Starting phenix.real_space_refine on Wed Jan 15 05:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8q_37356/01_2025/8w8q_37356_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8q_37356/01_2025/8w8q_37356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8q_37356/01_2025/8w8q_37356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8q_37356/01_2025/8w8q_37356.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8q_37356/01_2025/8w8q_37356_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8q_37356/01_2025/8w8q_37356_neut.cif" } resolution = 2.89 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= 0.001 sd= 0.005 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 49 5.16 5 C 5209 2.51 5 N 1417 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8168 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2283 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2579 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.95, per 1000 atoms: 0.61 Number of scatterers: 8168 At special positions: 0 Unit cell: (77.848, 124.136, 92.576, 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 49 16.00 O 1493 8.00 N 1417 7.00 C 5209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 42.9% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'C' and resid 27 through 59 removed outlier: 3.591A pdb=" N LYS C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 93 removed outlier: 3.732A pdb=" N PHE C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 100 through 135 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 168 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 201 through 228 Processing helix chain 'C' and resid 394 through 425 Proline residue: C 414 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.904A pdb=" N GLN C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 445 removed outlier: 3.637A pdb=" N ILE C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 455 Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 458 through 473 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.573A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.540A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.538A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.615A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.194A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.645A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 174 through 176 removed outlier: 3.585A pdb=" N SER C 183 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 176 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 181 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.404A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.425A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.512A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.333A 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: 3.526A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.861A 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: 3.614A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.370A 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: 3.600A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.163A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.324A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1269 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: 2.65 Time building geometry restraints manager: 2.23 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: 2098 1.33 - 1.45: 1585 1.45 - 1.57: 4592 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8342 Sorted by residual: bond pdb=" C CYS B 233 " pdb=" N PHE B 234 " ideal model delta sigma weight residual 1.331 1.231 0.099 1.41e-02 5.03e+03 4.94e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.32e-02 5.74e+03 1.01e+01 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.26e+00 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 8.96e+00 bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.59e+00 ... (remaining 8337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10931 1.97 - 3.95: 350 3.95 - 5.92: 35 5.92 - 7.89: 3 7.89 - 9.86: 2 Bond angle restraints: 11321 Sorted by residual: angle pdb=" CA THR B 274 " pdb=" CB THR B 274 " pdb=" OG1 THR B 274 " ideal model delta sigma weight residual 109.60 99.74 9.86 1.50e+00 4.44e-01 4.32e+01 angle pdb=" C CYS B 233 " pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 121.50 129.91 -8.41 1.43e+00 4.89e-01 3.46e+01 angle pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" C ASP A 284 " ideal model delta sigma weight residual 113.30 106.71 6.59 1.34e+00 5.57e-01 2.42e+01 angle pdb=" O ASP B 247 " pdb=" C ASP B 247 " pdb=" N ALA B 248 " ideal model delta sigma weight residual 122.39 127.12 -4.73 1.29e+00 6.01e-01 1.34e+01 angle pdb=" C ASP B 298 " pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " ideal model delta sigma weight residual 109.89 115.50 -5.61 1.60e+00 3.91e-01 1.23e+01 ... (remaining 11316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 4364 17.17 - 34.34: 445 34.34 - 51.51: 122 51.51 - 68.67: 27 68.67 - 85.84: 4 Dihedral angle restraints: 4962 sinusoidal: 1918 harmonic: 3044 Sorted by residual: dihedral pdb=" CA ILE C 201 " pdb=" C ILE C 201 " pdb=" N VAL C 202 " pdb=" CA VAL C 202 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 65.31 27.69 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 4959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1007 0.052 - 0.103: 204 0.103 - 0.155: 57 0.155 - 0.207: 17 0.207 - 0.258: 7 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU B 146 " pdb=" N LEU B 146 " pdb=" C LEU B 146 " pdb=" CB LEU B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1289 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 29 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ALA C 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 29 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS C 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 40 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ILE C 40 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 40 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 41 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 413 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 414 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.023 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1068 2.75 - 3.29: 7912 3.29 - 3.83: 14110 3.83 - 4.36: 16957 4.36 - 4.90: 29011 Nonbonded interactions: 69058 Sorted by model distance: nonbonded pdb=" O PHE C 200 " pdb=" OH TYR C 408 " model vdw 2.216 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.255 3.120 nonbonded pdb=" N GLU G 58 " pdb=" OE1 GLU G 58 " model vdw 2.259 3.120 nonbonded pdb=" O MET C 143 " pdb=" NH2 ARG A 38 " model vdw 2.281 3.120 nonbonded pdb=" O VAL C 88 " pdb=" OG1 THR C 91 " model vdw 2.290 3.040 ... (remaining 69053 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: 0.370 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.920 Find NCS groups from input model: 0.080 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.005 0.099 8342 Z= 0.330 Angle : 0.741 9.863 11321 Z= 0.492 Chirality : 0.051 0.258 1292 Planarity : 0.004 0.041 1435 Dihedral : 15.287 85.843 2981 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 21.53 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.25), residues: 1028 helix: 1.98 (0.25), residues: 407 sheet: 0.61 (0.33), residues: 219 loop : -0.60 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.006 0.001 HIS C 223 PHE 0.011 0.001 PHE A 376 TYR 0.015 0.001 TYR C 454 ARG 0.003 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.873 Fit side-chains REVERT: C 61 GLN cc_start: 0.7222 (mt0) cc_final: 0.6987 (tp40) REVERT: C 96 PHE cc_start: 0.6225 (m-80) cc_final: 0.5766 (t80) REVERT: C 183 SER cc_start: 0.8282 (t) cc_final: 0.7815 (p) REVERT: C 464 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 53 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: A 221 MET cc_start: 0.8966 (ttp) cc_final: 0.8424 (ttp) REVERT: B 59 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8429 (t80) outliers start: 15 outliers final: 5 residues processed: 138 average time/residue: 1.2975 time to fit residues: 189.2534 Evaluate side-chains 121 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 222 GLN C 223 HIS A 294 GLN A 357 HIS A 371 ASN B 9 GLN B 32 GLN B 88 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093279 restraints weight = 11227.969| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.10 r_work: 0.2970 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8342 Z= 0.178 Angle : 0.537 7.590 11321 Z= 0.290 Chirality : 0.041 0.159 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.812 53.027 1147 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.64 % Allowed : 20.16 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.25), residues: 1028 helix: 2.23 (0.25), residues: 411 sheet: 0.59 (0.33), residues: 222 loop : -0.53 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.013 0.001 PHE A 376 TYR 0.013 0.001 TYR C 454 ARG 0.004 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.004 Fit side-chains REVERT: C 61 GLN cc_start: 0.7362 (mt0) cc_final: 0.6961 (tp40) REVERT: C 96 PHE cc_start: 0.6315 (m-80) cc_final: 0.5663 (t80) REVERT: C 424 TRP cc_start: 0.6973 (m100) cc_final: 0.6700 (m-90) REVERT: A 221 MET cc_start: 0.8948 (ttp) cc_final: 0.8453 (ttp) REVERT: B 59 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8575 (t80) REVERT: B 198 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8368 (pp) REVERT: B 262 MET cc_start: 0.9185 (mtp) cc_final: 0.8719 (mmm) outliers start: 32 outliers final: 13 residues processed: 155 average time/residue: 1.2060 time to fit residues: 199.2107 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN C 223 HIS A 357 HIS B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092131 restraints weight = 11424.375| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.11 r_work: 0.2963 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8342 Z= 0.180 Angle : 0.517 7.491 11321 Z= 0.278 Chirality : 0.042 0.156 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.552 52.577 1139 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.99 % Allowed : 20.96 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1028 helix: 2.32 (0.24), residues: 411 sheet: 0.45 (0.32), residues: 227 loop : -0.45 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.012 0.001 TYR N 95 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.908 Fit side-chains REVERT: C 61 GLN cc_start: 0.7370 (mt0) cc_final: 0.6975 (tp-100) REVERT: C 96 PHE cc_start: 0.6247 (m-80) cc_final: 0.5565 (t80) REVERT: C 147 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7475 (tpp80) REVERT: C 440 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7400 (mp) REVERT: C 473 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.5688 (t80) REVERT: A 221 MET cc_start: 0.9105 (ttp) cc_final: 0.8584 (ttp) REVERT: B 59 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8579 (t80) REVERT: B 198 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8354 (pp) REVERT: B 262 MET cc_start: 0.9095 (mtp) cc_final: 0.8797 (mmm) REVERT: G 20 LYS cc_start: 0.8466 (ttmm) cc_final: 0.7942 (mttp) REVERT: G 42 GLU cc_start: 0.8261 (pp20) cc_final: 0.7975 (tm-30) outliers start: 35 outliers final: 14 residues processed: 151 average time/residue: 1.2440 time to fit residues: 199.3995 Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 29 GLN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.090133 restraints weight = 11437.541| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.10 r_work: 0.2919 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8342 Z= 0.265 Angle : 0.548 7.579 11321 Z= 0.296 Chirality : 0.043 0.169 1292 Planarity : 0.004 0.045 1435 Dihedral : 4.776 55.660 1139 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.58 % Allowed : 20.27 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.25), residues: 1028 helix: 2.25 (0.24), residues: 411 sheet: 0.38 (0.33), residues: 227 loop : -0.45 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS C 112 PHE 0.020 0.002 PHE C 41 TYR 0.015 0.002 TYR A 339 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.010 Fit side-chains REVERT: C 61 GLN cc_start: 0.7414 (mt0) cc_final: 0.7107 (tp40) REVERT: C 96 PHE cc_start: 0.6318 (m-80) cc_final: 0.5546 (t80) REVERT: C 147 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7556 (tpp80) REVERT: C 440 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A 221 MET cc_start: 0.9069 (ttp) cc_final: 0.8644 (ttp) REVERT: B 31 SER cc_start: 0.8223 (m) cc_final: 0.7938 (t) REVERT: B 59 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8563 (t80) REVERT: B 198 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8362 (pp) REVERT: B 262 MET cc_start: 0.9114 (mtp) cc_final: 0.8901 (mtp) REVERT: B 314 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8523 (ptm160) REVERT: G 42 GLU cc_start: 0.8274 (pp20) cc_final: 0.7968 (tm-30) REVERT: G 46 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8790 (mmtm) REVERT: N 43 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7927 (mttt) outliers start: 49 outliers final: 24 residues processed: 162 average time/residue: 1.1469 time to fit residues: 197.8754 Evaluate side-chains 150 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.0030 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 390 GLN B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092606 restraints weight = 11344.823| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.12 r_work: 0.2953 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8342 Z= 0.167 Angle : 0.513 7.194 11321 Z= 0.275 Chirality : 0.041 0.152 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.564 54.158 1139 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.44 % Allowed : 21.41 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1028 helix: 2.36 (0.24), residues: 411 sheet: 0.33 (0.33), residues: 228 loop : -0.41 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.012 0.001 TYR C 168 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 1.277 Fit side-chains REVERT: C 61 GLN cc_start: 0.7345 (mt0) cc_final: 0.7074 (tp40) REVERT: C 96 PHE cc_start: 0.6342 (m-80) cc_final: 0.5483 (t80) REVERT: C 147 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7429 (tpp80) REVERT: C 440 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7380 (mp) REVERT: A 221 MET cc_start: 0.9046 (ttp) cc_final: 0.8667 (ttp) REVERT: B 59 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8514 (t80) REVERT: B 198 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8345 (pp) REVERT: B 217 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8003 (pmm) REVERT: B 262 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8835 (mtp) REVERT: N 43 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7889 (mttt) outliers start: 39 outliers final: 19 residues processed: 149 average time/residue: 1.2843 time to fit residues: 202.7032 Evaluate side-chains 142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS B 9 GLN B 237 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091439 restraints weight = 11310.615| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.10 r_work: 0.2943 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8342 Z= 0.211 Angle : 0.533 7.296 11321 Z= 0.286 Chirality : 0.042 0.177 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.536 55.489 1137 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.56 % Allowed : 21.64 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.25), residues: 1028 helix: 2.31 (0.24), residues: 411 sheet: 0.39 (0.33), residues: 226 loop : -0.43 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.013 0.001 TYR N 95 ARG 0.002 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.993 Fit side-chains REVERT: C 96 PHE cc_start: 0.6399 (m-80) cc_final: 0.5513 (t80) REVERT: C 147 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7505 (tpp80) REVERT: C 440 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7376 (mp) REVERT: A 221 MET cc_start: 0.9039 (ttp) cc_final: 0.8686 (ttp) REVERT: B 59 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8558 (t80) REVERT: B 198 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8331 (pp) REVERT: B 217 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8057 (pmm) REVERT: B 262 MET cc_start: 0.9030 (mtp) cc_final: 0.8821 (mtp) REVERT: N 43 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7888 (mttt) outliers start: 40 outliers final: 22 residues processed: 150 average time/residue: 1.2269 time to fit residues: 195.3286 Evaluate side-chains 144 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.0070 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 84 optimal weight: 0.0670 chunk 80 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 68 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 223 HIS B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095887 restraints weight = 11245.870| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.12 r_work: 0.3012 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8342 Z= 0.142 Angle : 0.510 7.211 11321 Z= 0.270 Chirality : 0.040 0.162 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.249 53.191 1137 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.53 % Allowed : 22.32 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.25), residues: 1028 helix: 2.39 (0.24), residues: 417 sheet: 0.43 (0.33), residues: 221 loop : -0.46 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.011 0.001 TYR C 168 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.972 Fit side-chains REVERT: C 41 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7060 (p90) REVERT: C 96 PHE cc_start: 0.6438 (m-80) cc_final: 0.5581 (t80) REVERT: C 440 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7329 (mp) REVERT: C 463 LYS cc_start: 0.8902 (tppt) cc_final: 0.8584 (tppt) REVERT: C 473 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.5451 (t80) REVERT: A 221 MET cc_start: 0.8981 (ttp) cc_final: 0.8652 (ttp) REVERT: B 3 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6420 (tm-30) REVERT: B 59 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8487 (t80) REVERT: B 198 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8325 (pp) REVERT: B 217 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7895 (pmm) REVERT: B 262 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8747 (mtp) outliers start: 31 outliers final: 16 residues processed: 139 average time/residue: 1.2970 time to fit residues: 191.2405 Evaluate side-chains 139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 PHE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.9242 > 50: distance: 22 - 27: 10.343 distance: 27 - 28: 17.626 distance: 27 - 33: 21.062 distance: 28 - 29: 25.015 distance: 28 - 31: 15.103 distance: 29 - 30: 30.331 distance: 29 - 34: 9.760 distance: 31 - 32: 21.001 distance: 32 - 33: 23.931 distance: 34 - 35: 14.615 distance: 35 - 36: 11.041 distance: 35 - 38: 17.776 distance: 36 - 37: 7.372 distance: 36 - 42: 28.324 distance: 38 - 39: 18.366 distance: 39 - 40: 24.358 distance: 39 - 41: 17.386 distance: 42 - 43: 37.011 distance: 43 - 44: 21.228 distance: 43 - 46: 9.701 distance: 44 - 45: 40.924 distance: 44 - 53: 7.775 distance: 46 - 47: 12.617 distance: 47 - 48: 36.493 distance: 47 - 49: 12.463 distance: 48 - 50: 5.039 distance: 49 - 51: 20.055 distance: 50 - 52: 7.006 distance: 51 - 52: 18.855 distance: 53 - 54: 9.181 distance: 54 - 55: 31.555 distance: 54 - 57: 20.417 distance: 55 - 56: 35.653 distance: 55 - 67: 24.964 distance: 57 - 58: 18.757 distance: 58 - 59: 7.057 distance: 58 - 60: 11.037 distance: 59 - 61: 5.534 distance: 60 - 62: 10.063 distance: 60 - 63: 15.397 distance: 61 - 62: 15.695 distance: 62 - 64: 14.396 distance: 63 - 65: 13.153 distance: 64 - 66: 15.611 distance: 65 - 66: 11.231 distance: 67 - 68: 28.563 distance: 67 - 73: 19.535 distance: 68 - 69: 39.148 distance: 68 - 71: 34.561 distance: 69 - 70: 24.855 distance: 69 - 74: 17.749 distance: 71 - 72: 42.246 distance: 72 - 73: 31.128 distance: 74 - 75: 6.313 distance: 75 - 76: 5.984 distance: 75 - 78: 21.061 distance: 76 - 77: 20.246 distance: 76 - 82: 33.633 distance: 78 - 79: 25.711 distance: 79 - 80: 12.527 distance: 79 - 81: 35.900 distance: 83 - 84: 12.196 distance: 83 - 86: 11.812 distance: 84 - 85: 28.368 distance: 84 - 90: 13.564 distance: 85 - 117: 21.733 distance: 86 - 87: 22.198 distance: 87 - 88: 7.787 distance: 87 - 89: 14.499 distance: 90 - 91: 24.419 distance: 91 - 92: 17.221 distance: 91 - 94: 23.103 distance: 92 - 93: 10.692 distance: 92 - 96: 24.680 distance: 93 - 123: 26.437 distance: 94 - 95: 10.045 distance: 96 - 97: 14.887 distance: 97 - 98: 13.324 distance: 97 - 100: 6.455 distance: 98 - 99: 25.146 distance: 98 - 106: 17.693 distance: 99 - 130: 17.953 distance: 100 - 101: 22.142 distance: 101 - 102: 36.797 distance: 101 - 103: 24.414 distance: 102 - 104: 13.320 distance: 103 - 105: 6.111 distance: 104 - 105: 48.023 distance: 106 - 107: 6.457 distance: 107 - 108: 13.123 distance: 107 - 110: 11.624 distance: 108 - 109: 18.286 distance: 108 - 117: 9.011 distance: 109 - 134: 17.550 distance: 110 - 111: 15.638 distance: 111 - 112: 10.106 distance: 111 - 113: 12.348 distance: 112 - 114: 12.057 distance: 113 - 115: 6.571 distance: 114 - 116: 11.509 distance: 115 - 116: 10.409