Starting phenix.real_space_refine on Sat Jan 18 19:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bht_44552/01_2025/9bht_44552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bht_44552/01_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_44552/01_2025/9bht_44552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bht_44552/01_2025/9bht_44552.map" model { file = "/net/cci-nas-00/data/ceres_data/9bht_44552/01_2025/9bht_44552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bht_44552/01_2025/9bht_44552.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 10.45, per 1000 atoms: 0.82 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.68 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: 3.97 Time building geometry restraints manager: 4.02 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 350 or resid 501)) selection = (chain 'F' and (resid 84 through 261 or resid 274 through 350 or resid 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 314 or resid 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 305 or \ resid 501)) selection = (chain 'D' and (resid 18 through 63 or resid 70 through 305 or resid 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: 14.820 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.390 Process input model: 34.200 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.950 ------------------------------------------------------------------------------- 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 12973 Z= 0.370 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.030 0.002 TRP A 307 HIS 0.010 0.001 HIS A 317 PHE 0.032 0.002 PHE C 21 TYR 0.033 0.002 TYR A 305 ARG 0.012 0.001 ARG F 244 *********************** 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 : 1.679 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: 0.3113 time to fit residues: 99.3604 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 : 1.555 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 218 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 158 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.042596 restraints weight = 86919.330| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 5.71 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 12973 Z= 0.257 Angle : 0.899 31.555 17547 Z= 0.410 Chirality : 0.048 0.202 1971 Planarity : 0.006 0.179 2221 Dihedral : 12.447 170.253 1773 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.69 % Favored : 93.78 % Rotamer: Outliers : 6.44 % Allowed : 25.85 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1528 helix: 0.96 (0.20), residues: 655 sheet: 0.19 (0.36), residues: 205 loop : -1.49 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 307 HIS 0.006 0.001 HIS C 204 PHE 0.025 0.002 PHE B 148 TYR 0.019 0.002 TYR C 29 ARG 0.005 0.001 ARG C 194 *********************** 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 230 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 139 time to evaluate : 1.637 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 192 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6183 (ptm-80) REVERT: A 218 LEU cc_start: 0.8901 (mm) cc_final: 0.8676 (mm) REVERT: A 292 MET cc_start: 0.8459 (mmt) cc_final: 0.8149 (mmp) REVERT: B 101 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8513 (ptt90) REVERT: B 160 TYR cc_start: 0.8402 (t80) cc_final: 0.8165 (t80) REVERT: B 177 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: B 290 MET cc_start: 0.9037 (mmm) cc_final: 0.8637 (mmm) REVERT: C 28 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9159 (mt) REVERT: C 198 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8264 (tm-30) REVERT: D 21 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8570 (p90) REVERT: D 82 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 200 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8407 (mpp) REVERT: D 282 MET cc_start: 0.8701 (tpp) cc_final: 0.8283 (tpp) REVERT: D 290 ASN cc_start: 0.9438 (OUTLIER) cc_final: 0.9172 (m110) REVERT: E 66 MET cc_start: 0.8671 (mtt) cc_final: 0.8134 (mtt) REVERT: E 80 HIS cc_start: 0.7738 (t70) cc_final: 0.7430 (t70) REVERT: E 222 PHE cc_start: 0.6972 (m-80) cc_final: 0.6721 (m-80) REVERT: E 284 MET cc_start: 0.8179 (mmt) cc_final: 0.7572 (mmt) REVERT: E 285 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9263 (mp) REVERT: E 296 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9243 (mmmm) REVERT: F 197 PHE cc_start: 0.8907 (m-80) cc_final: 0.7800 (m-80) REVERT: F 215 MET cc_start: 0.9124 (mtm) cc_final: 0.8887 (mtm) outliers start: 91 outliers final: 33 residues processed: 219 average time/residue: 0.2576 time to fit residues: 82.8358 Evaluate side-chains 159 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 110 VAL 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 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 193 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 290 ASN 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 82 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 197 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 285 LEU 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 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.0470 chunk 116 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.2220 ------------------------------------------------------------------------------- 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 D 35 GLN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 290 ASN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.051418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.041322 restraints weight = 88240.113| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 5.61 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12973 Z= 0.266 Angle : 0.855 31.981 17547 Z= 0.384 Chirality : 0.046 0.206 1971 Planarity : 0.005 0.163 2221 Dihedral : 12.105 167.346 1757 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.43 % Favored : 94.04 % Rotamer: Outliers : 4.53 % Allowed : 26.56 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1528 helix: 1.11 (0.20), residues: 654 sheet: -0.07 (0.34), residues: 218 loop : -1.39 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 307 HIS 0.008 0.001 HIS F 178 PHE 0.019 0.002 PHE F 85 TYR 0.015 0.002 TYR C 297 ARG 0.005 0.000 ARG D 145 *********************** 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 182 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 118 time to evaluate : 1.541 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: A 292 MET cc_start: 0.8527 (mmt) cc_final: 0.8216 (mmp) REVERT: B 32 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6248 (m-10) REVERT: B 101 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8439 (ptt90) REVERT: B 177 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8301 (mtm) REVERT: B 290 MET cc_start: 0.9137 (mmm) cc_final: 0.8749 (mmm) REVERT: C 198 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 200 MET cc_start: 0.8669 (mpp) cc_final: 0.8333 (mpp) REVERT: D 282 MET cc_start: 0.8613 (tpp) cc_final: 0.8101 (tpp) REVERT: E 66 MET cc_start: 0.8665 (mtt) cc_final: 0.8371 (mtt) REVERT: E 80 HIS cc_start: 0.7823 (t70) cc_final: 0.7576 (t70) REVERT: E 83 MET cc_start: 0.8399 (tpp) cc_final: 0.8163 (tpp) REVERT: E 145 ARG cc_start: 0.8546 (ptm-80) cc_final: 0.8226 (ptm-80) REVERT: E 244 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9262 (m) REVERT: E 296 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9264 (mmmm) REVERT: F 197 PHE cc_start: 0.9413 (m-80) cc_final: 0.8477 (m-80) REVERT: F 215 MET cc_start: 0.9073 (mtm) cc_final: 0.8846 (mtm) REVERT: F 292 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9170 (mmp) outliers start: 64 outliers final: 33 residues processed: 172 average time/residue: 0.2464 time to fit residues: 62.3603 Evaluate side-chains 150 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 32 PHE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 177 MET 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 148 CYS 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 C residue 290 ASN 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 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 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 292 MET 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 81 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN 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 = 0.3713 r_free = 0.3713 target = 0.050181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.040241 restraints weight = 88468.670| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 5.44 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12973 Z= 0.297 Angle : 0.848 32.788 17547 Z= 0.381 Chirality : 0.046 0.166 1971 Planarity : 0.005 0.150 2221 Dihedral : 11.938 166.613 1755 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.63 % Favored : 93.85 % Rotamer: Outliers : 5.17 % Allowed : 25.00 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1528 helix: 1.31 (0.20), residues: 653 sheet: -0.13 (0.33), residues: 218 loop : -1.34 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 265 HIS 0.015 0.001 HIS F 178 PHE 0.011 0.002 PHE E 222 TYR 0.021 0.002 TYR C 29 ARG 0.007 0.001 ARG D 145 *********************** 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 177 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 104 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8553 (mt) REVERT: A 218 LEU cc_start: 0.8901 (mm) cc_final: 0.8526 (mm) REVERT: A 292 MET cc_start: 0.8552 (mmt) cc_final: 0.8256 (mmp) REVERT: B 32 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6292 (m-10) REVERT: B 101 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8507 (ptt90) REVERT: B 177 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8127 (mtm) REVERT: B 290 MET cc_start: 0.9133 (mmm) cc_final: 0.8808 (mmm) REVERT: C 198 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 35 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8567 (tm-30) REVERT: D 82 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: D 200 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8272 (mpp) REVERT: D 282 MET cc_start: 0.8557 (tpp) cc_final: 0.8115 (tpp) REVERT: E 80 HIS cc_start: 0.8008 (t70) cc_final: 0.7648 (t70) REVERT: E 83 MET cc_start: 0.8534 (tpp) cc_final: 0.8234 (tpp) REVERT: E 145 ARG cc_start: 0.8598 (ptm-80) cc_final: 0.8197 (ptm-80) REVERT: E 244 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9253 (m) REVERT: E 296 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9248 (mmmm) REVERT: F 197 PHE cc_start: 0.9376 (m-80) cc_final: 0.8273 (m-80) REVERT: F 215 MET cc_start: 0.9087 (mtm) cc_final: 0.8873 (mtm) REVERT: F 292 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9083 (mmp) outliers start: 73 outliers final: 34 residues processed: 167 average time/residue: 0.2669 time to fit residues: 66.5835 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 : 1.473 ------------------------------------------------------------------------------- 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 166 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 331 MET 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 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 177 MET 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 122 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 148 CYS 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 290 ASN Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 175 VAL 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 292 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 F residue 246 ILE Chi-restraints excluded: chain F residue 292 MET 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 119 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.051213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.041176 restraints weight = 88081.466| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 5.52 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12973 Z= 0.206 Angle : 0.813 32.673 17547 Z= 0.362 Chirality : 0.045 0.185 1971 Planarity : 0.004 0.106 2221 Dihedral : 11.476 168.066 1748 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.24 % Favored : 94.31 % Rotamer: Outliers : 3.90 % Allowed : 26.42 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1528 helix: 1.45 (0.20), residues: 658 sheet: 0.01 (0.33), residues: 217 loop : -1.28 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 265 HIS 0.004 0.001 HIS A 330 PHE 0.019 0.001 PHE A 320 TYR 0.017 0.002 TYR C 29 ARG 0.004 0.000 ARG C 248 *********************** 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 163 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 108 time to evaluate : 1.623 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: A 218 LEU cc_start: 0.8875 (mm) cc_final: 0.8467 (mm) REVERT: A 292 MET cc_start: 0.8580 (mmt) cc_final: 0.8288 (mmp) REVERT: B 79 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7468 (pp30) REVERT: B 83 MET cc_start: 0.7776 (mmm) cc_final: 0.7562 (mmm) REVERT: B 101 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8444 (ptt90) REVERT: B 290 MET cc_start: 0.9114 (mmm) cc_final: 0.8830 (mmm) REVERT: C 187 MET cc_start: 0.8556 (mpp) cc_final: 0.8031 (mpp) REVERT: C 198 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8296 (tm-30) REVERT: D 35 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8563 (tm-30) REVERT: D 82 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: D 200 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8294 (mpp) REVERT: D 282 MET cc_start: 0.8534 (tpp) cc_final: 0.8175 (tpp) REVERT: E 80 HIS cc_start: 0.7929 (t70) cc_final: 0.7593 (t70) REVERT: E 83 MET cc_start: 0.8522 (tpp) cc_final: 0.8308 (tpp) REVERT: E 244 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9209 (m) REVERT: F 197 PHE cc_start: 0.9336 (m-80) cc_final: 0.8280 (m-80) REVERT: F 215 MET cc_start: 0.9068 (mtm) cc_final: 0.8855 (mtm) REVERT: F 292 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9064 (mmp) outliers start: 55 outliers final: 36 residues processed: 154 average time/residue: 0.2370 time to fit residues: 55.2888 Evaluate side-chains 145 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 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 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 141 LEU Chi-restraints excluded: chain B residue 177 MET 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 232 VAL Chi-restraints excluded: chain D residue 44 VAL 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.050968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.040952 restraints weight = 89686.533| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 5.59 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12973 Z= 0.193 Angle : 0.817 33.388 17547 Z= 0.360 Chirality : 0.045 0.229 1971 Planarity : 0.004 0.047 2221 Dihedral : 11.364 167.730 1748 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.04 % Favored : 94.63 % Rotamer: Outliers : 3.82 % Allowed : 27.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1528 helix: 1.50 (0.20), residues: 660 sheet: -0.01 (0.33), residues: 221 loop : -1.17 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 265 HIS 0.007 0.001 HIS B 81 PHE 0.020 0.001 PHE B 148 TYR 0.014 0.001 TYR D 151 ARG 0.004 0.000 ARG C 248 *********************** 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 162 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8525 (mm) REVERT: A 292 MET cc_start: 0.8520 (mmt) cc_final: 0.8182 (mmp) REVERT: B 101 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8468 (ptt90) REVERT: B 290 MET cc_start: 0.9151 (mmm) cc_final: 0.8877 (mmm) REVERT: C 187 MET cc_start: 0.8508 (mpp) cc_final: 0.7958 (mpp) REVERT: C 198 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8284 (tm-30) REVERT: D 35 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8618 (tm-30) REVERT: D 82 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: D 200 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8175 (mpp) REVERT: D 282 MET cc_start: 0.8563 (tpp) cc_final: 0.8194 (tpp) REVERT: E 80 HIS cc_start: 0.8023 (t70) cc_final: 0.7653 (t70) REVERT: E 83 MET cc_start: 0.8581 (tpp) cc_final: 0.8332 (tpp) REVERT: E 244 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9173 (m) REVERT: F 197 PHE cc_start: 0.9337 (m-80) cc_final: 0.8230 (m-80) REVERT: F 215 MET cc_start: 0.9015 (mtm) cc_final: 0.8790 (mtm) REVERT: F 292 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9110 (mmp) outliers start: 54 outliers final: 38 residues processed: 153 average time/residue: 0.2404 time to fit residues: 55.3176 Evaluate side-chains 150 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain A residue 218 LEU 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 177 MET 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 232 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 82 GLU 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 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 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 270 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 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 = 0.3718 r_free = 0.3718 target = 0.050175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.040277 restraints weight = 88559.495| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 5.43 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12973 Z= 0.252 Angle : 0.824 35.959 17547 Z= 0.366 Chirality : 0.045 0.199 1971 Planarity : 0.004 0.046 2221 Dihedral : 11.352 168.275 1748 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.24 % Favored : 94.44 % Rotamer: Outliers : 3.97 % Allowed : 27.27 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1528 helix: 1.53 (0.20), residues: 660 sheet: 0.18 (0.33), residues: 209 loop : -1.22 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 265 HIS 0.005 0.001 HIS A 330 PHE 0.020 0.001 PHE E 222 TYR 0.022 0.002 TYR B 263 ARG 0.004 0.000 ARG C 248 *********************** 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 162 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 106 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 292 MET cc_start: 0.8393 (mmt) cc_final: 0.8060 (mmp) REVERT: B 101 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8491 (ptt90) REVERT: B 290 MET cc_start: 0.9100 (mmm) cc_final: 0.8862 (mmm) REVERT: C 187 MET cc_start: 0.8545 (mpp) cc_final: 0.7963 (mpp) REVERT: C 198 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 229 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8952 (mtpp) REVERT: D 35 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8610 (tm-30) REVERT: D 82 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: D 200 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8139 (mpp) REVERT: D 282 MET cc_start: 0.8518 (tpp) cc_final: 0.8204 (tpp) REVERT: E 80 HIS cc_start: 0.7976 (t70) cc_final: 0.7684 (t70) REVERT: E 83 MET cc_start: 0.8563 (tpp) cc_final: 0.8357 (tpp) REVERT: E 222 PHE cc_start: 0.6988 (m-80) cc_final: 0.6514 (m-80) REVERT: E 244 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9164 (m) REVERT: E 296 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9231 (mmmm) REVERT: F 197 PHE cc_start: 0.9346 (m-80) cc_final: 0.8211 (m-80) REVERT: F 215 MET cc_start: 0.9026 (mtm) cc_final: 0.8812 (mtm) REVERT: F 292 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9123 (mmp) outliers start: 56 outliers final: 38 residues processed: 152 average time/residue: 0.2531 time to fit residues: 57.5387 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 : 1.689 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE 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 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 D residue 44 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 82 GLU 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 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 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 270 VAL Chi-restraints excluded: chain E residue 296 LYS 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 57 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN B 131 GLN B 132 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS D 116 GLN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.049480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.039551 restraints weight = 92065.656| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 5.48 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12973 Z= 0.310 Angle : 0.708 11.479 17547 Z= 0.347 Chirality : 0.046 0.207 1971 Planarity : 0.004 0.049 2221 Dihedral : 11.462 168.413 1748 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.63 % Favored : 94.04 % Rotamer: Outliers : 4.39 % Allowed : 27.05 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1528 helix: 1.48 (0.20), residues: 660 sheet: 0.09 (0.33), residues: 209 loop : -1.23 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 115 HIS 0.005 0.001 HIS F 205 PHE 0.024 0.002 PHE B 148 TYR 0.023 0.002 TYR B 263 ARG 0.004 0.000 ARG C 248 *********************** 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 165 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 103 time to evaluate : 1.555 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: A 292 MET cc_start: 0.8482 (mmt) cc_final: 0.8143 (mmp) REVERT: B 101 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8538 (ptt90) REVERT: B 131 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: B 290 MET cc_start: 0.9182 (mmm) cc_final: 0.8937 (mmm) REVERT: C 187 MET cc_start: 0.8688 (mpp) cc_final: 0.8075 (mpp) REVERT: C 198 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8421 (tm-30) REVERT: C 229 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8934 (mtpp) REVERT: D 35 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8690 (tm-30) REVERT: D 82 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: D 200 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8102 (mpp) REVERT: D 282 MET cc_start: 0.8685 (tpp) cc_final: 0.8289 (tpp) REVERT: E 80 HIS cc_start: 0.8048 (t70) cc_final: 0.7691 (t70) REVERT: E 244 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9155 (m) REVERT: F 87 LEU cc_start: 0.9344 (mt) cc_final: 0.9046 (pt) REVERT: F 197 PHE cc_start: 0.9364 (m-80) cc_final: 0.8437 (m-80) REVERT: F 215 MET cc_start: 0.9056 (mtm) cc_final: 0.8846 (mtm) REVERT: F 292 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.9134 (mmp) outliers start: 62 outliers final: 44 residues processed: 155 average time/residue: 0.2381 time to fit residues: 55.9094 Evaluate side-chains 152 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain A residue 149 THR 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 131 GLN Chi-restraints excluded: chain B residue 141 LEU 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 105 PHE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 137 THR 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 D residue 44 VAL 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 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 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 270 VAL Chi-restraints excluded: chain E residue 285 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 125 optimal weight: 0.0170 chunk 139 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.050225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.040295 restraints weight = 89576.159| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 5.49 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12973 Z= 0.207 Angle : 0.708 14.070 17547 Z= 0.339 Chirality : 0.046 0.350 1971 Planarity : 0.004 0.050 2221 Dihedral : 11.433 169.270 1748 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.50 % Favored : 94.18 % Rotamer: Outliers : 3.19 % Allowed : 27.90 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1528 helix: 1.49 (0.20), residues: 660 sheet: 0.23 (0.33), residues: 208 loop : -1.16 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 115 HIS 0.008 0.001 HIS B 80 PHE 0.018 0.001 PHE C 167 TYR 0.027 0.002 TYR B 263 ARG 0.005 0.000 ARG C 248 *********************** 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 147 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8456 (mmt) cc_final: 0.8116 (mmp) REVERT: B 101 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8535 (ptt90) REVERT: B 128 TYR cc_start: 0.8317 (t80) cc_final: 0.8065 (t80) REVERT: B 290 MET cc_start: 0.9207 (mmm) cc_final: 0.8971 (mmm) REVERT: C 187 MET cc_start: 0.8634 (mpp) cc_final: 0.8002 (mpp) REVERT: C 198 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 229 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8933 (mtpp) REVERT: D 35 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8694 (tm-30) REVERT: D 82 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: D 200 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8117 (mpp) REVERT: D 282 MET cc_start: 0.8693 (tpp) cc_final: 0.8353 (tpp) REVERT: E 145 ARG cc_start: 0.8520 (ptm-80) cc_final: 0.8093 (ptm-80) REVERT: E 244 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9148 (m) REVERT: F 87 LEU cc_start: 0.9329 (mt) cc_final: 0.9021 (pt) REVERT: F 197 PHE cc_start: 0.9339 (m-80) cc_final: 0.8413 (m-80) REVERT: F 292 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.9259 (mmp) outliers start: 45 outliers final: 36 residues processed: 138 average time/residue: 0.2449 time to fit residues: 51.1094 Evaluate side-chains 143 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 149 THR 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 144 CYS 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 D residue 42 MET 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 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 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 270 VAL Chi-restraints excluded: chain E residue 285 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 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 80 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 13 optimal weight: 0.0270 chunk 152 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 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 = 0.3739 r_free = 0.3739 target = 0.050967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.041075 restraints weight = 90900.858| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 5.55 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12973 Z= 0.185 Angle : 0.701 13.268 17547 Z= 0.335 Chirality : 0.046 0.321 1971 Planarity : 0.004 0.053 2221 Dihedral : 11.369 169.956 1748 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.10 % Favored : 94.57 % Rotamer: Outliers : 3.05 % Allowed : 28.26 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1528 helix: 1.53 (0.20), residues: 660 sheet: 0.31 (0.33), residues: 211 loop : -1.10 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 115 HIS 0.004 0.001 HIS F 205 PHE 0.031 0.001 PHE B 148 TYR 0.024 0.002 TYR D 151 ARG 0.009 0.000 ARG C 248 ********************** 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 146 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8420 (mmt) cc_final: 0.8068 (mmp) REVERT: B 101 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8500 (ptt90) REVERT: B 128 TYR cc_start: 0.8371 (t80) cc_final: 0.8104 (t80) REVERT: B 290 MET cc_start: 0.9230 (mmm) cc_final: 0.9027 (mmm) REVERT: C 187 MET cc_start: 0.8577 (mpp) cc_final: 0.7956 (mpp) REVERT: C 198 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8295 (tm-30) REVERT: D 35 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8730 (tm-30) REVERT: D 200 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8135 (mpp) REVERT: D 282 MET cc_start: 0.8748 (tpp) cc_final: 0.8391 (tpp) REVERT: E 145 ARG cc_start: 0.8477 (ptm-80) cc_final: 0.7990 (ptm-80) REVERT: E 244 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9114 (m) REVERT: F 197 PHE cc_start: 0.9342 (m-80) cc_final: 0.8221 (m-80) REVERT: F 292 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9032 (mmp) outliers start: 43 outliers final: 31 residues processed: 137 average time/residue: 0.2443 time to fit residues: 49.8877 Evaluate side-chains 135 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 149 THR 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 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 D residue 44 VAL Chi-restraints excluded: chain D residue 77 LYS 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 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 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 270 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 287 VAL Chi-restraints excluded: chain F residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 167 GLN ** 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 = 0.050953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.041096 restraints weight = 90670.368| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 5.56 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12973 Z= 0.193 Angle : 0.707 12.655 17547 Z= 0.339 Chirality : 0.046 0.316 1971 Planarity : 0.004 0.052 2221 Dihedral : 11.323 169.827 1748 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.78 % Favored : 94.90 % Rotamer: Outliers : 2.83 % Allowed : 28.19 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1528 helix: 1.61 (0.20), residues: 651 sheet: 0.36 (0.33), residues: 211 loop : -1.04 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.001 PHE C 167 TYR 0.029 0.002 TYR C 29 ARG 0.003 0.000 ARG D 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5113.04 seconds wall clock time: 95 minutes 1.77 seconds (5701.77 seconds total)