Starting phenix.real_space_refine on Wed Jan 15 09:17:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6u_42999/01_2025/8v6u_42999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6u_42999/01_2025/8v6u_42999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6u_42999/01_2025/8v6u_42999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6u_42999/01_2025/8v6u_42999.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6u_42999/01_2025/8v6u_42999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6u_42999/01_2025/8v6u_42999.cif" } resolution = 3.0 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= 0.018 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 53 5.16 5 C 5264 2.51 5 N 1389 2.21 5 O 1505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8211 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1999 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1656 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2466 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1716 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'YEQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.68 Number of scatterers: 8211 At special positions: 0 Unit cell: (90.272, 118.048, 132.804, 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 53 16.00 O 1505 8.00 N 1389 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 38.3% alpha, 24.5% 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 78 through 102 removed outlier: 3.710A pdb=" N ALA A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.682A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 179 removed outlier: 3.787A pdb=" N TRP A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.522A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 removed outlier: 4.167A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.851A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 317 through 349 removed outlier: 3.501A pdb=" N MET A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.580A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 removed outlier: 3.634A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.611A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.989A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.522A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.570A pdb=" N ASN B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 184 through 203 removed outlier: 4.134A pdb=" N ARG B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.555A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.972A pdb=" N GLN C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 23 removed outlier: 4.256A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.015A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 5.095A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.285A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.585A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.937A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.774A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.691A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 217 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.655A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.631A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.161A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.622A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.622A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1125 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: 2.37 Time building geometry restraints manager: 2.35 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: 2136 1.33 - 1.46: 1841 1.46 - 1.59: 4326 1.59 - 1.71: 1 1.71 - 1.84: 78 Bond restraints: 8382 Sorted by residual: bond pdb=" C02 YEQ A 501 " pdb=" N03 YEQ A 501 " ideal model delta sigma weight residual 1.454 1.209 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C06 YEQ A 501 " pdb=" C07 YEQ A 501 " ideal model delta sigma weight residual 1.528 1.422 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C05 YEQ A 501 " pdb=" C06 YEQ A 501 " ideal model delta sigma weight residual 1.534 1.455 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C07 YEQ A 501 " pdb=" C09 YEQ A 501 " ideal model delta sigma weight residual 1.507 1.581 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C12 YEQ A 501 " pdb=" O13 YEQ A 501 " ideal model delta sigma weight residual 1.350 1.423 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 8377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 10511 3.09 - 6.18: 864 6.18 - 9.26: 22 9.26 - 12.35: 2 12.35 - 15.44: 1 Bond angle restraints: 11400 Sorted by residual: angle pdb=" CA ASP C 186 " pdb=" CB ASP C 186 " pdb=" CG ASP C 186 " ideal model delta sigma weight residual 112.60 121.20 -8.60 1.00e+00 1.00e+00 7.39e+01 angle pdb=" C PHE E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta sigma weight residual 120.29 130.02 -9.73 1.42e+00 4.96e-01 4.70e+01 angle pdb=" CA ASP C 228 " pdb=" CB ASP C 228 " pdb=" CG ASP C 228 " ideal model delta sigma weight residual 112.60 119.28 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" CA PHE E 68 " pdb=" CB PHE E 68 " pdb=" CG PHE E 68 " ideal model delta sigma weight residual 113.80 119.57 -5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" CA ASP C 163 " pdb=" CB ASP C 163 " pdb=" CG ASP C 163 " ideal model delta sigma weight residual 112.60 117.89 -5.29 1.00e+00 1.00e+00 2.80e+01 ... (remaining 11395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4503 18.00 - 35.99: 328 35.99 - 53.98: 77 53.98 - 71.98: 9 71.98 - 89.97: 6 Dihedral angle restraints: 4923 sinusoidal: 1766 harmonic: 3157 Sorted by residual: dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER E 52 " pdb=" C SER E 52 " pdb=" N SER E 53 " pdb=" CA SER E 53 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA THR C 165 " pdb=" C THR C 165 " pdb=" N CYS C 166 " pdb=" CA CYS C 166 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 4920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 986 0.088 - 0.176: 289 0.176 - 0.263: 47 0.263 - 0.351: 7 0.351 - 0.439: 6 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CA PHE C 292 " pdb=" N PHE C 292 " pdb=" C PHE C 292 " pdb=" CB PHE C 292 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA THR C 164 " pdb=" N THR C 164 " pdb=" C THR C 164 " pdb=" CB THR C 164 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA SER C 334 " pdb=" N SER C 334 " pdb=" C SER C 334 " pdb=" CB SER C 334 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1332 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " 0.138 2.00e-02 2.50e+03 7.53e-02 1.42e+02 pdb=" CG TRP C 332 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " -0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " 0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 94 " -0.121 2.00e-02 2.50e+03 6.85e-02 9.39e+01 pdb=" CG TYR E 94 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 94 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR E 94 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 94 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 94 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR E 94 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 94 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 82 " -0.120 2.00e-02 2.50e+03 5.71e-02 8.15e+01 pdb=" CG TRP C 82 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 82 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP C 82 " 0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP C 82 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP C 82 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 82 " 0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 82 " -0.058 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 82 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 82 " -0.051 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 13 2.58 - 3.16: 6055 3.16 - 3.74: 11828 3.74 - 4.32: 16339 4.32 - 4.90: 28229 Nonbonded interactions: 62464 Sorted by model distance: nonbonded pdb=" OD1 ASP A 172 " pdb=" OH TYR B 243 " model vdw 1.999 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.212 3.040 nonbonded pdb=" O ILE A 197 " pdb=" OG1 THR A 201 " model vdw 2.337 3.040 nonbonded pdb=" O SER A 219 " pdb=" OG SER A 219 " model vdw 2.464 3.040 nonbonded pdb=" C06 YEQ A 501 " pdb=" C15 YEQ A 501 " model vdw 2.499 2.992 ... (remaining 62459 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.690 Find NCS groups from input model: 0.100 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.011 0.245 8382 Z= 0.751 Angle : 1.670 15.442 11400 Z= 1.100 Chirality : 0.086 0.439 1335 Planarity : 0.012 0.115 1432 Dihedral : 14.064 89.972 2875 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 1.31 % Allowed : 11.53 % Favored : 87.16 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.23 % 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: 0.40 (0.25), residues: 1064 helix: 0.58 (0.27), residues: 349 sheet: 1.45 (0.34), residues: 222 loop : -0.48 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.138 0.018 TRP C 332 HIS 0.015 0.004 HIS C 62 PHE 0.068 0.008 PHE C 151 TYR 0.121 0.016 TYR E 94 ARG 0.005 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.906 Fit side-chains REVERT: A 208 MET cc_start: 0.7086 (mmm) cc_final: 0.6841 (mmm) REVERT: A 242 SER cc_start: 0.8572 (p) cc_final: 0.8240 (p) REVERT: B 22 ASN cc_start: 0.7935 (t0) cc_final: 0.7673 (m110) REVERT: B 200 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7390 (tt) REVERT: C 35 ASN cc_start: 0.7678 (t0) cc_final: 0.7068 (m-40) REVERT: C 156 GLN cc_start: 0.8643 (mt0) cc_final: 0.8419 (mt0) REVERT: C 333 ASP cc_start: 0.7362 (p0) cc_final: 0.7067 (p0) REVERT: E 215 TYR cc_start: 0.7622 (m-80) cc_final: 0.7350 (m-80) outliers start: 11 outliers final: 9 residues processed: 161 average time/residue: 1.2661 time to fit residues: 216.8443 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.0020 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 183 HIS B 146 GLN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.115832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101896 restraints weight = 15590.951| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.84 r_work: 0.3373 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8382 Z= 0.240 Angle : 0.630 9.075 11400 Z= 0.336 Chirality : 0.045 0.144 1335 Planarity : 0.004 0.037 1432 Dihedral : 6.701 57.794 1202 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.92 % Allowed : 16.88 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.97 (0.26), residues: 1064 helix: 1.43 (0.28), residues: 358 sheet: 1.23 (0.31), residues: 267 loop : -0.33 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.009 0.002 HIS B 209 PHE 0.016 0.002 PHE C 151 TYR 0.017 0.001 TYR E 178 ARG 0.003 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.897 Fit side-chains REVERT: A 242 SER cc_start: 0.8594 (p) cc_final: 0.8246 (p) REVERT: B 10 LYS cc_start: 0.7326 (tttm) cc_final: 0.7019 (mtmt) REVERT: B 80 ASN cc_start: 0.7044 (p0) cc_final: 0.6778 (p0) REVERT: C 35 ASN cc_start: 0.7945 (t0) cc_final: 0.7459 (m-40) REVERT: C 156 GLN cc_start: 0.8932 (mt0) cc_final: 0.8657 (mt0) REVERT: C 333 ASP cc_start: 0.7432 (p0) cc_final: 0.7138 (p0) REVERT: D 51 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6579 (tp) REVERT: E 215 TYR cc_start: 0.7791 (m-80) cc_final: 0.7566 (m-80) outliers start: 33 outliers final: 12 residues processed: 141 average time/residue: 1.0577 time to fit residues: 159.8713 Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS C 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099074 restraints weight = 15947.784| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.84 r_work: 0.3346 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8382 Z= 0.318 Angle : 0.660 10.746 11400 Z= 0.347 Chirality : 0.046 0.153 1335 Planarity : 0.005 0.050 1432 Dihedral : 6.003 58.513 1190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.11 % Allowed : 18.79 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.80 (0.26), residues: 1064 helix: 1.53 (0.28), residues: 351 sheet: 0.92 (0.31), residues: 273 loop : -0.49 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 82 HIS 0.009 0.002 HIS B 209 PHE 0.021 0.002 PHE C 151 TYR 0.018 0.002 TYR E 178 ARG 0.006 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.952 Fit side-chains REVERT: B 24 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.7757 (ttp-110) REVERT: C 23 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7690 (tmmm) REVERT: C 35 ASN cc_start: 0.7990 (t0) cc_final: 0.7674 (t0) REVERT: C 156 GLN cc_start: 0.8945 (mt0) cc_final: 0.8649 (mt0) REVERT: C 217 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7599 (ppp) REVERT: C 226 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: C 315 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8355 (m) REVERT: D 51 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6818 (tm) outliers start: 43 outliers final: 18 residues processed: 142 average time/residue: 1.0019 time to fit residues: 153.7486 Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 61.531 > 50: distance: 15 - 19: 4.235 distance: 16 - 35: 19.083 distance: 19 - 20: 3.557 distance: 19 - 25: 6.645 distance: 20 - 21: 6.977 distance: 20 - 23: 6.013 distance: 21 - 22: 14.595 distance: 21 - 26: 13.009 distance: 22 - 46: 31.077 distance: 23 - 24: 5.173 distance: 24 - 25: 11.339 distance: 26 - 27: 8.089 distance: 27 - 28: 7.230 distance: 27 - 30: 10.632 distance: 28 - 29: 5.132 distance: 28 - 35: 12.650 distance: 29 - 51: 18.342 distance: 30 - 31: 7.819 distance: 31 - 32: 7.433 distance: 32 - 33: 9.478 distance: 32 - 34: 3.713 distance: 35 - 36: 5.523 distance: 36 - 37: 7.080 distance: 36 - 39: 10.984 distance: 37 - 38: 12.107 distance: 37 - 46: 5.934 distance: 39 - 40: 5.005 distance: 40 - 41: 9.662 distance: 40 - 42: 5.437 distance: 41 - 43: 7.168 distance: 42 - 44: 6.320 distance: 43 - 45: 6.031 distance: 44 - 45: 8.664 distance: 46 - 47: 15.336 distance: 47 - 48: 37.002 distance: 47 - 50: 22.963 distance: 48 - 49: 17.913 distance: 48 - 51: 14.477 distance: 51 - 52: 17.759 distance: 52 - 53: 3.341 distance: 52 - 55: 16.747 distance: 53 - 54: 17.279 distance: 53 - 56: 14.459 distance: 56 - 57: 12.992 distance: 57 - 58: 12.963 distance: 57 - 60: 4.776 distance: 58 - 59: 12.702 distance: 58 - 68: 8.344 distance: 60 - 61: 6.324 distance: 61 - 63: 6.268 distance: 62 - 64: 5.177 distance: 64 - 66: 6.084 distance: 65 - 66: 4.658 distance: 66 - 67: 3.604 distance: 68 - 69: 7.921 distance: 69 - 70: 8.880 distance: 69 - 72: 4.968 distance: 70 - 71: 16.676 distance: 70 - 75: 8.742 distance: 72 - 73: 11.006 distance: 72 - 74: 9.552 distance: 75 - 76: 9.084 distance: 76 - 77: 17.939 distance: 76 - 79: 19.815 distance: 77 - 78: 18.901 distance: 77 - 82: 12.168 distance: 79 - 80: 19.265 distance: 79 - 81: 5.891 distance: 82 - 83: 7.782 distance: 82 - 88: 4.548 distance: 83 - 84: 6.330 distance: 83 - 86: 8.043 distance: 84 - 85: 18.651 distance: 86 - 87: 10.076 distance: 87 - 88: 15.849 distance: 89 - 90: 7.320 distance: 90 - 91: 4.624 distance: 91 - 92: 13.940 distance: 91 - 97: 6.404 distance: 93 - 94: 7.183 distance: 94 - 96: 4.498