Starting phenix.real_space_refine on Sun Nov 17 03:18:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bht_44552/11_2024/9bht_44552.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bht_44552/11_2024/9bht_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bht_44552/11_2024/9bht_44552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bht_44552/11_2024/9bht_44552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bht_44552/11_2024/9bht_44552.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bht_44552/11_2024/9bht_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-5513/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: 9.39, per 1000 atoms: 0.74 Number of scatterers: 12725 At special positions: 0 Unit cell: (61.202, 74.994, 258.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 14 15.00 O 2410 8.00 N 2203 7.00 C 8024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.7 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: 1.48 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: 3.88 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 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: 30.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.120 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 12973 Z= 0.370 Angle : 1.129 36.928 17547 Z= 0.573 Chirality : 0.053 0.357 1971 Planarity : 0.008 0.256 2221 Dihedral : 19.394 168.535 4883 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 1.05 % Allowed : 5.96 % Favored : 93.00 % Rotamer: Outliers : 2.05 % Allowed : 33.00 % Favored : 64.94 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1528 helix: 0.60 (0.20), residues: 647 sheet: 0.14 (0.34), residues: 212 loop : -1.73 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 307 HIS 0.010 0.001 HIS A 317 PHE 0.032 0.002 PHE C 21 TYR 0.033 0.002 TYR A 305 ARG 0.012 0.001 ARG F 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 1.569 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: 0.3057 time to fit residues: 96.8850 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 : 1.414 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 12973 Z= 0.257 Angle : 0.899 31.555 17547 Z= 0.410 Chirality : 0.048 0.202 1971 Planarity : 0.006 0.179 2221 Dihedral : 12.447 170.253 1773 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.69 % Favored : 93.78 % Rotamer: Outliers : 6.44 % Allowed : 25.85 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1528 helix: 0.96 (0.20), residues: 655 sheet: 0.19 (0.36), residues: 205 loop : -1.49 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 307 HIS 0.006 0.001 HIS C 204 PHE 0.025 0.002 PHE B 148 TYR 0.019 0.002 TYR C 29 ARG 0.005 0.001 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 139 time to evaluate : 1.413 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: D 200 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7955 (mpp) REVERT: E 66 MET cc_start: 0.7659 (mtt) cc_final: 0.7061 (mtt) REVERT: E 233 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7919 (p0) REVERT: E 284 MET cc_start: 0.7620 (mmt) cc_final: 0.7384 (mmt) outliers start: 91 outliers final: 33 residues processed: 219 average time/residue: 0.2514 time to fit residues: 80.0533 Evaluate side-chains 150 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 149 THR 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 110 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 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 74 ARG Chi-restraints excluded: chain D residue 77 LYS 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 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 233 ASN Chi-restraints excluded: chain E residue 258 VAL 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 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12973 Z= 0.241 Angle : 0.863 31.738 17547 Z= 0.387 Chirality : 0.046 0.226 1971 Planarity : 0.005 0.163 2221 Dihedral : 12.124 168.219 1755 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.63 % Favored : 93.85 % Rotamer: Outliers : 3.90 % Allowed : 27.20 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1528 helix: 1.10 (0.20), residues: 653 sheet: 0.02 (0.34), residues: 218 loop : -1.37 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 307 HIS 0.011 0.001 HIS F 178 PHE 0.017 0.002 PHE C 167 TYR 0.013 0.001 TYR C 297 ARG 0.003 0.000 ARG C 226 *********************** 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 174 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 1.610 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: E 236 MET cc_start: 0.7594 (ppp) cc_final: 0.7313 (ppp) REVERT: F 292 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8030 (mmp) outliers start: 55 outliers final: 29 residues processed: 166 average time/residue: 0.2395 time to fit residues: 58.8310 Evaluate side-chains 142 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 274 GLN 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 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 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 83 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 285 LEU 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 138 optimal weight: 0.0970 chunk 105 optimal weight: 0.2980 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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** ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12973 Z= 0.197 Angle : 0.834 31.951 17547 Z= 0.371 Chirality : 0.045 0.175 1971 Planarity : 0.005 0.150 2221 Dihedral : 11.953 168.145 1755 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.24 % Favored : 94.24 % Rotamer: Outliers : 3.82 % Allowed : 25.50 % Favored : 70.68 % 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: 0.05 (0.22), residues: 1528 helix: 1.27 (0.20), residues: 653 sheet: 0.05 (0.34), residues: 218 loop : -1.25 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.006 0.001 HIS F 178 PHE 0.015 0.001 PHE D 21 TYR 0.018 0.002 TYR A 152 ARG 0.003 0.000 ARG F 175 *********************** 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: 54 poor density : 116 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8157 (mt) REVERT: D 282 MET cc_start: 0.7558 (mmt) cc_final: 0.7340 (tpp) REVERT: F 292 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7928 (mmp) outliers start: 54 outliers final: 34 residues processed: 160 average time/residue: 0.2373 time to fit residues: 56.5315 Evaluate side-chains 142 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 134 GLU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 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 83 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 110 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12973 Z= 0.191 Angle : 0.822 32.592 17547 Z= 0.365 Chirality : 0.045 0.189 1971 Planarity : 0.004 0.100 2221 Dihedral : 11.734 167.563 1755 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.30 % Favored : 94.24 % Rotamer: Outliers : 3.97 % Allowed : 25.28 % Favored : 70.75 % 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: 0.15 (0.22), residues: 1528 helix: 1.34 (0.20), residues: 659 sheet: 0.12 (0.34), residues: 218 loop : -1.21 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 265 HIS 0.008 0.001 HIS B 80 PHE 0.022 0.001 PHE B 148 TYR 0.023 0.002 TYR A 152 ARG 0.006 0.000 ARG F 245 *********************** 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 171 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 115 time to evaluate : 1.581 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: F 292 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7950 (mmp) outliers start: 56 outliers final: 36 residues processed: 160 average time/residue: 0.2415 time to fit residues: 58.2570 Evaluate side-chains 147 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain 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 109 SER Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 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 83 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0370 chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 149 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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** ** C 198 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12973 Z= 0.192 Angle : 0.821 33.357 17547 Z= 0.363 Chirality : 0.045 0.224 1971 Planarity : 0.004 0.050 2221 Dihedral : 11.570 168.529 1755 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.84 % Favored : 94.76 % Rotamer: Outliers : 3.40 % Allowed : 26.13 % Favored : 70.47 % 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: 0.25 (0.22), residues: 1528 helix: 1.45 (0.20), residues: 659 sheet: 0.18 (0.34), residues: 218 loop : -1.19 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 265 HIS 0.005 0.001 HIS D 172 PHE 0.026 0.001 PHE B 148 TYR 0.017 0.001 TYR A 152 ARG 0.003 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 1.611 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: C 229 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8761 (ttpp) REVERT: F 292 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7950 (mmp) outliers start: 48 outliers final: 32 residues processed: 148 average time/residue: 0.2381 time to fit residues: 52.5525 Evaluate side-chains 141 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 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 109 SER Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 229 LYS 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 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 143 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12973 Z= 0.217 Angle : 0.808 35.979 17547 Z= 0.360 Chirality : 0.045 0.206 1971 Planarity : 0.004 0.049 2221 Dihedral : 11.429 168.825 1755 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.91 % Favored : 94.70 % Rotamer: Outliers : 3.40 % Allowed : 26.63 % Favored : 69.97 % 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: 0.33 (0.22), residues: 1528 helix: 1.53 (0.20), residues: 661 sheet: 0.01 (0.33), residues: 231 loop : -1.12 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 265 HIS 0.005 0.001 HIS D 281 PHE 0.033 0.002 PHE B 148 TYR 0.026 0.002 TYR C 29 ARG 0.003 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 1.387 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 236 MET cc_start: 0.7951 (mmm) cc_final: 0.7746 (mmp) REVERT: F 292 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7940 (mmp) outliers start: 48 outliers final: 39 residues processed: 143 average time/residue: 0.2593 time to fit residues: 54.4519 Evaluate side-chains 142 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 274 GLN 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 66 MET Chi-restraints excluded: chain B residue 88 LEU 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 120 ASN Chi-restraints excluded: chain C residue 188 THR 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 74 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain 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 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 Chi-restraints excluded: chain F residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.1832 > 50: distance: 23 - 30: 33.100 distance: 30 - 31: 19.543 distance: 30 - 77: 27.963 distance: 31 - 32: 34.466 distance: 31 - 34: 34.056 distance: 32 - 33: 20.474 distance: 32 - 38: 29.406 distance: 33 - 74: 29.275 distance: 34 - 35: 9.713 distance: 34 - 36: 24.789 distance: 35 - 37: 21.957 distance: 38 - 39: 20.524 distance: 39 - 40: 13.569 distance: 39 - 42: 38.816 distance: 40 - 41: 25.530 distance: 40 - 47: 35.692 distance: 42 - 43: 26.747 distance: 43 - 44: 41.381 distance: 44 - 45: 41.674 distance: 45 - 46: 40.053 distance: 47 - 48: 40.118 distance: 48 - 49: 26.563 distance: 48 - 51: 55.958 distance: 49 - 50: 45.009 distance: 49 - 55: 21.234 distance: 51 - 52: 22.310 distance: 52 - 53: 28.481 distance: 52 - 54: 45.003 distance: 55 - 56: 40.048 distance: 56 - 57: 38.863 distance: 57 - 58: 40.367 distance: 57 - 59: 59.303 distance: 59 - 60: 36.061 distance: 60 - 61: 11.787 distance: 60 - 63: 32.843 distance: 61 - 62: 46.042 distance: 61 - 64: 21.489 distance: 64 - 65: 47.440 distance: 65 - 66: 41.169 distance: 65 - 68: 27.511 distance: 66 - 67: 32.200 distance: 66 - 69: 14.796 distance: 69 - 70: 30.782 distance: 70 - 71: 17.230 distance: 71 - 72: 30.859 distance: 71 - 74: 26.982 distance: 74 - 75: 31.228 distance: 75 - 76: 24.574 distance: 75 - 78: 23.715 distance: 76 - 77: 17.557 distance: 76 - 81: 11.629 distance: 78 - 79: 6.280 distance: 78 - 80: 32.005 distance: 81 - 82: 21.191 distance: 82 - 83: 15.346 distance: 82 - 85: 11.206 distance: 83 - 84: 27.737 distance: 83 - 90: 24.023 distance: 85 - 86: 44.707 distance: 86 - 87: 24.148 distance: 87 - 88: 7.514 distance: 88 - 89: 12.729 distance: 90 - 91: 10.524 distance: 91 - 92: 22.846 distance: 91 - 94: 41.923 distance: 92 - 93: 10.486 distance: 92 - 95: 21.447