Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:56:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/12_2022/8efo_28086_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/12_2022/8efo_28086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/12_2022/8efo_28086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/12_2022/8efo_28086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/12_2022/8efo_28086_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efo_28086/12_2022/8efo_28086_updated_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "R ARG 181": "NH1" <-> "NH2" Residue "R ARG 184": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 278": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Residue "M ARG 350": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 11708 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} 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: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 156 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 193 Unusual residues: {'8QY': 1, 'CLR': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 137 Unusual residues: {'8QY': 1, 'CLR': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.88, per 1000 atoms: 0.59 Number of scatterers: 11708 At special positions: 0 Unit cell: (104, 110.24, 149.76, 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 2090 8.00 N 1900 7.00 C 7618 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=2.03 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: 4.58 Conformation dependent library (CDL) restraints added in 1.9 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 17 sheets defined 45.0% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.503A pdb=" N VAL R 96 " --> pdb=" O MET R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 132 removed outlier: 3.613A pdb=" N TYR R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 139 through 172 removed outlier: 3.509A pdb=" N ILE R 144 " --> pdb=" O ILE R 140 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.514A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 4.166A 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 242 Processing helix chain 'R' and resid 244 through 263 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: 3.574A pdb=" N HIS R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 4.172A 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 removed outlier: 3.528A pdb=" N CYS R 348 " --> pdb=" O ASN R 344 " (cutoff:3.500A) 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 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.663A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (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 removed outlier: 3.576A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.713A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.663A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.608A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 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 68 through 97 removed outlier: 3.503A pdb=" N VAL M 96 " --> pdb=" O MET M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 132 removed outlier: 3.613A pdb=" N TYR M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.510A pdb=" N ILE M 144 " --> pdb=" O ILE M 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.513A pdb=" N LEU M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 4.166A 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 242 Processing helix chain 'M' and resid 244 through 263 Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 338 removed outlier: 3.573A pdb=" N HIS M 321 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 4.172A 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 removed outlier: 3.528A pdb=" N CYS M 348 " --> pdb=" O ASN M 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 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 324 removed outlier: 6.832A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.861A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.565A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.217A 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: 6.768A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.752A 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: 7.050A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.502A 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: 6.701A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.453A 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: 6.628A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.664A 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: 6.703A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.629A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.535A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER E 120 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 92 through 99 removed outlier: 5.658A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.335A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 156 through 158 Processing sheet with id= P, first strand: chain 'E' and resid 227 through 232 removed outlier: 3.501A pdb=" N ILE E 190 " --> pdb=" O TRP E 177 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 208 through 213 601 hydrogen bonds defined for protein. 1755 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: 3.72 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2738 1.33 - 1.46: 2741 1.46 - 1.58: 6358 1.58 - 1.70: 0 1.70 - 1.83: 149 Bond restraints: 11986 Sorted by residual: bond pdb=" C19 8QY M 401 " pdb=" O20 8QY M 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" C19 8QY R 401 " pdb=" O20 8QY R 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C02 8QY M 401 " pdb=" N12 8QY M 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C02 8QY R 401 " pdb=" N12 8QY R 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.94e+00 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 91.75 - 100.20: 10 100.20 - 108.66: 734 108.66 - 117.11: 7944 117.11 - 125.57: 7433 125.57 - 134.02: 189 Bond angle restraints: 16310 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 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ASP A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 120.63 126.54 -5.91 1.61e+00 3.86e-01 1.35e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 128.08 -4.61 1.53e+00 4.27e-01 9.08e+00 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 110.23 114.59 -4.36 1.45e+00 4.76e-01 9.03e+00 ... (remaining 16305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.83: 6297 9.83 - 19.65: 581 19.65 - 29.48: 74 29.48 - 39.31: 37 39.31 - 49.14: 8 Dihedral angle restraints: 6997 sinusoidal: 2784 harmonic: 4213 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 57.75 35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS R 142 " pdb=" SG CYS R 142 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual 93.00 124.29 -31.29 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 6994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1695 0.086 - 0.172: 169 0.172 - 0.259: 24 0.259 - 0.345: 10 0.345 - 0.431: 10 Chirality restraints: 1908 Sorted by residual: chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.64e+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 -2.75 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1905 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " -0.008 2.00e-02 2.50e+03 1.37e-02 4.71e+00 pdb=" CG TRP E 111 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 232 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ILE B 232 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 232 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 233 " 0.011 2.00e-02 2.50e+03 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1746 2.77 - 3.30: 11049 3.30 - 3.84: 19733 3.84 - 4.37: 23239 4.37 - 4.90: 40066 Nonbonded interactions: 95833 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.241 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.323 2.440 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.331 2.440 nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.331 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.336 2.440 ... (remaining 95828 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' and (resid 66 through 352 or resid 401 through 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 7618 2.51 5 N 1900 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.900 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 33.500 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 0.052 11986 Z= 0.284 Angle : 0.852 9.597 16310 Z= 0.452 Chirality : 0.065 0.431 1908 Planarity : 0.005 0.053 1965 Dihedral : 8.023 49.136 4264 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.93 (0.19), residues: 1423 helix: -0.48 (0.16), residues: 629 sheet: 0.09 (0.30), residues: 263 loop : -0.95 (0.23), residues: 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 371 average time/residue: 1.0574 time to fit residues: 427.6257 Evaluate side-chains 218 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1446 time to fit residues: 2.0956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN A 22 ASN A 188 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 91 HIS B 220 GLN B 259 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN M 126 GLN M 173 HIS ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 11986 Z= 0.265 Angle : 0.586 8.733 16310 Z= 0.307 Chirality : 0.042 0.189 1908 Planarity : 0.004 0.038 1965 Dihedral : 5.725 59.188 1663 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.74 (0.20), residues: 1423 helix: 1.55 (0.18), residues: 649 sheet: 0.23 (0.29), residues: 272 loop : -0.70 (0.25), residues: 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 250 average time/residue: 1.1585 time to fit residues: 314.8504 Evaluate side-chains 193 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 2 average time/residue: 0.1226 time to fit residues: 2.2543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 106 optimal weight: 0.0970 chunk 87 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN M 193 ASN M 225 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 11986 Z= 0.152 Angle : 0.494 9.016 16310 Z= 0.258 Chirality : 0.039 0.148 1908 Planarity : 0.003 0.035 1965 Dihedral : 5.208 53.123 1663 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.27 (0.21), residues: 1423 helix: 2.09 (0.19), residues: 651 sheet: 0.18 (0.30), residues: 279 loop : -0.39 (0.26), residues: 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 225 average time/residue: 1.1482 time to fit residues: 281.2304 Evaluate side-chains 197 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.3544 time to fit residues: 3.4915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 187 GLN M 111 ASN M 126 GLN M 193 ASN M 225 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 11986 Z= 0.357 Angle : 0.615 9.309 16310 Z= 0.317 Chirality : 0.043 0.176 1908 Planarity : 0.004 0.047 1965 Dihedral : 6.061 59.164 1663 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.20 (0.21), residues: 1423 helix: 1.98 (0.19), residues: 652 sheet: 0.20 (0.30), residues: 275 loop : -0.38 (0.27), residues: 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 201 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 26 residues processed: 235 average time/residue: 1.1655 time to fit residues: 298.6246 Evaluate side-chains 207 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 8 average time/residue: 0.2804 time to fit residues: 4.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 0.0050 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11986 Z= 0.182 Angle : 0.507 7.892 16310 Z= 0.263 Chirality : 0.039 0.151 1908 Planarity : 0.003 0.036 1965 Dihedral : 5.484 53.173 1663 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.42 (0.22), residues: 1423 helix: 2.22 (0.19), residues: 652 sheet: 0.25 (0.30), residues: 273 loop : -0.33 (0.27), residues: 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.145 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 216 average time/residue: 1.0438 time to fit residues: 246.1183 Evaluate side-chains 203 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.3677 time to fit residues: 3.7294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN M 225 HIS M 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 11986 Z= 0.419 Angle : 0.649 10.268 16310 Z= 0.331 Chirality : 0.044 0.204 1908 Planarity : 0.005 0.045 1965 Dihedral : 6.575 60.493 1663 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 4.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.03 (0.21), residues: 1423 helix: 1.81 (0.19), residues: 662 sheet: 0.02 (0.31), residues: 262 loop : -0.40 (0.27), residues: 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 196 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 34 residues processed: 234 average time/residue: 1.1014 time to fit residues: 280.8724 Evaluate side-chains 213 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 7 average time/residue: 0.4775 time to fit residues: 5.8591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 0.0060 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 156 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11986 Z= 0.185 Angle : 0.535 9.421 16310 Z= 0.273 Chirality : 0.039 0.152 1908 Planarity : 0.004 0.037 1965 Dihedral : 5.768 57.868 1663 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.30 (0.22), residues: 1423 helix: 2.12 (0.19), residues: 660 sheet: 0.10 (0.31), residues: 259 loop : -0.36 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 1.549 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 32 residues processed: 235 average time/residue: 1.1003 time to fit residues: 282.2175 Evaluate side-chains 215 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 7 average time/residue: 0.6854 time to fit residues: 7.3677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11986 Z= 0.222 Angle : 0.557 10.248 16310 Z= 0.283 Chirality : 0.040 0.151 1908 Planarity : 0.004 0.063 1965 Dihedral : 5.740 57.423 1663 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.33 (0.22), residues: 1423 helix: 2.26 (0.19), residues: 654 sheet: -0.05 (0.30), residues: 268 loop : -0.40 (0.27), residues: 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 1.360 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 34 residues processed: 219 average time/residue: 1.1593 time to fit residues: 277.8250 Evaluate side-chains 213 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 28 residues processed: 6 average time/residue: 0.7184 time to fit residues: 6.7074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11986 Z= 0.213 Angle : 0.543 10.981 16310 Z= 0.280 Chirality : 0.040 0.145 1908 Planarity : 0.004 0.048 1965 Dihedral : 5.665 57.499 1663 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.34 (0.22), residues: 1423 helix: 2.27 (0.19), residues: 654 sheet: -0.06 (0.30), residues: 268 loop : -0.37 (0.27), residues: 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.356 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 32 residues processed: 214 average time/residue: 1.0902 time to fit residues: 255.7057 Evaluate side-chains 205 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 5 average time/residue: 0.6056 time to fit residues: 5.4088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 140 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 ASN ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11986 Z= 0.209 Angle : 0.547 9.543 16310 Z= 0.280 Chirality : 0.040 0.149 1908 Planarity : 0.004 0.066 1965 Dihedral : 5.606 57.227 1663 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.34 (0.22), residues: 1423 helix: 2.27 (0.19), residues: 654 sheet: -0.15 (0.30), residues: 274 loop : -0.32 (0.27), residues: 495 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 1.530 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 29 residues processed: 207 average time/residue: 1.1224 time to fit residues: 253.7978 Evaluate side-chains 202 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.4737 time to fit residues: 3.6183 ------------------------------------------------------------------------------- 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-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-dev-4807/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-dev-4807/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: 52.7783 > 50: distance: 20 - 24: 16.095 distance: 24 - 25: 15.943 distance: 25 - 26: 11.641 distance: 25 - 28: 5.180 distance: 26 - 27: 16.039 distance: 26 - 34: 18.107 distance: 28 - 29: 14.527 distance: 29 - 30: 13.715 distance: 29 - 31: 9.815 distance: 30 - 32: 7.113 distance: 31 - 33: 9.444 distance: 32 - 33: 9.464 distance: 34 - 35: 45.631 distance: 34 - 40: 30.230 distance: 35 - 36: 27.624 distance: 35 - 38: 31.900 distance: 36 - 37: 21.274 distance: 36 - 41: 40.087 distance: 38 - 39: 14.215 distance: 39 - 40: 10.278 distance: 41 - 42: 40.165 distance: 42 - 43: 11.396 distance: 42 - 45: 24.722 distance: 43 - 44: 12.977 distance: 43 - 48: 4.556 distance: 44 - 88: 4.193 distance: 45 - 46: 39.228 distance: 45 - 47: 24.983 distance: 48 - 49: 5.724 distance: 49 - 50: 12.220 distance: 49 - 52: 5.443 distance: 50 - 51: 5.108 distance: 50 - 62: 7.001 distance: 51 - 97: 9.844 distance: 52 - 53: 7.948 distance: 53 - 54: 10.871 distance: 53 - 55: 7.531 distance: 54 - 56: 11.766 distance: 55 - 57: 14.961 distance: 55 - 58: 8.267 distance: 56 - 57: 11.538 distance: 57 - 59: 10.871 distance: 58 - 60: 4.847 distance: 59 - 61: 4.256 distance: 60 - 61: 8.033 distance: 62 - 63: 3.297 distance: 63 - 64: 8.201 distance: 63 - 66: 7.050 distance: 64 - 65: 5.543 distance: 64 - 74: 7.363 distance: 65 - 105: 20.536 distance: 66 - 67: 6.954 distance: 67 - 68: 5.058 distance: 68 - 70: 13.582 distance: 69 - 71: 8.922 distance: 70 - 72: 18.647 distance: 71 - 72: 17.032 distance: 72 - 73: 18.238 distance: 74 - 75: 8.009 distance: 75 - 76: 4.715 distance: 75 - 78: 10.983 distance: 76 - 77: 14.321 distance: 76 - 88: 9.801 distance: 77 - 113: 17.912 distance: 78 - 79: 8.396 distance: 79 - 80: 4.482 distance: 80 - 82: 16.831 distance: 81 - 83: 11.854 distance: 81 - 84: 13.732 distance: 82 - 83: 22.788 distance: 83 - 85: 17.837 distance: 84 - 86: 8.190 distance: 85 - 87: 13.069 distance: 86 - 87: 7.394 distance: 88 - 89: 16.179 distance: 89 - 90: 6.415 distance: 89 - 92: 7.509 distance: 90 - 91: 18.097 distance: 90 - 97: 12.151 distance: 91 - 121: 9.646 distance: 92 - 93: 7.631 distance: 93 - 94: 9.155 distance: 94 - 95: 7.770 distance: 94 - 96: 7.360 distance: 97 - 98: 11.463 distance: 98 - 99: 5.481 distance: 98 - 101: 15.495 distance: 99 - 100: 13.504 distance: 99 - 105: 22.032 distance: 100 - 130: 15.505 distance: 101 - 102: 15.046 distance: 102 - 103: 16.578 distance: 102 - 104: 10.389 distance: 105 - 106: 25.392 distance: 106 - 107: 24.648 distance: 106 - 109: 13.077 distance: 107 - 108: 9.516 distance: 107 - 113: 20.237 distance: 108 - 138: 4.865 distance: 109 - 110: 20.096 distance: 110 - 111: 11.657 distance: 110 - 112: 11.746 distance: 113 - 114: 11.081 distance: 114 - 115: 10.324 distance: 114 - 117: 12.180 distance: 115 - 116: 10.143 distance: 115 - 121: 9.375 distance: 116 - 144: 6.426 distance: 117 - 118: 26.804 distance: 118 - 119: 8.468 distance: 118 - 120: 20.593