Starting phenix.real_space_refine on Sat Dec 9 18:53:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/12_2023/8f7q_28907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/12_2023/8f7q_28907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/12_2023/8f7q_28907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/12_2023/8f7q_28907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/12_2023/8f7q_28907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/12_2023/8f7q_28907_updated.pdb" } resolution = 3.22 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= 0.009 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 100 5.16 5 C 7797 2.51 5 N 1949 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 184": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 282": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Residue "M ARG 350": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11994 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "M" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.37, per 1000 atoms: 0.53 Number of scatterers: 11994 At special positions: 0 Unit cell: (111.384, 112.455, 152.082, 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 100 16.00 O 2148 8.00 N 1949 7.00 C 7797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.72 Conformation dependent library (CDL) restraints added in 2.3 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 15 sheets defined 45.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'R' and resid 67 through 97 Processing helix chain 'R' and resid 104 through 121 Processing helix chain 'R' and resid 123 through 132 Processing helix chain 'R' and resid 139 through 172 Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.597A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 4.080A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 227 through 263 removed outlier: 5.177A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 271 through 307 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 314 through 338 removed outlier: 3.858A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 343 through 351 Processing helix chain 'P' and resid 13 through 20 Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.650A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.531A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'M' and resid 67 through 97 Processing helix chain 'M' and resid 104 through 132 removed outlier: 3.909A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Proline residue: M 124 - end of helix Processing helix chain 'M' and resid 139 through 172 removed outlier: 3.619A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.795A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 3.811A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 227 through 263 removed outlier: 5.087A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix removed outlier: 3.652A pdb=" N SER M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 339 removed outlier: 3.874A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 343 through 351 Processing helix chain 'Q' and resid 13 through 20 Processing helix chain 'F' and resid 337 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 208 through 213 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.891A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.758A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.611A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.722A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.100A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.833A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.841A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.776A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.621A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.924A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 156 through 160 Processing sheet with id= N, first strand: chain 'E' and resid 226 through 232 removed outlier: 5.919A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG E 181 " --> pdb=" O PRO E 186 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 208 through 213 637 hydrogen bonds defined for protein. 1860 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: 3.42 Time building geometry restraints manager: 6.00 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: 3659 1.34 - 1.46: 2776 1.46 - 1.58: 5694 1.58 - 1.70: 0 1.70 - 1.82: 149 Bond restraints: 12278 Sorted by residual: bond pdb=" C ASN R 334 " pdb=" N PRO R 335 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" C LEU M 202 " pdb=" N PRO M 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.50e+00 bond pdb=" C LEU R 202 " pdb=" N PRO R 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.36e-02 5.41e+03 3.85e+00 bond pdb=" C LEU R 123 " pdb=" N PRO R 124 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.49e+00 bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.33e+00 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.42: 334 106.42 - 113.33: 6878 113.33 - 120.25: 4319 120.25 - 127.16: 5039 127.16 - 134.08: 133 Bond angle restraints: 16703 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.02 131.81 -6.79 1.76e+00 3.23e-01 1.49e+01 angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 117.47 -7.66 2.21e+00 2.05e-01 1.20e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 124.82 130.67 -5.85 1.78e+00 3.16e-01 1.08e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 125.66 131.62 -5.96 1.85e+00 2.92e-01 1.04e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 124.82 130.46 -5.64 1.78e+00 3.16e-01 1.00e+01 ... (remaining 16698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 7365 14.13 - 28.27: 321 28.27 - 42.40: 55 42.40 - 56.53: 4 56.53 - 70.67: 3 Dihedral angle restraints: 7748 sinusoidal: 3414 harmonic: 4334 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.92 21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1709 0.082 - 0.165: 192 0.165 - 0.247: 31 0.247 - 0.330: 10 0.330 - 0.412: 11 Chirality restraints: 1953 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 1950 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL M 336 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C VAL M 336 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL M 336 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU M 337 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 236 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 219 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ARG E 219 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG E 219 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 220 " 0.011 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2283 2.79 - 3.32: 10970 3.32 - 3.84: 19468 3.84 - 4.37: 21844 4.37 - 4.90: 39479 Nonbonded interactions: 94044 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.262 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.276 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.314 2.440 nonbonded pdb=" O ILE M 292 " pdb=" OG1 THR M 296 " model vdw 2.360 2.440 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 219 " model vdw 2.360 2.440 ... (remaining 94039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 3.830 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: 3.750 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 35.030 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.004 0.063 12278 Z= 0.283 Angle : 0.868 9.050 16703 Z= 0.475 Chirality : 0.065 0.412 1953 Planarity : 0.006 0.050 2013 Dihedral : 8.264 70.668 4937 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.89 (0.20), residues: 1462 helix: 1.88 (0.17), residues: 668 sheet: 0.50 (0.30), residues: 283 loop : -1.10 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.006 0.001 HIS E 35 PHE 0.032 0.002 PHE Q 18 TYR 0.028 0.002 TYR R 301 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.402 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2855 time to fit residues: 90.1943 Evaluate side-chains 148 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 75 GLN B 88 ASN B 91 HIS B 230 ASN B 237 ASN B 266 HIS E 180 GLN E 187 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12278 Z= 0.226 Angle : 0.521 7.463 16703 Z= 0.271 Chirality : 0.040 0.157 1953 Planarity : 0.004 0.051 2013 Dihedral : 5.371 56.124 2256 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.70 % Allowed : 6.48 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.92 (0.21), residues: 1462 helix: 2.85 (0.18), residues: 687 sheet: 0.68 (0.29), residues: 290 loop : -0.72 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS E 233 PHE 0.011 0.001 PHE A 189 TYR 0.017 0.002 TYR R 301 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.397 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 171 average time/residue: 0.2414 time to fit residues: 59.3795 Evaluate side-chains 145 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1079 time to fit residues: 4.1498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 239 ASN E 82 GLN E 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12278 Z= 0.214 Angle : 0.499 6.350 16703 Z= 0.261 Chirality : 0.039 0.155 1953 Planarity : 0.004 0.045 2013 Dihedral : 5.378 54.978 2256 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.62 % Allowed : 7.41 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 2.08 (0.21), residues: 1462 helix: 3.06 (0.18), residues: 681 sheet: 0.67 (0.30), residues: 281 loop : -0.64 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS E 233 PHE 0.010 0.001 PHE P 4 TYR 0.014 0.001 TYR E 94 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.411 Fit side-chains outliers start: 21 outliers final: 6 residues processed: 154 average time/residue: 0.2684 time to fit residues: 60.8858 Evaluate side-chains 140 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1180 time to fit residues: 3.4785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 82 GLN E 187 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12278 Z= 0.177 Angle : 0.471 6.591 16703 Z= 0.244 Chirality : 0.038 0.151 1953 Planarity : 0.004 0.041 2013 Dihedral : 5.232 59.189 2256 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.08 % Allowed : 8.64 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 2.14 (0.21), residues: 1462 helix: 3.13 (0.18), residues: 681 sheet: 0.60 (0.30), residues: 282 loop : -0.56 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS E 233 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR E 94 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.361 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 150 average time/residue: 0.2503 time to fit residues: 54.8902 Evaluate side-chains 143 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1102 time to fit residues: 3.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 82 GLN E 187 GLN M 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12278 Z= 0.280 Angle : 0.535 8.312 16703 Z= 0.277 Chirality : 0.040 0.161 1953 Planarity : 0.004 0.042 2013 Dihedral : 5.679 57.641 2256 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.23 % Allowed : 9.18 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.85 (0.21), residues: 1462 helix: 2.83 (0.18), residues: 681 sheet: 0.49 (0.30), residues: 282 loop : -0.64 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS R 321 PHE 0.015 0.001 PHE E 240 TYR 0.019 0.002 TYR E 94 ARG 0.003 0.000 ARG R 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.432 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 158 average time/residue: 0.2588 time to fit residues: 59.9475 Evaluate side-chains 142 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1115 time to fit residues: 3.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 187 GLN M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12278 Z= 0.165 Angle : 0.470 7.385 16703 Z= 0.243 Chirality : 0.038 0.143 1953 Planarity : 0.003 0.037 2013 Dihedral : 5.452 58.906 2256 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.69 % Allowed : 10.57 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.96 (0.21), residues: 1462 helix: 2.92 (0.18), residues: 678 sheet: 0.50 (0.30), residues: 288 loop : -0.54 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.404 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 148 average time/residue: 0.2467 time to fit residues: 53.1986 Evaluate side-chains 145 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1209 time to fit residues: 3.6646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN M 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12278 Z= 0.246 Angle : 0.512 9.673 16703 Z= 0.263 Chirality : 0.039 0.146 1953 Planarity : 0.004 0.040 2013 Dihedral : 5.660 59.942 2256 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.46 % Allowed : 10.80 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.85 (0.21), residues: 1462 helix: 2.78 (0.18), residues: 684 sheet: 0.55 (0.30), residues: 283 loop : -0.63 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 PHE 0.014 0.001 PHE E 240 TYR 0.015 0.001 TYR E 94 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.356 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 139 average time/residue: 0.2379 time to fit residues: 48.6983 Evaluate side-chains 133 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1126 time to fit residues: 2.7898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12278 Z= 0.165 Angle : 0.467 6.949 16703 Z= 0.242 Chirality : 0.038 0.160 1953 Planarity : 0.003 0.038 2013 Dihedral : 5.387 58.954 2256 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.54 % Allowed : 10.73 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.93 (0.22), residues: 1462 helix: 2.88 (0.18), residues: 684 sheet: 0.53 (0.30), residues: 286 loop : -0.59 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR B 59 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.434 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 141 average time/residue: 0.2351 time to fit residues: 49.1216 Evaluate side-chains 131 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1082 time to fit residues: 2.7100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.0270 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12278 Z= 0.199 Angle : 0.480 6.858 16703 Z= 0.249 Chirality : 0.038 0.148 1953 Planarity : 0.004 0.039 2013 Dihedral : 5.423 58.381 2256 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.31 % Allowed : 11.27 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.91 (0.22), residues: 1462 helix: 2.88 (0.18), residues: 684 sheet: 0.57 (0.30), residues: 278 loop : -0.66 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.011 0.001 PHE B 241 TYR 0.017 0.001 TYR B 59 ARG 0.008 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.371 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 137 average time/residue: 0.2417 time to fit residues: 49.0342 Evaluate side-chains 133 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1269 time to fit residues: 2.4461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 0.0370 chunk 114 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 111 ASN M 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12278 Z= 0.134 Angle : 0.459 10.676 16703 Z= 0.235 Chirality : 0.037 0.138 1953 Planarity : 0.004 0.040 2013 Dihedral : 5.119 56.499 2256 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 2.05 (0.22), residues: 1462 helix: 3.02 (0.19), residues: 684 sheet: 0.56 (0.30), residues: 283 loop : -0.58 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS R 321 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR R 151 ARG 0.010 0.000 ARG E 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2473 time to fit residues: 49.7729 Evaluate side-chains 128 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.116 > 50: distance: 17 - 21: 15.356 distance: 21 - 22: 17.752 distance: 22 - 23: 13.027 distance: 22 - 25: 41.148 distance: 23 - 24: 41.611 distance: 25 - 26: 12.580 distance: 26 - 27: 17.079 distance: 26 - 28: 16.561 distance: 27 - 29: 15.274 distance: 28 - 30: 16.430 distance: 29 - 30: 17.889 distance: 31 - 32: 5.937 distance: 31 - 37: 32.293 distance: 32 - 33: 28.137 distance: 32 - 35: 25.228 distance: 33 - 34: 19.251 distance: 33 - 38: 9.314 distance: 35 - 36: 53.808 distance: 38 - 39: 36.081 distance: 39 - 40: 21.968 distance: 39 - 42: 17.487 distance: 40 - 41: 37.266 distance: 40 - 45: 13.268 distance: 41 - 85: 30.669 distance: 42 - 43: 34.868 distance: 42 - 44: 34.916 distance: 45 - 46: 12.297 distance: 46 - 47: 17.259 distance: 46 - 49: 13.339 distance: 47 - 48: 26.921 distance: 47 - 59: 17.459 distance: 48 - 94: 30.534 distance: 49 - 50: 16.192 distance: 50 - 51: 14.597 distance: 50 - 52: 8.367 distance: 51 - 53: 18.159 distance: 52 - 54: 14.414 distance: 52 - 55: 7.268 distance: 53 - 54: 10.087 distance: 54 - 56: 7.868 distance: 55 - 57: 6.397 distance: 56 - 58: 6.890 distance: 57 - 58: 12.629 distance: 59 - 60: 10.584 distance: 60 - 61: 5.312 distance: 60 - 63: 22.021 distance: 61 - 62: 19.174 distance: 61 - 71: 10.927 distance: 62 - 102: 25.014 distance: 63 - 64: 7.997 distance: 64 - 65: 7.576 distance: 64 - 66: 36.219 distance: 65 - 67: 4.450 distance: 66 - 68: 12.457 distance: 67 - 69: 30.042 distance: 68 - 69: 19.614 distance: 69 - 70: 10.106 distance: 72 - 73: 15.704 distance: 72 - 75: 16.225 distance: 73 - 74: 28.261 distance: 73 - 85: 3.339 distance: 74 - 110: 29.823 distance: 75 - 76: 12.457 distance: 76 - 77: 11.717 distance: 76 - 78: 18.365 distance: 77 - 79: 30.341 distance: 78 - 80: 17.974 distance: 78 - 81: 15.812 distance: 79 - 80: 8.714 distance: 80 - 82: 18.940 distance: 81 - 83: 18.378 distance: 82 - 84: 10.723 distance: 83 - 84: 9.457 distance: 85 - 86: 7.136 distance: 86 - 87: 11.358 distance: 86 - 89: 23.763 distance: 87 - 88: 10.527 distance: 87 - 94: 24.566 distance: 88 - 118: 20.392 distance: 89 - 90: 23.250 distance: 90 - 91: 19.199 distance: 91 - 92: 6.105 distance: 91 - 93: 17.896 distance: 94 - 95: 19.150 distance: 95 - 96: 5.422 distance: 95 - 98: 15.860 distance: 96 - 97: 25.352 distance: 96 - 102: 4.414 distance: 97 - 127: 15.381 distance: 98 - 99: 14.908 distance: 99 - 100: 15.419 distance: 99 - 101: 26.710 distance: 102 - 103: 5.022 distance: 103 - 104: 16.539 distance: 103 - 106: 19.643 distance: 104 - 105: 41.732 distance: 104 - 110: 20.721 distance: 105 - 135: 30.935 distance: 106 - 107: 22.598 distance: 107 - 108: 25.769 distance: 107 - 109: 26.131 distance: 110 - 111: 10.042 distance: 111 - 112: 20.923 distance: 111 - 114: 21.425 distance: 112 - 113: 19.676 distance: 112 - 118: 15.397 distance: 113 - 140: 20.913 distance: 114 - 115: 27.284 distance: 115 - 116: 16.300 distance: 115 - 117: 42.058