Starting phenix.real_space_refine on Thu Mar 13 20:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d77_30603/03_2025/7d77_30603.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d77_30603/03_2025/7d77_30603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2025/7d77_30603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2025/7d77_30603.map" model { file = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2025/7d77_30603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2025/7d77_30603.cif" } resolution = 2.9 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= 0.014 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 56 5.16 5 C 5645 2.51 5 N 1466 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8785 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2097 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 4, 'TRANS': 260} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 154 Unusual residues: {'CLR': 2, 'HCY': 1, 'PLM': 2, 'Y01': 1} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 5.70, per 1000 atoms: 0.65 Number of scatterers: 8785 At special positions: 0 Unit cell: (105.456, 126.75, 112.554, 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 56 16.00 O 1618 8.00 N 1466 7.00 C 5645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 338 " - pdb=" SG CYS R 420 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 15 sheets defined 33.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.950A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.622A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.908A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.765A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'R' and resid 264 through 297 removed outlier: 4.068A pdb=" N PHE R 282 " --> pdb=" O VAL R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 303 removed outlier: 3.850A pdb=" N GLU R 303 " --> pdb=" O PHE R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 329 Processing helix chain 'R' and resid 334 through 368 removed outlier: 3.816A pdb=" N CYS R 338 " --> pdb=" O SER R 334 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA R 340 " --> pdb=" O ALA R 336 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA R 360 " --> pdb=" O MET R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 400 Proline residue: R 390 - end of helix removed outlier: 3.723A pdb=" N ALA R 400 " --> pdb=" O GLY R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 428 through 435 removed outlier: 4.323A pdb=" N TYR R 432 " --> pdb=" O MET R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 461 Processing helix chain 'R' and resid 471 through 495 removed outlier: 3.673A pdb=" N LYS R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 477 " --> pdb=" O ARG R 473 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 525 removed outlier: 3.549A pdb=" N PHE R 506 " --> pdb=" O THR R 502 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE R 517 " --> pdb=" O GLN R 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.503A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.503A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.449A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.521A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.884A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.835A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.709A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.801A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.451A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 403 through 409 removed outlier: 3.577A pdb=" N LEU R 417 " --> pdb=" O ILE R 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.627A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.440A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147 405 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1407 1.32 - 1.45: 2518 1.45 - 1.58: 4964 1.58 - 1.70: 8 1.70 - 1.83: 80 Bond restraints: 8977 Sorted by residual: bond pdb=" CAS Y01 R 601 " pdb=" CAU Y01 R 601 " ideal model delta sigma weight residual 1.530 1.304 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 1.550 1.375 0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" CAS Y01 R 601 " pdb=" CBF Y01 R 601 " ideal model delta sigma weight residual 1.533 1.363 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" CBF Y01 R 601 " pdb=" CBH Y01 R 601 " ideal model delta sigma weight residual 1.550 1.689 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CAP Y01 R 601 " pdb=" CAQ Y01 R 601 " ideal model delta sigma weight residual 1.541 1.654 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 8972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 11902 2.20 - 4.39: 213 4.39 - 6.59: 34 6.59 - 8.78: 10 8.78 - 10.98: 4 Bond angle restraints: 12163 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 132.52 -10.98 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N ARG R 411 " pdb=" CA ARG R 411 " pdb=" C ARG R 411 " ideal model delta sigma weight residual 112.54 105.87 6.67 1.22e+00 6.72e-01 2.99e+01 angle pdb=" CBD Y01 R 601 " pdb=" CBG Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 115.11 105.59 9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N ASN A 295 " pdb=" CA ASN A 295 " pdb=" C ASN A 295 " ideal model delta sigma weight residual 108.52 113.97 -5.45 1.74e+00 3.30e-01 9.82e+00 angle pdb=" CBB Y01 R 601 " pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 119.27 110.15 9.12 3.00e+00 1.11e-01 9.24e+00 ... (remaining 12158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 5114 21.33 - 42.66: 323 42.66 - 63.99: 32 63.99 - 85.32: 10 85.32 - 106.65: 2 Dihedral angle restraints: 5481 sinusoidal: 2302 harmonic: 3179 Sorted by residual: dihedral pdb=" CB CYS R 338 " pdb=" SG CYS R 338 " pdb=" SG CYS R 420 " pdb=" CB CYS R 420 " ideal model delta sinusoidal sigma weight residual -86.00 -33.18 -52.82 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA GLN A 52 " pdb=" C GLN A 52 " pdb=" N MET A 53 " pdb=" CA MET A 53 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR A 188 " pdb=" C THR A 188 " pdb=" N HIS A 189 " pdb=" CA HIS A 189 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1314 0.109 - 0.217: 53 0.217 - 0.326: 7 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CBG Y01 R 601 " pdb=" CAQ Y01 R 601 " pdb=" CBD Y01 R 601 " pdb=" CBI Y01 R 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1374 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HCY R 604 " -0.022 2.00e-02 2.50e+03 7.73e-02 7.46e+01 pdb=" C3 HCY R 604 " 0.095 2.00e-02 2.50e+03 pdb=" C4 HCY R 604 " -0.121 2.00e-02 2.50e+03 pdb=" C5 HCY R 604 " -0.023 2.00e-02 2.50e+03 pdb=" C6 HCY R 604 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 235 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C PHE B 235 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE B 235 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO B 236 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 410 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASP R 410 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP R 410 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 411 " 0.012 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 154 2.67 - 3.22: 8050 3.22 - 3.78: 12843 3.78 - 4.34: 18190 4.34 - 4.90: 31345 Nonbonded interactions: 70582 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.107 3.040 nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 228 " model vdw 2.132 3.120 nonbonded pdb=" O THR R 397 " pdb=" OG SER R 402 " model vdw 2.135 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.136 3.040 nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.157 3.040 ... (remaining 70577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.170 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.008 0.226 8977 Z= 0.560 Angle : 0.778 10.977 12163 Z= 0.404 Chirality : 0.056 0.543 1377 Planarity : 0.004 0.077 1511 Dihedral : 13.717 106.650 3435 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.58 (0.22), residues: 1091 helix: -0.32 (0.25), residues: 352 sheet: -1.90 (0.28), residues: 274 loop : -2.64 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 339 HIS 0.008 0.001 HIS R 309 PHE 0.016 0.002 PHE A 190 TYR 0.015 0.002 TYR S 178 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7774 (ttp80) REVERT: B 124 TYR cc_start: 0.8912 (m-80) cc_final: 0.8592 (m-80) REVERT: B 130 GLU cc_start: 0.7681 (mp0) cc_final: 0.7465 (mp0) REVERT: B 138 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 153 ASP cc_start: 0.7626 (m-30) cc_final: 0.7394 (m-30) REVERT: R 447 MET cc_start: 0.6609 (mmt) cc_final: 0.6388 (mpt) REVERT: S 168 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7522 (mtt90) REVERT: S 174 GLN cc_start: 0.8810 (pt0) cc_final: 0.8591 (pt0) REVERT: S 194 SER cc_start: 0.8264 (t) cc_final: 0.8025 (p) outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 1.3624 time to fit residues: 201.8454 Evaluate side-chains 97 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN R 362 HIS S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.165700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115855 restraints weight = 9661.296| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.72 r_work: 0.3114 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8977 Z= 0.170 Angle : 0.539 7.862 12163 Z= 0.280 Chirality : 0.042 0.151 1377 Planarity : 0.003 0.038 1511 Dihedral : 7.326 58.919 1508 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.72 % Allowed : 11.17 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.09 (0.24), residues: 1091 helix: 1.46 (0.28), residues: 355 sheet: -1.38 (0.28), residues: 269 loop : -2.05 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 169 HIS 0.005 0.001 HIS R 309 PHE 0.023 0.001 PHE R 285 TYR 0.020 0.001 TYR B 105 ARG 0.004 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.976 Fit side-chains REVERT: A 43 ASN cc_start: 0.7570 (t0) cc_final: 0.7199 (t0) REVERT: A 248 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.7011 (tt) REVERT: A 341 ASP cc_start: 0.8138 (t70) cc_final: 0.7896 (t0) REVERT: B 19 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7776 (ttp80) REVERT: B 138 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8572 (mt-10) REVERT: B 153 ASP cc_start: 0.7603 (m-30) cc_final: 0.7401 (m-30) REVERT: B 155 ASN cc_start: 0.7995 (t0) cc_final: 0.7707 (t0) REVERT: B 175 GLN cc_start: 0.8265 (mm110) cc_final: 0.7802 (mm110) REVERT: B 197 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7993 (ttm110) REVERT: B 214 ARG cc_start: 0.7677 (mpt90) cc_final: 0.7420 (mpt90) REVERT: R 459 THR cc_start: 0.8104 (t) cc_final: 0.7821 (p) REVERT: S 194 SER cc_start: 0.7960 (t) cc_final: 0.7753 (p) outliers start: 16 outliers final: 7 residues processed: 134 average time/residue: 1.2136 time to fit residues: 173.8254 Evaluate side-chains 116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain S residue 82 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113068 restraints weight = 9861.078| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.72 r_work: 0.3077 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8977 Z= 0.296 Angle : 0.568 7.270 12163 Z= 0.294 Chirality : 0.043 0.150 1377 Planarity : 0.003 0.038 1511 Dihedral : 7.345 59.396 1508 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.15 % Allowed : 13.96 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1091 helix: 1.81 (0.28), residues: 355 sheet: -1.15 (0.28), residues: 276 loop : -1.83 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS R 309 PHE 0.021 0.001 PHE R 292 TYR 0.021 0.001 TYR B 105 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.010 Fit side-chains REVERT: A 43 ASN cc_start: 0.7557 (t0) cc_final: 0.7227 (t0) REVERT: A 341 ASP cc_start: 0.8218 (t70) cc_final: 0.7970 (t0) REVERT: B 138 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8574 (mt-10) REVERT: B 155 ASN cc_start: 0.8121 (t0) cc_final: 0.7831 (t0) REVERT: B 175 GLN cc_start: 0.8335 (mm110) cc_final: 0.8077 (mm110) REVERT: R 447 MET cc_start: 0.7014 (mmt) cc_final: 0.6785 (mpt) REVERT: S 194 SER cc_start: 0.8049 (t) cc_final: 0.7847 (p) outliers start: 20 outliers final: 12 residues processed: 125 average time/residue: 1.2606 time to fit residues: 168.0600 Evaluate side-chains 115 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain S residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114417 restraints weight = 9696.124| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.71 r_work: 0.3096 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8977 Z= 0.222 Angle : 0.536 7.917 12163 Z= 0.279 Chirality : 0.042 0.198 1377 Planarity : 0.003 0.037 1511 Dihedral : 7.120 59.793 1508 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.36 % Allowed : 14.72 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.42 (0.25), residues: 1091 helix: 2.02 (0.28), residues: 358 sheet: -0.95 (0.28), residues: 276 loop : -1.74 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 309 PHE 0.024 0.001 PHE R 285 TYR 0.016 0.001 TYR B 105 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.752 Fit side-chains REVERT: A 43 ASN cc_start: 0.7534 (t0) cc_final: 0.7177 (t0) REVERT: A 341 ASP cc_start: 0.8214 (t70) cc_final: 0.7957 (t0) REVERT: B 138 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8512 (mt-10) REVERT: B 155 ASN cc_start: 0.8107 (t0) cc_final: 0.7801 (t0) REVERT: B 175 GLN cc_start: 0.8358 (mm110) cc_final: 0.7956 (mm110) REVERT: B 197 ARG cc_start: 0.8221 (ttm110) cc_final: 0.8018 (ttm110) REVERT: B 214 ARG cc_start: 0.7463 (mpt90) cc_final: 0.7151 (mpt90) REVERT: B 217 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6818 (ptt) REVERT: S 211 ASP cc_start: 0.8418 (m-30) cc_final: 0.7803 (m-30) outliers start: 22 outliers final: 14 residues processed: 123 average time/residue: 1.1710 time to fit residues: 154.5388 Evaluate side-chains 119 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.32 > 50: distance: 12 - 14: 7.932 distance: 14 - 15: 9.384 distance: 15 - 16: 20.257 distance: 15 - 18: 8.123 distance: 16 - 17: 6.251 distance: 16 - 22: 20.500 distance: 18 - 19: 7.935 distance: 19 - 20: 6.886 distance: 19 - 21: 14.619 distance: 22 - 23: 10.356 distance: 23 - 24: 17.382 distance: 23 - 26: 8.543 distance: 24 - 25: 14.461 distance: 24 - 29: 11.879 distance: 26 - 27: 13.532 distance: 26 - 28: 16.394 distance: 29 - 30: 13.541 distance: 30 - 31: 16.539 distance: 30 - 33: 24.646 distance: 31 - 32: 37.456 distance: 31 - 38: 23.784 distance: 33 - 34: 8.084 distance: 34 - 35: 14.705 distance: 35 - 36: 23.928 distance: 35 - 37: 15.531 distance: 38 - 39: 12.893 distance: 38 - 44: 11.635 distance: 39 - 40: 30.373 distance: 39 - 42: 16.560 distance: 40 - 41: 31.481 distance: 40 - 45: 50.320 distance: 43 - 44: 14.024 distance: 45 - 46: 18.915 distance: 46 - 47: 5.846 distance: 47 - 48: 9.438 distance: 47 - 49: 6.719 distance: 49 - 50: 9.883 distance: 50 - 51: 18.469 distance: 51 - 52: 4.474 distance: 51 - 53: 16.536 distance: 53 - 54: 5.651 distance: 54 - 55: 15.612 distance: 54 - 57: 17.262 distance: 55 - 56: 19.410 distance: 55 - 59: 9.819 distance: 57 - 58: 17.049 distance: 59 - 60: 10.823 distance: 59 - 126: 6.467 distance: 60 - 61: 8.944 distance: 60 - 63: 6.610 distance: 61 - 62: 15.126 distance: 61 - 70: 16.692 distance: 63 - 64: 7.467 distance: 64 - 65: 7.789 distance: 65 - 66: 3.251 distance: 67 - 68: 5.112 distance: 67 - 69: 5.167 distance: 70 - 71: 15.142 distance: 71 - 72: 30.980 distance: 71 - 74: 20.893 distance: 72 - 73: 13.865 distance: 72 - 79: 27.367 distance: 74 - 75: 11.019 distance: 75 - 76: 22.801 distance: 76 - 77: 9.621 distance: 77 - 78: 24.126 distance: 79 - 80: 12.808 distance: 79 - 112: 10.115 distance: 80 - 81: 15.924 distance: 80 - 83: 10.761 distance: 81 - 82: 11.262 distance: 81 - 87: 9.403 distance: 82 - 109: 7.792 distance: 83 - 84: 3.769 distance: 84 - 85: 13.184 distance: 84 - 86: 6.648