Starting phenix.real_space_refine on Wed Jun 11 10:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bht_44552/06_2025/9bht_44552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bht_44552/06_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_44552/06_2025/9bht_44552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bht_44552/06_2025/9bht_44552.map" model { file = "/net/cci-nas-00/data/ceres_data/9bht_44552/06_2025/9bht_44552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bht_44552/06_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-5710/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: 10.37, per 1000 atoms: 0.81 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: 4.56 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: 1.26 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: 3.63 Time building geometry restraints manager: 4.45 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: 12.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.890 Find NCS groups from input model: 0.600 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 12975 Z= 0.304 Angle : 1.129 36.928 17547 Z= 0.573 Chirality : 0.053 0.357 1971 Planarity : 0.008 0.256 2221 Dihedral : 19.394 168.535 4883 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 1.05 % Allowed : 5.96 % Favored : 93.00 % Rotamer: Outliers : 2.05 % Allowed : 33.00 % Favored : 64.94 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.16288 ( 597) hydrogen bonds : angle 6.51274 ( 1686) covalent geometry : bond 0.00552 (12973) covalent geometry : angle 1.12861 (17547) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 232 average time/residue: 0.4143 time to fit residues: 131.5354 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 : 1.761 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.042592 restraints weight = 86919.284| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 5.69 r_work (final): 0.3412 ------------------------------------------------------------------------------- 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 12975 Z= 0.168 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 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 597) hydrogen bonds : angle 5.25345 ( 1686) covalent geometry : bond 0.00385 (12973) covalent geometry : angle 0.89921 (17547) Misc. bond : bond 0.00115 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 139 time to evaluate : 1.441 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: 0.7083 (OUTLIER) cc_final: 0.6186 (ptm-80) REVERT: A 218 LEU cc_start: 0.8900 (mm) cc_final: 0.8675 (mm) REVERT: A 292 MET cc_start: 0.8460 (mmt) cc_final: 0.8150 (mmp) REVERT: B 101 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8514 (ptt90) REVERT: B 160 TYR cc_start: 0.8401 (t80) cc_final: 0.8166 (t80) REVERT: B 177 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: B 290 MET cc_start: 0.9026 (mmm) cc_final: 0.8631 (mmm) REVERT: C 28 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9158 (mt) REVERT: C 198 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8267 (tm-30) REVERT: D 21 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8565 (p90) REVERT: D 82 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: D 200 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8408 (mpp) REVERT: D 282 MET cc_start: 0.8692 (tpp) cc_final: 0.8278 (tpp) REVERT: D 290 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.9175 (m110) REVERT: E 66 MET cc_start: 0.8670 (mtt) cc_final: 0.8129 (mtt) REVERT: E 80 HIS cc_start: 0.7741 (t70) cc_final: 0.7432 (t70) REVERT: E 222 PHE cc_start: 0.6972 (m-80) cc_final: 0.6724 (m-80) REVERT: E 284 MET cc_start: 0.8172 (mmt) cc_final: 0.7567 (mmt) REVERT: E 285 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9263 (mp) REVERT: E 296 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9241 (mmmm) REVERT: F 197 PHE cc_start: 0.8908 (m-80) cc_final: 0.7803 (m-80) REVERT: F 215 MET cc_start: 0.9123 (mtm) cc_final: 0.8887 (mtm) outliers start: 91 outliers final: 33 residues processed: 219 average time/residue: 0.2343 time to fit residues: 74.5296 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 : 1.631 ------------------------------------------------------------------------------- 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: 8.9990 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.051078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.041024 restraints weight = 88748.006| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.56 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12975 Z= 0.205 Angle : 0.867 32.106 17547 Z= 0.391 Chirality : 0.047 0.262 1971 Planarity : 0.006 0.163 2221 Dihedral : 12.149 167.472 1757 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.50 % Favored : 93.98 % Rotamer: Outliers : 4.53 % Allowed : 26.91 % Favored : 68.56 % 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: -0.19 (0.21), residues: 1528 helix: 1.10 (0.20), residues: 654 sheet: -0.09 (0.34), residues: 218 loop : -1.41 (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 D 21 TYR 0.015 0.002 TYR C 297 ARG 0.006 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 597) hydrogen bonds : angle 5.18858 ( 1686) covalent geometry : bond 0.00455 (12973) covalent geometry : angle 0.86737 (17547) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 1.636 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: 0.8547 (mmt) cc_final: 0.8220 (mmp) REVERT: B 32 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6188 (m-10) REVERT: B 101 ARG cc_start: 0.8857 (mtm180) cc_final: 0.8465 (ptt90) REVERT: B 177 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8267 (mtm) REVERT: B 290 MET cc_start: 0.9112 (mmm) cc_final: 0.8731 (mmm) REVERT: C 28 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9289 (mt) REVERT: C 198 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 82 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: D 200 MET cc_start: 0.8715 (mpp) cc_final: 0.8401 (mpp) REVERT: D 282 MET cc_start: 0.8620 (tpp) cc_final: 0.8120 (tpp) REVERT: E 66 MET cc_start: 0.8656 (mtt) cc_final: 0.8262 (mtt) REVERT: E 80 HIS cc_start: 0.7855 (t70) cc_final: 0.7621 (t70) REVERT: E 244 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9290 (m) REVERT: E 296 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9267 (mmmm) REVERT: F 197 PHE cc_start: 0.9406 (m-80) cc_final: 0.8383 (m-80) REVERT: F 215 MET cc_start: 0.9097 (mtm) cc_final: 0.8866 (mtm) REVERT: F 292 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9190 (mmp) outliers start: 64 outliers final: 32 residues processed: 171 average time/residue: 0.2362 time to fit residues: 60.0111 Evaluate side-chains 149 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 B residue 32 PHE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 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 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 82 GLU Chi-restraints excluded: chain D residue 83 THR 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: 3.9990 chunk 105 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 131 optimal weight: 0.0770 chunk 55 optimal weight: 0.0970 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.051833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.041783 restraints weight = 87309.001| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 5.60 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12975 Z= 0.136 Angle : 0.833 32.117 17547 Z= 0.370 Chirality : 0.045 0.233 1971 Planarity : 0.005 0.150 2221 Dihedral : 11.860 167.788 1755 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.04 % Favored : 94.44 % Rotamer: Outliers : 4.11 % Allowed : 25.99 % Favored : 69.90 % 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: 0.06 (0.22), residues: 1528 helix: 1.36 (0.20), residues: 653 sheet: -0.05 (0.33), residues: 218 loop : -1.29 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.011 0.001 HIS F 178 PHE 0.012 0.001 PHE C 167 TYR 0.019 0.002 TYR C 29 ARG 0.004 0.000 ARG F 175 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 597) hydrogen bonds : angle 5.01411 ( 1686) covalent geometry : bond 0.00307 (12973) covalent geometry : angle 0.83275 (17547) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 112 time to evaluate : 1.976 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 166 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8487 (mt) REVERT: A 218 LEU cc_start: 0.8799 (mm) cc_final: 0.8422 (mm) REVERT: A 292 MET cc_start: 0.8488 (mmt) cc_final: 0.8211 (mmp) REVERT: B 79 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7353 (pp30) REVERT: B 101 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8281 (ptt-90) REVERT: C 198 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8271 (tm-30) REVERT: D 200 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8333 (mpp) REVERT: D 282 MET cc_start: 0.8511 (tpp) cc_final: 0.8079 (tpp) REVERT: E 80 HIS cc_start: 0.8026 (t70) cc_final: 0.7788 (t70) REVERT: E 145 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.8180 (ptm-80) REVERT: E 244 VAL cc_start: 0.9461 (OUTLIER) cc_final: 0.9223 (m) REVERT: F 197 PHE cc_start: 0.9359 (m-80) cc_final: 0.8280 (m-80) REVERT: F 215 MET cc_start: 0.9039 (mtm) cc_final: 0.8799 (mtm) REVERT: F 249 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8675 (pt0) REVERT: F 292 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9021 (mmp) outliers start: 58 outliers final: 31 residues processed: 159 average time/residue: 0.2477 time to fit residues: 59.1625 Evaluate side-chains 145 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain 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 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 148 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain 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 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 119 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** 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 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.050193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.040207 restraints weight = 88522.150| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 5.54 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12975 Z= 0.209 Angle : 0.836 33.097 17547 Z= 0.376 Chirality : 0.046 0.191 1971 Planarity : 0.005 0.102 2221 Dihedral : 11.784 165.856 1755 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.76 % Favored : 93.78 % Rotamer: Outliers : 4.60 % Allowed : 25.64 % Favored : 69.76 % 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: 0.14 (0.22), residues: 1528 helix: 1.49 (0.20), residues: 658 sheet: 0.11 (0.34), residues: 206 loop : -1.38 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.006 0.001 HIS B 81 PHE 0.013 0.002 PHE C 167 TYR 0.018 0.002 TYR C 29 ARG 0.005 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 597) hydrogen bonds : angle 5.07609 ( 1686) covalent geometry : bond 0.00452 (12973) covalent geometry : angle 0.83597 (17547) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 105 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 218 LEU cc_start: 0.8869 (mm) cc_final: 0.8491 (mm) REVERT: A 292 MET cc_start: 0.8553 (mmt) cc_final: 0.8264 (mmp) REVERT: B 101 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8538 (ptt90) REVERT: C 198 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8362 (tm-30) REVERT: D 82 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: D 200 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8409 (mpp) REVERT: D 282 MET cc_start: 0.8515 (tpp) cc_final: 0.8096 (tpp) REVERT: E 145 ARG cc_start: 0.8619 (ptm-80) cc_final: 0.8222 (ptm-80) REVERT: E 244 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9219 (m) REVERT: F 197 PHE cc_start: 0.9381 (m-80) cc_final: 0.8329 (m-80) REVERT: F 292 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9108 (mmp) outliers start: 65 outliers final: 36 residues processed: 157 average time/residue: 0.2379 time to fit residues: 55.4182 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 : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 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 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 120 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 CYS 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 C residue 236 VAL Chi-restraints excluded: chain C residue 290 ASN 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 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 284 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 25 optimal weight: 0.9980 chunk 121 optimal weight: 0.3980 chunk 30 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 0.0010 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 0.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** 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 = 0.3754 r_free = 0.3754 target = 0.051559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.041628 restraints weight = 89287.260| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 5.51 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12975 Z= 0.124 Angle : 0.827 32.788 17547 Z= 0.365 Chirality : 0.046 0.258 1971 Planarity : 0.004 0.051 2221 Dihedral : 11.412 169.055 1748 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.91 % Favored : 94.76 % Rotamer: Outliers : 3.47 % Allowed : 26.91 % Favored : 69.62 % 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: 0.23 (0.22), residues: 1528 helix: 1.49 (0.20), residues: 661 sheet: 0.01 (0.34), residues: 219 loop : -1.22 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 115 HIS 0.004 0.001 HIS D 172 PHE 0.020 0.001 PHE B 148 TYR 0.018 0.001 TYR F 168 ARG 0.003 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 597) hydrogen bonds : angle 4.95725 ( 1686) covalent geometry : bond 0.00275 (12973) covalent geometry : angle 0.82705 (17547) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 106 time to evaluate : 1.441 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: 0.8525 (mmt) cc_final: 0.8210 (mmp) REVERT: B 101 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8414 (ptt90) REVERT: C 187 MET cc_start: 0.8508 (mpp) cc_final: 0.7989 (mpp) REVERT: C 198 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8265 (tm-30) REVERT: D 82 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: D 200 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8329 (mpp) REVERT: D 282 MET cc_start: 0.8607 (tpp) cc_final: 0.8289 (tpp) REVERT: E 244 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9216 (m) REVERT: F 197 PHE cc_start: 0.9328 (m-80) cc_final: 0.8200 (m-80) REVERT: F 292 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9123 (mmp) outliers start: 49 outliers final: 30 residues processed: 146 average time/residue: 0.2254 time to fit residues: 49.2418 Evaluate side-chains 140 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 274 GLN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 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 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 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: 7.9990 chunk 19 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.050977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.041090 restraints weight = 88098.671| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 5.50 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12975 Z= 0.144 Angle : 0.826 34.617 17547 Z= 0.366 Chirality : 0.046 0.266 1971 Planarity : 0.004 0.048 2221 Dihedral : 11.353 168.278 1748 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.37 % Favored : 94.31 % Rotamer: Outliers : 3.40 % Allowed : 27.05 % Favored : 69.55 % 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: 0.35 (0.22), residues: 1528 helix: 1.60 (0.20), residues: 655 sheet: 0.23 (0.34), residues: 209 loop : -1.19 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.004 0.001 HIS A 330 PHE 0.018 0.001 PHE E 222 TYR 0.027 0.001 TYR B 263 ARG 0.003 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 597) hydrogen bonds : angle 4.96844 ( 1686) covalent geometry : bond 0.00320 (12973) covalent geometry : angle 0.82571 (17547) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 1.680 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: 0.8474 (mmt) cc_final: 0.8156 (mmp) REVERT: B 101 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8432 (ptt90) REVERT: C 187 MET cc_start: 0.8578 (mpp) cc_final: 0.8070 (mpp) REVERT: C 198 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 82 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: D 200 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8296 (mpp) REVERT: D 282 MET cc_start: 0.8581 (tpp) cc_final: 0.8221 (tpp) REVERT: E 244 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9139 (m) REVERT: F 197 PHE cc_start: 0.9361 (m-80) cc_final: 0.8242 (m-80) REVERT: F 292 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9110 (mmp) outliers start: 48 outliers final: 38 residues processed: 142 average time/residue: 0.2267 time to fit residues: 48.4743 Evaluate side-chains 147 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 331 MET 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 141 LEU 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 C residue 229 LYS 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 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 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 284 MET Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3719 r_free = 0.3719 target = 0.050003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.040221 restraints weight = 90800.938| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 5.40 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12975 Z= 0.192 Angle : 0.708 11.075 17547 Z= 0.345 Chirality : 0.046 0.257 1971 Planarity : 0.004 0.048 2221 Dihedral : 11.435 168.593 1748 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 3.82 % Allowed : 27.12 % Favored : 69.05 % 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: 0.34 (0.22), residues: 1528 helix: 1.61 (0.20), residues: 654 sheet: 0.25 (0.33), residues: 208 loop : -1.21 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.004 0.001 HIS F 205 PHE 0.023 0.002 PHE B 148 TYR 0.028 0.002 TYR B 263 ARG 0.003 0.000 ARG C 253 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 597) hydrogen bonds : angle 5.07495 ( 1686) covalent geometry : bond 0.00418 (12973) covalent geometry : angle 0.70832 (17547) Misc. bond : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 1.697 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: 0.8484 (mmt) cc_final: 0.8149 (mmp) REVERT: B 101 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8521 (ptt90) REVERT: C 187 MET cc_start: 0.8638 (mpp) cc_final: 0.8104 (mpp) REVERT: C 198 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 82 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: D 200 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8244 (mpp) REVERT: D 282 MET cc_start: 0.8604 (tpp) cc_final: 0.8292 (tpp) REVERT: E 145 ARG cc_start: 0.8502 (ptm-80) cc_final: 0.8019 (ptm-80) REVERT: E 244 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9140 (m) REVERT: F 197 PHE cc_start: 0.9376 (m-80) cc_final: 0.8252 (m-80) REVERT: F 292 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.9145 (mmp) outliers start: 54 outliers final: 42 residues processed: 147 average time/residue: 0.2535 time to fit residues: 56.6237 Evaluate side-chains 147 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 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 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 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 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 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 284 MET Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 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: 1.9990 chunk 139 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 96 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.050754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.040855 restraints weight = 88825.436| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 5.47 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12975 Z= 0.141 Angle : 0.699 12.439 17547 Z= 0.339 Chirality : 0.047 0.349 1971 Planarity : 0.004 0.048 2221 Dihedral : 11.404 169.829 1748 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.37 % Favored : 94.31 % Rotamer: Outliers : 3.33 % Allowed : 27.55 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.37 (0.22), residues: 1528 helix: 1.60 (0.20), residues: 654 sheet: 0.27 (0.33), residues: 210 loop : -1.16 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.003 0.001 HIS C 293 PHE 0.019 0.001 PHE C 167 TYR 0.026 0.001 TYR B 263 ARG 0.006 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 597) hydrogen bonds : angle 5.07038 ( 1686) covalent geometry : bond 0.00313 (12973) covalent geometry : angle 0.69911 (17547) Misc. bond : bond 0.00118 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 1.864 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: 0.8456 (mmt) cc_final: 0.8131 (mmp) REVERT: B 101 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8526 (ptt90) REVERT: B 128 TYR cc_start: 0.8367 (t80) cc_final: 0.8110 (t80) REVERT: C 187 MET cc_start: 0.8613 (mpp) cc_final: 0.8029 (mpp) REVERT: C 198 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 200 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8290 (mpp) REVERT: D 282 MET cc_start: 0.8677 (tpp) cc_final: 0.8334 (tpp) REVERT: E 145 ARG cc_start: 0.8491 (ptm-80) cc_final: 0.8069 (ptm-80) REVERT: E 244 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9094 (m) REVERT: F 197 PHE cc_start: 0.9349 (m-80) cc_final: 0.8226 (m-80) REVERT: F 292 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9171 (mmp) outliers start: 47 outliers final: 37 residues processed: 143 average time/residue: 0.2899 time to fit residues: 63.6274 Evaluate side-chains 142 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 43 VAL 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 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 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 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 80 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.1980 chunk 148 optimal weight: 3.9990 chunk 149 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.050924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.041018 restraints weight = 89868.184| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 5.61 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12975 Z= 0.134 Angle : 0.727 12.372 17547 Z= 0.353 Chirality : 0.046 0.300 1971 Planarity : 0.004 0.048 2221 Dihedral : 11.361 169.973 1748 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.91 % Favored : 94.76 % Rotamer: Outliers : 2.90 % Allowed : 27.97 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.43 (0.22), residues: 1528 helix: 1.60 (0.20), residues: 654 sheet: 0.32 (0.33), residues: 211 loop : -1.08 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.004 0.001 HIS F 205 PHE 0.030 0.001 PHE B 148 TYR 0.026 0.002 TYR C 29 ARG 0.005 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 597) hydrogen bonds : angle 5.06002 ( 1686) covalent geometry : bond 0.00302 (12973) covalent geometry : angle 0.72701 (17547) Misc. bond : bond 0.00074 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8535 (mmt) cc_final: 0.8212 (mmp) REVERT: B 101 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8477 (ptt90) REVERT: B 128 TYR cc_start: 0.8339 (t80) cc_final: 0.8088 (t80) REVERT: C 187 MET cc_start: 0.8622 (mpp) cc_final: 0.8037 (mpp) REVERT: C 198 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8283 (tm-30) REVERT: D 200 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8256 (mpp) REVERT: D 282 MET cc_start: 0.8727 (tpp) cc_final: 0.8392 (tpp) REVERT: E 145 ARG cc_start: 0.8521 (ptm-80) cc_final: 0.8046 (ptm-80) REVERT: E 244 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.9109 (m) REVERT: E 257 MET cc_start: 0.9060 (tpp) cc_final: 0.8734 (tpp) REVERT: F 197 PHE cc_start: 0.9357 (m-80) cc_final: 0.8235 (m-80) REVERT: F 292 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.9157 (mmp) outliers start: 41 outliers final: 34 residues processed: 134 average time/residue: 0.2368 time to fit residues: 48.4681 Evaluate side-chains 139 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 109 SER 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 42 MET 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 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 35 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.050802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.040837 restraints weight = 90797.073| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 5.58 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12975 Z= 0.148 Angle : 0.721 12.311 17547 Z= 0.346 Chirality : 0.046 0.289 1971 Planarity : 0.004 0.048 2221 Dihedral : 11.325 170.078 1748 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.24 % Favored : 94.44 % Rotamer: Outliers : 3.12 % Allowed : 28.05 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.22), residues: 1528 helix: 1.56 (0.20), residues: 661 sheet: 0.34 (0.33), residues: 213 loop : -1.09 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 265 HIS 0.004 0.001 HIS F 205 PHE 0.020 0.001 PHE C 167 TYR 0.022 0.002 TYR C 29 ARG 0.004 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 597) hydrogen bonds : angle 5.01373 ( 1686) covalent geometry : bond 0.00335 (12973) covalent geometry : angle 0.72061 (17547) Misc. bond : bond 0.00081 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7349.77 seconds wall clock time: 133 minutes 40.73 seconds (8020.73 seconds total)