihedral : 11.363 169.668 1751 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.10 % Favored : 94.63 % Rotamer: Outliers : 3.12 % Allowed : 27.69 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.22), residues: 1528 helix: 1.61 (0.20), residues: 658 sheet: 0.05 (0.33), residues: 220 loop : -1.10 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 248 TYR 0.025 0.001 TYR C 29 PHE 0.017 0.001 PHE C 167 TRP 0.010 0.001 TRP D 115 HIS 0.011 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00293 (12973) covalent geometry : angle 0.83555 (17547) hydrogen bonds : bond 0.03459 ( 597) hydrogen bonds : angle 5.01144 ( 1686) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8525 (mmt) cc_final: 0.8175 (mmp) REVERT: B 101 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8459 (ptt90) REVERT: C 187 MET cc_start: 0.8584 (mpp) cc_final: 0.8011 (mpp) REVERT: C 229 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8944 (mtpp) REVERT: D 82 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: D 135 MET cc_start: 0.8782 (tmm) cc_final: 0.8481 (tmm) REVERT: D 282 MET cc_start: 0.8601 (tpp) cc_final: 0.8257 (tpp) REVERT: F 88 MET cc_start: 0.8930 (ppp) cc_final: 0.8025 (ppp) REVERT: F 197 PHE cc_start: 0.9251 (m-80) cc_final: 0.8019 (m-80) REVERT: F 215 MET cc_start: 0.8973 (mtm) cc_final: 0.8756 (mtm) outliers start: 44 outliers final: 36 residues processed: 141 average time/residue: 0.0924 time to fit residues: 19.5687 Evaluate side-chains 143 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 0.0070 chunk 128 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.051399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.041627 restraints weight = 87674.830| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 5.49 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12975 Z= 0.126 Angle : 0.706 12.030 17547 Z= 0.342 Chirality : 0.045 0.212 1971 Planarity : 0.004 0.048 2221 Dihedral : 11.325 169.743 1748 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.84 % Favored : 94.83 % Rotamer: Outliers : 3.19 % Allowed : 27.62 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.22), residues: 1528 helix: 1.59 (0.20), residues: 663 sheet: 0.09 (0.33), residues: 221 loop : -1.03 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.011 0.001 TYR C 297 PHE 0.032 0.001 PHE B 148 TRP 0.009 0.001 TRP D 115 HIS 0.012 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00282 (12973) covalent geometry : angle 0.70557 (17547) hydrogen bonds : bond 0.03365 ( 597) hydrogen bonds : angle 4.93613 ( 1686) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8481 (mmt) cc_final: 0.8131 (mmp) REVERT: B 101 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8470 (ptt90) REVERT: C 187 MET cc_start: 0.8562 (mpp) cc_final: 0.7987 (mpp) REVERT: C 229 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8947 (mtpp) REVERT: D 135 MET cc_start: 0.8738 (tmm) cc_final: 0.8399 (tmm) REVERT: D 282 MET cc_start: 0.8650 (tpp) cc_final: 0.8312 (tpp) REVERT: E 145 ARG cc_start: 0.8498 (ptm-80) cc_final: 0.8075 (ptm-80) REVERT: F 87 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9118 (tp) REVERT: F 88 MET cc_start: 0.8914 (ppp) cc_final: 0.7976 (ppp) REVERT: F 197 PHE cc_start: 0.9278 (m-80) cc_final: 0.7769 (m-80) REVERT: F 215 MET cc_start: 0.8974 (mtm) cc_final: 0.8768 (mtm) outliers start: 45 outliers final: 36 residues processed: 140 average time/residue: 0.0889 time to fit residues: 18.8427 Evaluate side-chains 142 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN B 132 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.049549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.039802 restraints weight = 92095.827| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 5.43 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12975 Z= 0.240 Angle : 0.751 12.221 17547 Z= 0.371 Chirality : 0.047 0.222 1971 Planarity : 0.004 0.047 2221 Dihedral : 11.357 168.451 1748 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 3.26 % Allowed : 27.97 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1528 helix: 1.47 (0.20), residues: 661 sheet: -0.34 (0.31), residues: 238 loop : -1.08 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 248 TYR 0.015 0.002 TYR F 176 PHE 0.035 0.002 PHE F 85 TRP 0.010 0.002 TRP D 115 HIS 0.015 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00523 (12973) covalent geometry : angle 0.75082 (17547) hydrogen bonds : bond 0.03880 ( 597) hydrogen bonds : angle 5.16015 ( 1686) Misc. bond : bond 0.00037 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8491 (mmt) cc_final: 0.8146 (mmp) REVERT: B 101 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8484 (ptt90) REVERT: B 131 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: C 187 MET cc_start: 0.8747 (mpp) cc_final: 0.8140 (mpp) REVERT: D 135 MET cc_start: 0.8791 (tmm) cc_final: 0.8050 (tmm) REVERT: D 282 MET cc_start: 0.8640 (tpp) cc_final: 0.8381 (tpp) REVERT: E 145 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8143 (ptm-80) REVERT: F 88 MET cc_start: 0.8955 (ppp) cc_final: 0.8200 (ppp) REVERT: F 215 MET cc_start: 0.8991 (mtm) cc_final: 0.8786 (mtm) outliers start: 46 outliers final: 41 residues processed: 140 average time/residue: 0.0836 time to fit residues: 17.8349 Evaluate side-chains 144 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 82 ASN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.050742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.040855 restraints weight = 91641.457| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 5.55 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12975 Z= 0.145 Angle : 0.732 12.545 17547 Z= 0.358 Chirality : 0.046 0.230 1971 Planarity : 0.004 0.047 2221 Dihedral : 11.328 170.608 1748 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 3.12 % Allowed : 28.05 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1528 helix: 1.58 (0.20), residues: 655 sheet: -0.13 (0.32), residues: 225 loop : -1.09 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.028 0.002 TYR B 263 PHE 0.034 0.002 PHE B 148 TRP 0.010 0.001 TRP D 115 HIS 0.012 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00326 (12973) covalent geometry : angle 0.73178 (17547) hydrogen bonds : bond 0.03599 ( 597) hydrogen bonds : angle 5.11976 ( 1686) Misc. bond : bond 0.00105 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.21 seconds wall clock time: 38 minutes 49.25 seconds (2329.25 seconds total)