Starting phenix.real_space_refine on Wed Jan 15 19:27:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuq_43536/01_2025/8vuq_43536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuq_43536/01_2025/8vuq_43536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vuq_43536/01_2025/8vuq_43536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuq_43536/01_2025/8vuq_43536.map" model { file = "/net/cci-nas-00/data/ceres_data/8vuq_43536/01_2025/8vuq_43536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuq_43536/01_2025/8vuq_43536.cif" } resolution = 3.85 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5500 2.51 5 N 1492 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2789 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2697 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "G" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1617 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1554 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.11, per 1000 atoms: 0.71 Number of scatterers: 8657 At special positions: 0 Unit cell: (107, 113.848, 124.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1629 8.00 N 1492 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 149 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 19 sheets defined 24.9% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.570A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.937A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.554A pdb=" N PHE A 102 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.506A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.797A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.518A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.659A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.502A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.757A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.832A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.095A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.613A pdb=" N SER B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.933A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 4.312A pdb=" N GLN B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.675A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.672A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.872A pdb=" N VAL B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 196 through 198 No H-bonds generated for 'chain 'G' and resid 196 through 198' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.768A pdb=" N ASN I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 removed outlier: 3.751A pdb=" N ALA I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 removed outlier: 3.749A pdb=" N HIS I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.502A pdb=" N LEU A 33 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.734A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.731A pdb=" N VAL A 167 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.734A pdb=" N ASN A 341 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 344 " --> pdb=" O ASN A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 72 removed outlier: 7.047A pdb=" N ALA B 37 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.878A pdb=" N PHE B 170 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL B 279 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 364 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.572A pdb=" N VAL B 341 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 348 " --> pdb=" O VAL B 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.857A pdb=" N LEU G 81 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 60 removed outlier: 3.551A pdb=" N GLY G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 97 " --> pdb=" O HIS G 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G 190 " --> pdb=" O HIS G 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER G 186 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 159 through 163 Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.762A pdb=" N VAL I 10 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN I 39 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR I 90 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 18 through 20 removed outlier: 4.072A pdb=" N VAL I 18 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 78 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 66 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA I 173 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 155 removed outlier: 4.065A pdb=" N TRP I 148 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS I 149 " --> pdb=" O SER I 192 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER I 192 " --> pdb=" O LYS I 149 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2801 1.34 - 1.46: 2083 1.46 - 1.58: 3917 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 8863 Sorted by residual: bond pdb=" CB PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 1.506 1.587 -0.081 3.90e-02 6.57e+02 4.28e+00 bond pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 1.468 1.435 0.033 1.70e-02 3.46e+03 3.80e+00 bond pdb=" CG PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.18e+00 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CA ASN I 53 " pdb=" CB ASN I 53 " ideal model delta sigma weight residual 1.539 1.598 -0.058 4.88e-02 4.20e+02 1.43e+00 ... (remaining 8858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12010 2.82 - 5.64: 74 5.64 - 8.47: 8 8.47 - 11.29: 1 11.29 - 14.11: 1 Bond angle restraints: 12094 Sorted by residual: angle pdb=" CA PRO G 156 " pdb=" N PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 111.50 97.39 14.11 1.40e+00 5.10e-01 1.02e+02 angle pdb=" C THR I 83 " pdb=" CA THR I 83 " pdb=" CB THR I 83 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N PRO G 156 " pdb=" CD PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 103.80 98.76 5.04 1.20e+00 6.94e-01 1.76e+01 angle pdb=" CA THR I 83 " pdb=" C THR I 83 " pdb=" N GLU I 84 " ideal model delta sigma weight residual 119.52 116.77 2.75 7.90e-01 1.60e+00 1.21e+01 angle pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 112.00 107.37 4.63 1.40e+00 5.10e-01 1.09e+01 ... (remaining 12089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4498 17.96 - 35.91: 566 35.91 - 53.87: 147 53.87 - 71.82: 24 71.82 - 89.78: 12 Dihedral angle restraints: 5247 sinusoidal: 1891 harmonic: 3356 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PRO A 142 " pdb=" C PRO A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP I 138 " pdb=" CB ASP I 138 " pdb=" CG ASP I 138 " pdb=" OD1 ASP I 138 " ideal model delta sinusoidal sigma weight residual -30.00 -88.25 58.25 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 802 0.029 - 0.058: 393 0.058 - 0.087: 105 0.087 - 0.117: 82 0.117 - 0.146: 15 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB THR G 91 " pdb=" CA THR G 91 " pdb=" OG1 THR G 91 " pdb=" CG2 THR G 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 227 " pdb=" N ILE B 227 " pdb=" C ILE B 227 " pdb=" CB ILE B 227 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA VAL G 40 " pdb=" N VAL G 40 " pdb=" C VAL G 40 " pdb=" CB VAL G 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1394 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 155 " -0.089 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO G 156 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO G 156 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO G 156 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " -0.045 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 304 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 319 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.026 5.00e-02 4.00e+02 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 245 2.69 - 3.24: 8282 3.24 - 3.79: 12495 3.79 - 4.35: 15199 4.35 - 4.90: 26229 Nonbonded interactions: 62450 Sorted by model distance: nonbonded pdb=" O ASN I 53 " pdb=" ND2 ASN I 53 " model vdw 2.133 3.120 nonbonded pdb=" O MET I 3 " pdb=" OG SER I 25 " model vdw 2.146 3.040 nonbonded pdb=" O PHE B 195 " pdb=" N GLY B 197 " model vdw 2.163 3.120 nonbonded pdb=" OG SER A 93 " pdb=" OE2 GLU A 277 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN B 154 " pdb=" OG SER B 259 " model vdw 2.216 3.040 ... (remaining 62445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 13.290 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: 3.610 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.003 0.081 8863 Z= 0.184 Angle : 0.616 14.112 12094 Z= 0.328 Chirality : 0.042 0.146 1397 Planarity : 0.005 0.124 1541 Dihedral : 17.334 89.781 3071 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.06 % Favored : 87.51 % Rotamer: Outliers : 0.66 % Allowed : 35.83 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.68 (0.26), residues: 1153 helix: 0.75 (0.37), residues: 218 sheet: -1.03 (0.32), residues: 317 loop : -1.89 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 284 HIS 0.005 0.001 HIS B 332 PHE 0.009 0.001 PHE B 210 TYR 0.021 0.001 TYR B 321 ARG 0.004 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.902 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 132 average time/residue: 0.2254 time to fit residues: 41.4694 Evaluate side-chains 127 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113779 restraints weight = 15628.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110679 restraints weight = 15582.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112251 restraints weight = 16258.207| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.180 Angle : 0.591 7.916 12094 Z= 0.309 Chirality : 0.043 0.138 1397 Planarity : 0.004 0.077 1541 Dihedral : 4.134 22.203 1244 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.62 % Favored : 87.94 % Rotamer: Outliers : 5.73 % Allowed : 29.00 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.58 (0.26), residues: 1153 helix: 0.88 (0.35), residues: 246 sheet: -0.80 (0.32), residues: 316 loop : -2.09 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.003 0.001 HIS B 332 PHE 0.012 0.001 PHE B 210 TYR 0.012 0.001 TYR B 321 ARG 0.003 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8126 (ptm160) REVERT: A 162 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6912 (m90) REVERT: A 295 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8927 (tp) REVERT: G 49 SER cc_start: 0.8903 (p) cc_final: 0.8437 (m) REVERT: G 180 GLN cc_start: 0.5865 (pm20) cc_final: 0.3691 (tm-30) REVERT: I 53 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7953 (p0) outliers start: 52 outliers final: 29 residues processed: 174 average time/residue: 0.2081 time to fit residues: 50.5080 Evaluate side-chains 155 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN I 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114364 restraints weight = 15902.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111741 restraints weight = 16085.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113079 restraints weight = 16396.030| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8863 Z= 0.158 Angle : 0.566 7.620 12094 Z= 0.292 Chirality : 0.043 0.143 1397 Planarity : 0.004 0.067 1541 Dihedral : 4.046 23.077 1241 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.75 % Favored : 88.81 % Rotamer: Outliers : 5.62 % Allowed : 29.22 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.55 (0.26), residues: 1153 helix: 0.92 (0.35), residues: 249 sheet: -0.91 (0.32), residues: 310 loop : -2.00 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS B 332 PHE 0.016 0.001 PHE A 152 TYR 0.012 0.001 TYR B 321 ARG 0.003 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8125 (ptm160) REVERT: B 206 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7798 (pp) REVERT: B 348 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8823 (pp) REVERT: B 378 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.7702 (t60) REVERT: G 49 SER cc_start: 0.9023 (p) cc_final: 0.8513 (m) outliers start: 51 outliers final: 31 residues processed: 167 average time/residue: 0.1940 time to fit residues: 45.5127 Evaluate side-chains 157 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.0010 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.149348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109855 restraints weight = 15837.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106834 restraints weight = 15155.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108169 restraints weight = 16192.392| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8863 Z= 0.267 Angle : 0.606 7.946 12094 Z= 0.313 Chirality : 0.044 0.164 1397 Planarity : 0.004 0.061 1541 Dihedral : 4.312 23.038 1241 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.62 % Favored : 85.95 % Rotamer: Outliers : 7.17 % Allowed : 28.67 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.67 (0.26), residues: 1153 helix: 0.71 (0.34), residues: 247 sheet: -0.95 (0.31), residues: 323 loop : -2.05 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 148 HIS 0.009 0.001 HIS A 293 PHE 0.017 0.002 PHE A 152 TYR 0.024 0.002 TYR B 180 ARG 0.004 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 130 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8149 (ptm160) REVERT: B 206 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7889 (pp) REVERT: B 207 ASP cc_start: 0.8378 (p0) cc_final: 0.8087 (p0) REVERT: B 348 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8794 (pp) REVERT: B 378 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7879 (t60) REVERT: I 24 ARG cc_start: 0.8760 (ttt90) cc_final: 0.8539 (ttt90) REVERT: I 53 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8041 (p0) outliers start: 65 outliers final: 50 residues processed: 180 average time/residue: 0.2017 time to fit residues: 50.2544 Evaluate side-chains 179 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 155 PHE Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112276 restraints weight = 15799.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110526 restraints weight = 14677.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111550 restraints weight = 14644.313| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.165 Angle : 0.578 7.885 12094 Z= 0.293 Chirality : 0.043 0.151 1397 Planarity : 0.004 0.058 1541 Dihedral : 4.172 22.171 1241 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.10 % Favored : 88.46 % Rotamer: Outliers : 6.50 % Allowed : 29.00 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.55 (0.26), residues: 1153 helix: 0.90 (0.34), residues: 249 sheet: -1.00 (0.32), residues: 309 loop : -1.93 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 148 HIS 0.006 0.001 HIS A 293 PHE 0.013 0.001 PHE A 152 TYR 0.012 0.001 TYR B 321 ARG 0.004 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8262 (ptm160) REVERT: B 206 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7828 (pp) REVERT: B 207 ASP cc_start: 0.8415 (p0) cc_final: 0.8091 (p0) REVERT: B 348 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8799 (pp) REVERT: B 378 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.7798 (t60) REVERT: I 53 ASN cc_start: 0.8245 (p0) cc_final: 0.7975 (p0) outliers start: 59 outliers final: 45 residues processed: 175 average time/residue: 0.2040 time to fit residues: 50.2837 Evaluate side-chains 176 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 134 CYS Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 0.0050 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111472 restraints weight = 15772.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110797 restraints weight = 14640.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111447 restraints weight = 14285.407| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.182 Angle : 0.587 7.696 12094 Z= 0.295 Chirality : 0.044 0.405 1397 Planarity : 0.004 0.053 1541 Dihedral : 4.147 21.812 1241 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.23 % Favored : 87.34 % Rotamer: Outliers : 6.50 % Allowed : 29.44 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.54 (0.26), residues: 1153 helix: 1.00 (0.34), residues: 244 sheet: -1.04 (0.31), residues: 311 loop : -1.91 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 284 HIS 0.007 0.001 HIS A 293 PHE 0.028 0.001 PHE B 186 TYR 0.018 0.001 TYR B 180 ARG 0.005 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 134 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8203 (ptm160) REVERT: B 206 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7785 (pp) REVERT: B 207 ASP cc_start: 0.8423 (p0) cc_final: 0.8119 (p0) REVERT: B 348 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8756 (pp) REVERT: B 378 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.7764 (t60) REVERT: I 53 ASN cc_start: 0.8320 (p0) cc_final: 0.8046 (p0) outliers start: 59 outliers final: 48 residues processed: 179 average time/residue: 0.1964 time to fit residues: 49.5843 Evaluate side-chains 176 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 72.6546 > 50: distance: 24 - 49: 32.231 distance: 27 - 46: 33.802 distance: 42 - 46: 35.123 distance: 46 - 47: 55.809 distance: 47 - 48: 40.613 distance: 47 - 50: 57.091 distance: 48 - 54: 40.087 distance: 50 - 51: 56.296 distance: 54 - 55: 41.378 distance: 55 - 56: 41.958 distance: 56 - 57: 15.593 distance: 56 - 61: 46.525 distance: 57 - 86: 39.215 distance: 58 - 59: 56.654 distance: 58 - 60: 40.191 distance: 61 - 67: 39.160 distance: 62 - 63: 56.678 distance: 62 - 65: 41.505 distance: 63 - 64: 55.905 distance: 63 - 68: 40.708 distance: 64 - 100: 55.852 distance: 65 - 66: 39.754 distance: 66 - 67: 39.174 distance: 69 - 70: 41.506 distance: 69 - 72: 41.151 distance: 70 - 71: 55.430 distance: 70 - 77: 40.296 distance: 71 - 109: 34.041 distance: 73 - 74: 39.563 distance: 74 - 75: 56.389 distance: 74 - 76: 69.467 distance: 77 - 78: 40.807 distance: 78 - 79: 39.470 distance: 78 - 81: 70.237 distance: 79 - 86: 56.565 distance: 81 - 82: 39.334 distance: 82 - 83: 55.781 distance: 83 - 85: 40.408 distance: 87 - 88: 39.671 distance: 87 - 90: 56.284 distance: 88 - 89: 55.897 distance: 88 - 100: 56.206 distance: 90 - 91: 23.759 distance: 91 - 92: 37.282 distance: 91 - 93: 54.587 distance: 92 - 94: 39.309 distance: 93 - 95: 60.855 distance: 94 - 95: 18.530 distance: 95 - 97: 18.659 distance: 96 - 98: 39.353 distance: 98 - 99: 56.433 distance: 100 - 101: 26.700 distance: 101 - 102: 42.743 distance: 101 - 104: 28.498 distance: 102 - 109: 66.116 distance: 104 - 105: 39.047 distance: 105 - 106: 56.818 distance: 106 - 107: 56.184 distance: 109 - 110: 6.069 distance: 110 - 111: 56.312 distance: 110 - 113: 55.229 distance: 111 - 112: 40.601 distance: 111 - 115: 55.521 distance: 115 - 116: 57.004 distance: 116 - 117: 55.199 distance: 116 - 119: 57.247 distance: 117 - 118: 40.533 distance: 117 - 125: 41.114 distance: 119 - 120: 39.788 distance: 120 - 121: 56.038 distance: 120 - 122: 56.717 distance: 126 - 127: 56.483 distance: 126 - 129: 40.492 distance: 127 - 128: 39.190 distance: 127 - 136: 34.993 distance: 129 - 130: 41.010 distance: 130 - 131: 62.958 distance: 131 - 132: 12.360 distance: 133 - 134: 40.101 distance: 133 - 135: 56.347